Kumar R


Full name : Kumar Rajnish

First name : Rajnish

Mail : Karolinska Institutet, Department NVS, Translational Alzheimer Neurobiology, Karolinska Institute, Novum 5th floor, Halsovagen 7, 14157 Huddinge

Zip Code :

City :

Country : Sweden

Email : rajnish.kumar@ki.se

Phone :

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References (68)

Title : Heterologous expression, biochemical characterization and prospects for insecticide biosensing potential of carboxylesterase Ha006a from Helicoverpa armigera - Kaur_2024_Pestic.Biochem.Physiol_200_105844
Author(s) : Kaur H , Rode S , Lonare S , Demiwal P , Narasimhappa P , Arun E , Kumar R , Das J , Ramamurthy PC , Sircar D , Sharma AK
Ref : Pestic Biochem Physiol , 200 :105844 , 2024
Abstract : Enzymes have attracted considerable scientific attention for their crucial role in detoxifying a wide range of harmful compounds. In today's global context, the extensive use of insecticides has emerged as a significant threat to the environment, sparking substantial concern. Insects, including economically important pests like Helicoverpa armigera, have developed resistance to conventional pest control methods through enzymes like carboxyl/cholinesterases. This study specifically focuses on a notable carboxyl/cholinesterase enzyme from Helicoverpa armigera (Ha006a), with the goal of harnessing its potential to combat environmental toxins. A total of six insecticides belonging to two different classes displayed varying inhibitory responses towards Ha006a, thereby rendering it effective in detoxifying a broader spectrum of insecticides. The significance of this research lies in discovering the bioremediation property of Ha006a, as it hydrolyzes synthetic pyrethroids (fenvalerate, lambda-cyhalothrin and deltamethrin) and sequesters organophosphate (paraoxon ethyl, profenofos, and chlorpyrifos) insecticides. Additionally, the interaction studies between organophosphate insecticides and Ha006a helped in the fabrication of a novel electroanalytical sensor using a modified carbon paste electrode (MCPE). This sensor boasts impressive sensitivity, with detection limits of 0.019 microM, 0.15 microM, and 0.025 microM for paraoxon ethyl, profenofos, and chlorpyrifos, respectively. This study provides a comprehensive biochemical and biophysical characterization of the purified esterase Ha006a, showcasing its potential to remediate different classes of insecticides.
ESTHER : Kaur_2024_Pestic.Biochem.Physiol_200_105844
PubMedSearch : Kaur_2024_Pestic.Biochem.Physiol_200_105844
PubMedID: 38582571
Gene_locus related to this paper: helam-d5g3e0

Title : Reconstructing curcumin biosynthesis in yeast reveals the implication of caffeoyl-shikimate esterase in phenylpropanoid metabolic flux - Utomo_2024_Metab.Eng__
Author(s) : Utomo JC , Barrell HB , Kumar R , Smith J , Brant MS , De la Hoz Siegler H , Ro DK
Ref : Metab Eng , : , 2024
Abstract : Curcumin is a polyphenolic natural product from the roots of turmeric (Curcuma longa). It has been a popular coloring and flavoring agent in food industries with known health benefits. The conventional phenylpropanoid pathway is known to proceed from phenylalanine via p-coumaroyl-CoA intermediate. Although hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) plays a key catalysis in the biosynthesis of phenylpropanoid products at the downstream of p-coumaric acid, a recent discovery of caffeoyl-shikimate esterase (CSE) showed that an alternative pathway exists. Here, the biosynthetic efficiency of the conventional and the alternative pathway in producing feruloyl-CoA was examined using curcumin production in yeast. A novel modular multiplex genome-edit (MMG)-CRISPR platform was developed to facilitate rapid integrations of up to eight genes into the yeast genome in two steps. Using this MMG-CRISPR platform and metabolic engineering strategies, the alternative CSE phenylpropanoid pathway consistently showed higher titers (2-19 folds) of curcumin production than the conventional pathway in engineered yeast strains. In shake flask cultures using a synthetic minimal medium without phenylalanine, the curcumin production titer reached up to 1.5 mg/L, which is three orders of magnitude (-4800-fold) improvement over non-engineered base strain. This is the first demonstration of de novo curcumin biosynthesis in yeast. Our work shows the critical role of CSE in improving the metabolic flux in yeast towards the phenylpropanoid biosynthetic pathway. In addition, we showcased the convenience and reliability of modular multiplex CRISPR/Cas9 genome editing in constructing complex synthetic pathways in yeast.
ESTHER : Utomo_2024_Metab.Eng__
PubMedSearch : Utomo_2024_Metab.Eng__
PubMedID: 38387678

Title : Chemical Composition of Piper nigrum L. Cultivar Guajarina Essential Oils and Their Biological Activity - Feitosa_2024_Molecules_29_
Author(s) : Feitosa BS , Ferreira OO , Franco CJP , Karakoti H , Kumar R , Cascaes MM , Jawarkar RD , Mali SN , Cruz JN , de Menezes IC , de Oliveira MS , de Aguiar Andrade EH
Ref : Molecules , 29 : , 2024
Abstract : The essential oils and aroma derived from the leaves (L), stems (St), and spikes (s) of Piper nigrum L. cv. Guajarina were extracted; the essential oils were extracted using hydrodistillation (HD), and steam distillation (SD), and the aroma was obtained by simultaneous distillation and extraction (SDE). Chemical constituents were identified and quantified using GC/MS and GC-FID. Preliminary biological activity was assessed by determining the toxicity against Artemia salina Leach larvae, calculating mortality rates, and determining lethal concentration values (LC(50)). The predominant compounds in essential oil samples included alpha-pinene (0-5.6%), beta-pinene (0-22.7%), limonene (0-19.3%), 35 linalool (0-5.3%), delta-elemene (0-10.1%), beta-caryophyllene (0.5-21.9%), gamma-elemene (7.5-33.9%), and curzerene (6.9-31.7%). Multivariate analysis, employing principal component analysis (PCA) and hierarchical cluster analysis (HCA), revealed three groups among the identified classes and two groups among individual compounds. The highest antioxidant activity was found for essential oils derived from the leaves (167.9 41 mg TE mL(-1)). Larvicidal potential against A. salina was observed in essential oils obtained from the leaves (LC50 6.40 microg mL(-1)) and spikes (LC(50) 6.44 microg mL(-1)). The in silico studies demonstrated that the main compounds can interact with acetylcholinesterase, thus showing the potential molecular interaction responsible for the toxicity of the essential oil in A. salina.
ESTHER : Feitosa_2024_Molecules_29_
PubMedSearch : Feitosa_2024_Molecules_29_
PubMedID: 38474459

Title : Effect of Curcumin and Coenzyme Q10 Alone and in Combination on Learning and Memory in an Animal Model of Alzheimer's Disease - Kumar_2023_Biomedicines_11_
Author(s) : Kumar P , Singh A , Kumar A , Kumar R , Pal R , Sachan AK , Dixit RK , Nath R
Ref : Biomedicines , 11 : , 2023
Abstract : The most frequent neurodegenerative illness among senior people and the main cause of dementia is Alzheimer's disease. The present dementia medications available only help with the symptoms of cognitive deficits and have several negative effects. The current study's goal is to assess the effects of curcumin and coenzyme Q10, two herbal medicines, both separately and in combination, on learning and memory before comparing them to the industry standard drug. A total of 42 adult healthy Wistar rats were used in our study. In this experiment, rats were given daily doses of 2.5 mg/kg of body weight of scopolamine hydrobromide for 7 days to induce Alzheimer's disease. On the eighth day, behavioural testing was conducted. Following testing, scopolamine and the test medications were given daily for the following 21 days. On days 29 and 30, behavioural testing was conducted once more, and then animals were slaughtered. Brain homogenate was produced for the estimation of molecular and biochemical markers. Curcumin has demonstrated a dose-response relationship, with a higher dose (200 mg/kg b.w. p.o.) being more effective than a lower dose (100 mg/kg b.w. p.o.). Similar to the greater dose of curcumin, coenzyme Q10 (200 mg/kg b.w. p.o.) has also been found to improve memory and learning. Higher doses of curcumin and coenzyme Q10 had more pronounced and meaningful effects. Acetylcholinesterase and TNF levels increased in scopolamine-induced memory impairment, but these effects were restored by the test medications, and improved by the combined therapy. These outcomes are comparable to those of the common medication memantine. As a result, we may infer from our results that curcumin at higher doses and its combination with coenzyme Q10 (200 mg/kg b.w. p.o.) have a significant impact on cognitive impairment in animal models of Alzheimer's disease and can be utilised alone or as an add-on therapy for the condition.
ESTHER : Kumar_2023_Biomedicines_11_
PubMedSearch : Kumar_2023_Biomedicines_11_
PubMedID: 37239093

Title : Chemical composition, pesticidal activities and in-silico investigation of Hedychium spicatum Sm. chloroform extract - Rawat_2023_An.Acad.Bras.Cienc_95_e20220964
Author(s) : Rawat A , Prakash OM , Nagarkoti K , Kumar R , Verma AK , Kumar S , Srivastava RM , Latwal M , Pandey G
Ref : An Acad Bras Cienc , 95 :e20220964 , 2023
Abstract : The present study aimed to identify the bioactive constituents in the chloroform extract of H. spicatum rhizomes (HS-RCLE), further evaluated for its in-vitro pesticidal activities validating via molecular docking techniques. GC/MS analysis of HS-RCLE identified 14 compounds contributing 84.1 % of the total composition. The extract was dominated by oxygenated sesquiterpenes (43.1 %) with curcumenone (25.2 %) and coronarin E (14.8 %) as the major compounds. The extract recorded 89.4 % egg hatchability inhibition and 82.6 % immobility of Meloidogyne incognita, 66.7 % insecticidal activity on Spodoptera litura, 100 % phytotoxic activity on Raphanus raphanistrum seeds, and 74.7 % anti-fungal activity on Curvularia lunata at the respective highest dose studied. The biological activities were furthermore validated by using docking studies on certain proteins/enzymes namely acetylcholinesterase (PBD ID: IC2O), carboxylesterase (PDB ID: 1CI8), acetohydroxyacid synthase (PBD ID: 1YHZ) and trihydroxy naphthalene reductase (PBD ID: 3HNR). The bioactivity of the major constituents of the extract was predicted with the help of in silico PASS studies. HS-RCLE was observed to be a viable alternative source of natural pesticidal agents and paves the way for further studies on its mechanistic approaches and field trials to ascertain its pesticidal studies.
ESTHER : Rawat_2023_An.Acad.Bras.Cienc_95_e20220964
PubMedSearch : Rawat_2023_An.Acad.Bras.Cienc_95_e20220964
PubMedID: 37466542

Title : Molecular Docking and Network Pharmacology Interaction Analysis of Gingko Biloba (EGB761) Extract with Dual Target Inhibitory Mechanism in Alzheimer's Disease - Singh_2023_J.Alzheimers.Dis__
Author(s) : Singh M , Jindal D , Kumar R , Pancham P , Haider S , Gupta V , Mani S , R R , Tiwari RK , Chanda S
Ref : J Alzheimers Dis , : , 2023
Abstract : BACKGROUND: Alzheimer's disease (AD) is the most common type of neurodegenerative dementia affecting people in their later years of life. The AD prevalence rate has significantly increased due to a lack of early detection technology and low therapeutic efficacy. Despite recent scientific advances, some aspects of AD pathological targets still require special attention. Certain traditionally consumed phytocompounds have been used for thousands of years to treat such pathologies. The standard extract of Gingko biloba (EGB761) is a combination of 13 macro phyto-compounds and various other micro phytocompounds that have shown greater therapeutic potential against the pathology of AD. OBJECTIVE: Strong physiological evidence of cognitive health preservation has been observed in elderly people who keep an active lifestyle. According to some theories, consuming certain medicinal extracts helps build cognitive reserve. We outline the research employing EGB761 as a dual target for AD. METHODS: This study investigates various inhibitory targets against AD using computational approaches such as molecular docking, network pharmacology, ADMET (full form), and bioactivity prediction of the selected compounds. RESULTS: After interaction studies were done for all the phytoconstituents of EGB761, it was concluded that all four of the phytocompounds (kaempferol, isorhamnetin, quercetin, and ginkgotoxin) showed the maximum inhibitory activity against acetylcholinesterase (AChE) and GSK3beta. CONCLUSION: The highly active phytocompounds of EGB761, especially quercetin, kaempferol, and isorhamnetin, have better activity against AChE and GSK3beta than its reported synthetic drug, according to molecular docking and network pharmacology research. These compounds may act on multiple targets in the protein network of AD. The AChE theory was primarily responsible for EGB761's therapeutic efficacy in treating AD.
ESTHER : Singh_2023_J.Alzheimers.Dis__
PubMedSearch : Singh_2023_J.Alzheimers.Dis__
PubMedID: 37066913

Title : Virtual screening and molecular dynamics simulation approach for the identification of potential multi-target directed ligands for the treatment of Alzheimer's disease - Jangid_2023_J.Biomol.Struct.Dyn__1
Author(s) : Jangid K , Devi B , Sahoo A , Kumar V , Dwivedi AR , Thareja S , Kumar R
Ref : J Biomol Struct Dyn , :1 , 2023
Abstract : Alzheimer's disease (AD) is a multifactorial neurological disorder characterized by memory loss and cognitive impairment. The currently available single-targeting drugs have miserably failed in the treatment of AD, and multi-target directed ligands (MTDLs) are being explored as an alternative treatment strategy. Cholinesterase and monoamine oxidase enzymes are reported to play a crucial role in the pathology of AD, and multipotent ligands targeting these two enzymes simultaneously are under various phases of design and development. Recent studies have revealed that computational approaches are robust and trusted tools for identifying novel therapeutics. The current research work is focused on the development of potential multi-target directed ligands that simultaneously inhibit acetylcholinesterase (AChE) and monoamine oxidase B (MAO-B) enzymes employing a structure-based virtual screening (SBVS) approach. The ASINEX database was screened after applying pan assay interference and drug-likeness filter to identify novel molecules using three docking precision criteria; High Throughput Virtual Screening (HTVS), Standard Precision (SP), and Extra Precision (XP). Additionally, binding free energy calculations, ADME, and molecular dynamic simulations were employed to get structural insights into the mechanism of protein-ligand binding and pharmacokinetic properties. Three lead molecules viz. AOP19078710, BAS00314308 and BDD26909696 were successfully identified with binding scores of -10.565, -10.543 & -8.066 kcal/mol against AChE and -11.019, -12.357 & -10.068 kcal/mol against MAO-B, better score as compared to the standard inhibitors. In the near future, these molecules will be synthesized and evaluated through in vitro and in vivo assays for their inhibition potential against AChE and MAO-B enzymes.
ESTHER : Jangid_2023_J.Biomol.Struct.Dyn__1
PubMedSearch : Jangid_2023_J.Biomol.Struct.Dyn__1
PubMedID: 37114423

Title : Chemical Composition, Preliminary Toxicity, and Antioxidant Potential of Piper marginatum Sensu Lato Essential Oils and Molecular Modeling Study - Feitosa_2023_Molecules_28_
Author(s) : Feitosa BS , Ferreira OO , Mali SN , Anand A , Cruz JN , Franco CJP , Mahawer SK , Kumar R , Cascaes MM , Oliveira MS , Andrade EHA
Ref : Molecules , 28 : , 2023
Abstract : The essential oils (OEs) of the leaves, stems, and spikes of P. marginatum were obtained by hydrodistillation, steam distillation, and simultaneous extraction. The chemical constituents were identified and quantified by GC/MS and GC-FID. The preliminary biological activity was determined by assessing the toxicity of the samples to Artemia salina Leach larvae and calculating the mortality rate and lethal concentration (LC(50)). The antioxidant activity of the EOs was determined by the DPPH radical scavenging method. Molecular modeling was performed using molecular docking and molecular dynamics, with acetylcholinesterase being the molecular target. The OES yields ranged from 1.49% to 1.83%. The EOs and aromatic constituents of P. marginatum are characterized by the high contents of (E)-isoosmorhizole (19.4-32.9%), 2-methoxy-4,5-methylenedioxypropiophenone (9.0-19.9%), isoosmorhizole (1.6-24.5%), and 2-methoxy-4,5-methylenedioxypropiophenone isomer (1.6-14.3%). The antioxidant potential was significant in the OE of the leaves and stems of P. marginatum extracted by SD in November (84.9 +/- 4.0 mg TE.mL(-1)) and the OEs of the leaves extracted by HD in March (126.8 +/- 12.3 mg TE.mL(-1)). Regarding the preliminary toxicity, the OEs of Pm-SD-L-St-Nov and Pm-HD-L-St-Nov had mortality higher than 80% in concentrations of 25 microg.mL(-1). This in silico study on essential oils elucidated the potential mechanism of interaction of the main compounds, which may serve as a basis for advances in this line of research.
ESTHER : Feitosa_2023_Molecules_28_
PubMedSearch : Feitosa_2023_Molecules_28_
PubMedID: 37570784

Title : Structural dynamics and mechanistic action guided engineering of lipolytic enzymes - Kumar_2023_J.Cell.Biochem__
Author(s) : Kumar R
Ref : Journal of Cellular Biochemistry , : , 2023
Abstract : Lipases have been established as important biocatalysts in several industrial applications, owing to their diverse substrate specificity. The availability of data on three-dimensional crystal structures for various lipases offers an opportunity for modulating their structural and functional aspects to design and engineer better versions of lipases. With the aim of investigating the structural components governing the extremophilic behavior of lipases, structural analysis of microbial lipases was performed using advanced bioinformatics and molecular dynamics simulation approaches. In sequences and functionally distinct alkaliphilic and thermophilic lipases were investigated for their functional properties to understand the distinguishing features of their structures. The alkaliphilic lipase from Bacillus subtilis (LipA) showed conformational changes in the loop region Ala132-Met137, subsequently, the active site residue His156 shows two conformations, toward the active site nucleophilic residues Ser77 and away from the Ser77. Interestingly, the active site of LipA is more solvent-exposed and can be correlated with the adoption of an open conformation which might extend and expose the active site region to solvents during the catalysis process. Furthermore, the MD simulation of thermophilic lipase from marine Streptomyces (MAS1) revealed the role of N- and C-terminal regions with disulfide bridges and identified a metal ion binding site that facilitates the enzyme stability. The novel thermo-alkaliphilic lipase can be designed to integrate the stability features of MAS1 into the alkaliphilic LipA. These structural-level intrinsic characteristics can be used for lipase engineering to amend the lipase activity and stability as per the requirements of the industrial processes.
ESTHER : Kumar_2023_J.Cell.Biochem__
PubMedSearch : Kumar_2023_J.Cell.Biochem__
PubMedID: 37087743

Title : Purification and characterization of extracellular lipase from a thermotolerant strain: Bacillus subtilis TTP-06 - Kaur_2023_3.Biotech_13_343
Author(s) : Kaur M , Kumar R , Katoch P , Gupta R
Ref : 3 Biotech , 13 :343 , 2023
Abstract : In current study, lipase from a thermotolerant Bacillus subtilis TTP-06 was purified in a stepwise manner by using ammonium sulfate precipitation and column chromatography. Thenceforth, it was subjected to sodium dodecyl sulfate- and native-polyacrylamide gel electrophoresis to check the homogeneity of the purified enzyme. The ideal substrate concentration, pH, temperature, reaction duration and lipase specificity were identified. With a yield of 11.02%, purified lipase displayed activity of 8.51 U/mg. Thenceforward, the homogeneously purified enzyme was considered to be a homo-dimer of 30 kDa subunits. Enzyme had K(m) and V(max) value of 9.498 mM and 19.92 mol mg(-1) min(-1), respectively. Additionally, the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) method was used to investigate the purified lipase and estimate its 3-D structure, which revealed a catalytic triad of serine, aspartate and histidine.
ESTHER : Kaur_2023_3.Biotech_13_343
PubMedSearch : Kaur_2023_3.Biotech_13_343
PubMedID: 37711229

Title : Prdx6 Regulates Nlrp3 Inflammasome Activation-Driven Inflammatory Response in Lens Epithelial Cells - Chhunchha_2023_Int.J.Mol.Sci_24_
Author(s) : Chhunchha B , Kumar R , Kubo E , Thakur P , Singh DP
Ref : Int J Mol Sci , 24 : , 2023
Abstract : The continuum of antioxidant response dysregulation in aging/oxidative stress-driven Nlrp3 inflammasome activation-mediated inflammatory response is associated with age-related diseases. Peroxiredoxin (Prdx) 6 is a key antioxidant that provides cytoprotection by regulating redox homeostasis. Herein, using lens epithelial cells (LECs) derived from the targeted inactivation of Prdx6 gene and aging lenses, we present molecular evidence that Prdx6-deficiency causes oxidative-driven Nlrp3 inflammasome activation, resulting in pyroptosis in aging/redox active cells wherein Prdx6 availability offsets the inflammatory process. We observed that Prdx6(-/-) and aging LECs harboring accumulated reactive oxygen species (ROS) showed augmented activation of Nlrp3 and bioactive inflammatory components, like Caspase-1, IL-1beta, ASC and Gasdermin-D. Similar to lipopolysaccharide treatment, oxidative exposure led to further ROS amplification with increased activation of the Nlrp3 inflammasome pathway. Mechanistically, we found that oxidative stress enhanced Kruppel-like factor 9 (Klf9) expression in aging/Prdx6(-/-) mLECs, leading to a Klf9-dependent increase in Nlrp3 transcription, while the elimination of ROS by the delivery of Prdx6 or by silencing Klf9 prevented the inflammatory response. Altogether, our data identify the biological significance of Prdx6 as an intrinsic checkpoint for regulating the cellular health of aging or redox active LECs and provide opportunities to develop antioxidant-based therapeutic(s) to prevent oxidative/aging-related diseases linked to aberrant Nlrp3 inflammasome activation.
ESTHER : Chhunchha_2023_Int.J.Mol.Sci_24_
PubMedSearch : Chhunchha_2023_Int.J.Mol.Sci_24_
PubMedID: 38003466

Title : ABHD11-AS1: An Emerging Long Non-Coding RNA (lncRNA) with Clinical Significance in Human Malignancies - Golla_2022_Noncoding.RNA_8_21
Author(s) : Golla U , Sesham K , Dallavalasa S , Manda NK , Unnam S , Sanapala AK , Nalla S , Kondam S , Kumar R
Ref : Noncoding RNA , 8 : , 2022
Abstract : The aberrant expression of lncRNAs has been linked to the development and progression of different cancers. One such lncRNA is ABHD11 antisense RNA 1 (ABHD11-AS1), which has recently gained attention for its significant role in human malignancies. ABHD11-AS1 is highly expressed in gastric, lung, breast, colorectal, thyroid, pancreas, ovary, endometrium, cervix, and bladder cancers. Several reports highlighted the clinical significance of ABHD11-AS1 in prognosis, diagnosis, prediction of cancer progression stage, and treatment response. Significantly, the levels of ABHD11-AS1 in gastric juice had been exhibited as a clinical biomarker for the assessment of gastric cancer, while its serum levels have prognostic potential in thyroid cancers. The ABHD11-AS1 has been reported to exert oncogenic effects by sponging different microRNAs (miRNAs), altering signaling pathways such as PI3K/Akt, epigenetic mechanisms, and N6-methyladenosine (m(6)A) RNA modification. In contrast, the mouse homolog of AHD11-AS1 (Abhd11os) overexpression had exhibited neuroprotective effects against mutant huntingtin-induced toxicity. Considering the emerging research reports, the authors attempted in this first review on ABHD11-AS1 to summarize and highlight its oncogenic potential and clinical significance in different human cancers. Lastly, we underlined the necessity for future mechanistic studies to unravel the role of ABHD11-AS1 in tumor development, prognosis, progression, and targeted therapeutic approaches.
ESTHER : Golla_2022_Noncoding.RNA_8_21
PubMedSearch : Golla_2022_Noncoding.RNA_8_21
PubMedID: 35314614
Gene_locus related to this paper: human-ABHD11

Title : Archaeal lipolytic enzymes: Current developments and further prospects - Meghwanshi_2022_Biotechnol.Adv__108054
Author(s) : Meghwanshi GK , Verma S , Srivastava V , Kumar R
Ref : Biotechnol Adv , :108054 , 2022
Abstract : Lipolytic enzymes include triacylglycerol lipases (EC and esterases (EC that catalyze the cleavage and formation of ester bonds. They are potential industrial biocatalysts because of their broad range of activities on natural and synthetic substrates, high stability in organic solvents, thermal stability, stability in highly acidic and alkaline pH conditions and enantio-, regio- and chemo-selectivity. They also have varied applications in different sectors, among which industrial biotechnology, the production of cleaning agents, and pharmaceuticals are the most important ones. Identifying extremophilic lipolytic enzymes is of paramount interest and is a growing field in academic and industrial research. This review is focused on the current knowledge and future avenues of investigation on lipolytic enzymes sourced from the underexploited archaeal domain. Archaea is a potential source for novel extremophilic enzymes, which have high demand in the industries. The archaeal lipases and esterases are clustered into different families based on their similarity/dissimilarity at the genetic level and protein structures. The updated information on characterized and putative lipase sequences has also been presented in this paper. Common structural scaffolds of archaeal lipases have been deduced and discussed in this review. However, huge diversity at the level of their genetic sequences has yet to be correlated with the structure-function relationship. Based on their biochemical properties, possible applications and future prospective of archaeal lipolytic enzymes have also been proposed.
ESTHER : Meghwanshi_2022_Biotechnol.Adv__108054
PubMedSearch : Meghwanshi_2022_Biotechnol.Adv__108054
PubMedID: 36307049

Title : Multi-Target-Directed Ligands as an Effective Strategy for the Treatment of Alzheimer's Disease - Kumar_2021_Curr.Med.Chem__
Author(s) : Kumar B , Thakur A , Dwivedi AR , Kumar R , Kumar V
Ref : Curr Med Chem , : , 2021
Abstract : Alzheimer's disease (AD) is a complex neurological disorder, and multiple pathological factors are believed to be involved in the genesis and progression of the disease. A number of hypotheses, including Acetylcholinesterase, Monoamine oxidase, beta-Amyloid, Tau protein, etc., have been proposed for the initiation and progression of the disease. At present, acetylcholine esterase inhibitors and memantine (NMDAR antagonist) are the only approved therapies for the symptomatic management of AD. Most of these single-target drugs have miserably failed in the treatment or halting the progression of the disease. Multi-factorial diseases like AD require complex treatment strategies that involve simultaneous modulation of a network of interacting targets. Since the last few years, Multi-Target-Directed Ligands (MTDLs) strategy, drugs that can simultaneously hit multiple targets, is being explored as an effective therapeutic approach for the treatment of AD. In the current review article, the authors have briefly described various pathogenic pathways associated with AD. The importance of Multi-Target-Directed Ligands and their design strategies in recently reported articles have been discussed in detail. Potent leads are identified through various structure-activity relationship studies, and their drug-like characteristics are described. Recently developed promising compounds have been summarized in the article. Some of these MTDLs with balanced activity profiles against different targets have the potential to be developed as drug candidates for the treatment of AD.
ESTHER : Kumar_2021_Curr.Med.Chem__
PubMedSearch : Kumar_2021_Curr.Med.Chem__
PubMedID: 33982650

Title : Characterization of deltamethrin, cypermethrin, coumaphos and ivermectin resistance in populations of Rhipicephalus microplus in India and efficacy of an antitick natural formulation prepared from Ageratum conyzoides - Kumar_2021_Ticks.Tick.Borne.Dis_12_101818
Author(s) : Kumar S , Sharma AK , Kumar B , Shakya M , Patel JA , Bisht N , Chigure GM , Singh K , Kumar R , Srivastava S , Rawat P , Ghosh S
Ref : Ticks Tick Borne Dis , 12 :101818 , 2021
Abstract : Rhipicephalus microplus is posing a serious threat to productive animal husbandry. Excessive use of synthetic chemicals in tick management has led to the development of resistant tick populations. Characterization of resistance to deltamethrin, cypermethrin, coumaphos and ivermectin in ticks is necessary to develop a suitable and sustainable control strategy. Based on adult immersion test and larval packet test, the resistance ratios (RR(50)) for adults and larvae of R. microplus populations from two Indian states ranged from 3.8 to 19.4 and 1.35-25.0 against deltamethrin, 0.061-26.3 and 0.22-19.2 against cypermethrin, and 0.2-9.5 and 0.01-3.1 against coumaphos, respectively, were recorded. Moreover, the RR(50) for adults ranged from 0.212 to 3.87 against ivermectin. The RR(50) for different acaricides was significantly (p<0.01) correlated with esterases, Glutathione S-transferase and monooxygenase activity. A point mutation at the 190th position of the domain II S4-5 linker region of the sodium channel gene in synthetic pyrethroids (SP) resistant populations was also detected. An antitick natural formulation prepared from the plant Azeratum conyzoides and containing two major compounds, Precocene-I (7methoxy-2, 2-dimethyl 2H-chromene) and Precocene II (6, 7-dimethoxy-2, 2-dimethyl- 3-chromene), was developed and tested against the resistant ticks. The LC(50) values of the natural formulation against the resistant populations were in the range of 4.31-5.33% irrespective of their RR(50) values. Multi-acaricide resistant populations of R. microplus are established in India and the A. conyzoides based natural formulation can be used for its management.
ESTHER : Kumar_2021_Ticks.Tick.Borne.Dis_12_101818
PubMedSearch : Kumar_2021_Ticks.Tick.Borne.Dis_12_101818
PubMedID: 34537543

Title : Deciphering the Behavioral Response of Meloidogyne incognita and Fusarium oxysporum Toward Mustard Essential Oil - Dutta_2021_Front.Plant.Sci_12_714730
Author(s) : Dutta A , Mandal A , Kundu A , Malik M , Chaudhary A , Khan MR , Shanmugam V , Rao U , Saha S , Patanjali N , Kumar R , Kumar A , Dash S , Singh PK , Singh A
Ref : Front Plant Sci , 12 :714730 , 2021
Abstract : Environmental concerns related to synthetic pesticides and the emphasis on the adoption of an integrated pest management concept as a cardinal principle have strengthened the focus of global research and development on botanical pesticides. A scientific understanding of the mode of action of biomolecules over a range of pests is key to the successful development of biopesticides. The present investigation focuses on the in silico protein-ligand interactions of allyl isothiocyanate (AITC), a major constituent of black mustard (Brassica nigra) essential oil (MEO) against two pests, namely, Meloidogyne incognita (Mi) and Fusarium oxysporum f. sp. lycopersici (Fol), that cause severe yield losses in agricultural crops, especially in vegetables. The in vitro bioassay results of MEO against Mi exhibited an exposure time dependent on the lethal concentration causing 50% mortality (LC(50)) values of 47.7, 30.3, and 20.4 microg ml(-1) at 24, 48, and 72 h of exposure, respectively. The study revealed short-term nematostatic activity at lower concentrations, with nematicidal activity at higher concentrations upon prolonged exposure. Black mustard essential oil displayed excellent in vitro Fol mycelial growth inhibition, with an effective concentration to cause 50% inhibition (EC(50)) value of 6.42 microg ml(-1). In order to decipher the mechanism of action of MEO, its major component, AITC (87.6%), which was identified by gas chromatography-mass spectrometry (GC-MS), was subjected to in silico docking and simulation studies against seven and eight putative target proteins of Mi and Fol, respectively. Allyl isothiocyanate exhibited the highest binding affinity with the binding sites of acetyl cholinesterase (AChE), followed by odorant response gene-1 (ODR1) and neuropeptide G-protein coupled receptor (nGPCR) in Mi, suggesting the possible suppression of neurotransmission and chemosensing functions. Among the target proteins of Fol, AITC was the most effective protein in blocking chitin synthase (CS), followed by 2,3-dihydroxy benzoic acid decarboxylase (6m53) and trypsinase (1try), thus inferring these as the principal molecular targets of fungal growth. Taken together, the study establishes the potential of MEO as a novel biopesticide lead, which will be utilized further to manage the Mi-Fol disease complex.
ESTHER : Dutta_2021_Front.Plant.Sci_12_714730
PubMedSearch : Dutta_2021_Front.Plant.Sci_12_714730
PubMedID: 34512695

Title : Ameliorative effect of myrcene in mouse model of Alzheimer's disease - Kumar_2021_Eur.J.Pharmacol_911_174529
Author(s) : Kumar R , Sharma N , Khurana N
Ref : European Journal of Pharmacology , 911 :174529 , 2021
Abstract : Myrcene (Myr) has been reported to show neuroprotective effects in cerebral ischemia. In this research work, we investigated the Myr effect on neurobehavioural, and neuropathological alteration in mice induced by Aluminium trichloride (AlCl(3)) and D - galactose. The administration of AlCl(3) (5 mg/kg; p. o.), and D - galactose (60 mg/kg; i. p.) for 90 days in mice resulted in spatial learning and memory deficits, cognitive decline, as well as neurotoxicity. The treatments with Myr low dose (100 mg/kg), Myr high dose (200 mg/kg), donepezil (2 mg/kg), and Myr low dose + donepezil (100 + 2 mg/kg) were administered via intraperitoneal route for 30 days significantly reversed the neurobehavioral, and neuropathological effects of AlCl(3) and D - galactose in mice. The results of behavioural tests such as Morris water maze, elevated plus maze, and locomotor; biochemical analysis such as malondialdehyde (MDA), glutathione (GSH), superoxide dismutase (SOD), catalase (CAT), nitrite, and acetylcholinesterase (AChE); and ELISA tests such as mouse beta - secretase (BACE), amyloid-beta peptide(1-42) (Abeta(1 - 42)), tumor necrosis factor - alpha (TNF-alpha), interleukin - 6 (IL-6), and brain-derived neurotrophic factor (BDNF) demonstrated a significant (p < 0.05) neuroprotective effect of the Myr and donepezil co-treatments. In addition, hematoxylin and eosin staining of the cerebral cortex and hippocampus revealed eosinophilic lesions and hyperchromatic nuclei in Alzheimer's disease mice, but treatments with Myr low dose, Myr high dose, donepezil, and Myr low dose + donepezil reversed these neurodegenerative effects. Myr showed these activities by enhancing synaptic plasticity and cholinergic activity, as well as reducing oxidative damage, neuroinflammation, Abeta(1-42) aggregations, and histopathological damage. Myr alone and in combination with donepezil may serve as a potential candidate for the treatment of Alzheimer's disease.
ESTHER : Kumar_2021_Eur.J.Pharmacol_911_174529
PubMedSearch : Kumar_2021_Eur.J.Pharmacol_911_174529
PubMedID: 34592305

Title : Current perspectives for microbial lipases from extremophiles and metagenomics - Verma_2021_Biochimie__
Author(s) : Verma S , Meghwanshi GK , Kumar R
Ref : Biochimie , : , 2021
Abstract : Microbial lipases are most broadly used biocatalysts for environmental and industrial applications. Lipases catalyze the hydrolysis and synthesis of long acyl chain esters and have a characteristic folding pattern of alpha/beta hydrolase with highly conserved catalytic triad (Serine, Aspartic/Glutamic acid and Histidine). Mesophilic lipases (optimal activity in neutral pH range, mesophilic temperature range, atmospheric pressure, normal salinity, non-radio-resistant, and instability in organic solvents) have been in use for many industrial biotransformation reactions. However, lipases from extremophiles can be used to design biotransformation reactions with higher yields, less byproducts or useful side products and have been predicted to catalyze those reactions also, which otherwise are not possible with the mesophilic lipases. The extremophile lipase perform activity at extremes of temperature, pH, salinity, and pressure which can be screened from metagenome and de novo lipase design using computational approaches. Despite structural similarity, they exhibit great diversity at the sequence level. This diversity is broader when lipases from the bacterial, archaeal, plant, and animal domains/kingdoms are compared. Furthermore, a great diversity of novel lipases exists and can be discovered from the analysis of the dark matter - the unexplored nucleotide/metagenomic databases. This review is an update on extremophilic microbial lipases, their diversity, structure, and classification. An overview on novel lipases which have been detected through analysis of the genomic dark matter (metagenome) has also been presented.
ESTHER : Verma_2021_Biochimie__
PubMedSearch : Verma_2021_Biochimie__
PubMedID: 33421499

Title : Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes - Talwar_2020_Sci.Rep_10_1151
Author(s) : Talwar C , Nagar S , Kumar R , Scaria J , Lal R , Negi RK
Ref : Sci Rep , 10 :1151 , 2020
Abstract : Devosia are well known for their dominance in soil habitats contaminated with various toxins and are best characterized for their bioremediation potential. In this study, we compared the genomes of 27 strains of Devosia with aim to understand their metabolic abilities. The analysis revealed their adaptive gene repertoire which was bared from 52% unique pan-gene content. A striking feature of all genomes was the abundance of oligo- and di-peptide permeases (oppABCDF and dppABCDF) with each genome harboring an average of 60.7 +/- 19.1 and 36.5 +/- 10.6 operon associated genes respectively. Apart from their primary role in nutrition, these permeases may help Devosia to sense environmental signals and in chemotaxis at stressed habitats. Through sequence similarity network analyses, we identified 29 Opp and 19 Dpp sequences that shared very little homology with any other sequence suggesting an expansive short peptidic transport system within Devosia. The substrate determining components of these permeases viz. OppA and DppA further displayed a large diversity that separated into 12 and 9 homologous clusters respectively in addition to large number of isolated nodes. We also dissected the genome scale positive evolution and found genes associated with growth (exopolyphosphatase, HesB_IscA_SufA family protein), detoxification (moeB, nifU-like domain protein, alpha/beta hydrolase), chemotaxis (cheB, luxR) and stress response (phoQ, uspA, luxR, sufE) were positively selected. The study highlights the genomic plasticity of the Devosia spp. for conferring adaptation, bioremediation and the potential to utilize a wide range of substrates. The widespread toxin-antitoxin loci and 'open' state of the pangenome provided evidence of plastic genomes and a much larger genetic repertoire of the genus which is yet uncovered.
ESTHER : Talwar_2020_Sci.Rep_10_1151
PubMedSearch : Talwar_2020_Sci.Rep_10_1151
PubMedID: 31980727

Title : Bacosides enrichment does not improve the anti-amnesic effect of Bacopa monnieri: behavioural and biochemical evidences - Arora_2020_Nat.Prod.Res__1
Author(s) : Arora R , Kumar R , Agarwal A , Gupta YK
Ref : Nat Prod Res , :1 , 2020
Abstract : Bacopa monnieri (L.) Wettst. (BM) has been traditionally used in Ayurveda for improving memory and cognitive deficits which is also evidenced through experimental and clinical studies. The neuropharmacological properties of BM are attributed to "bacosides", a complex mixture of saponin compounds. BM extracts enriched with bacosides offers commercial advantage due to perceived higher efficacy. However, there is no scientific data to support the same. In the present study, methanolic extract of BM (BME) was compared with bacosides enriched (BME-EF) vis a vis bacosides free fraction (BME-FF). Potential antioxidant and cholinesterase inhibitory activity has been evaluated using in vitro and in vivo methods. BME showed not only the highest anti-amnesic efficacy but also antioxidant and cholinesterase inhibitory activity, followed by either BME-FF or BME-EF. Interestingly, no significant differences were found in between the groups. These findings dispel the notion that bacosides enrichment enhances anti-amnesic efficacy and also suggests the contribution of other components.
ESTHER : Arora_2020_Nat.Prod.Res__1
PubMedSearch : Arora_2020_Nat.Prod.Res__1
PubMedID: 32924596

Title : Small molecule therapeutics for tauopathy in Alzheimer's disease: Walking on the path of most resistance - Wang_2020_Eur.J.Med.Chem__112915
Author(s) : Wang L , Bharti , Kumar R , Pavlov PF , Winblad B
Ref : Eur Journal of Medicinal Chemistry , :112915 , 2020
Abstract : Alzheimer's disease (AD) is the most common form of dementia characterized by presence of extracellular amyloid plaques and intracellular neurofibrillary tangles composed of tau protein. Currently there are close to 50 million people living with dementia and this figure is expected to increase to 75 million by 2030 putting a huge burden on the economy due to the health care cost. Considering the effects on quality of life of patients and the increasing burden on the economy, there is an enormous need of new disease modifying therapies to tackle this disease. The current therapies are dominated by only symptomatic treatments including cholinesterase inhibitors and N-methyl-D-aspartate receptor blockers but no disease modifying treatments exist so far. After several failed attempts to develop drugs against amyloidopathy, tau targeting approaches have been in the main focus of drug development against AD. After an overview of the tauopathy in AD, this review summarizes recent findings on the development of small molecules as therapeutics targeting tau modification, aggregation, and degradation, and tau-oriented multi-target directed ligands. Overall, this work aims to provide a comprehensive and critical overview of small molecules which are being explored as a lead candidate for discovering drugs against tauopathy in AD.
ESTHER : Wang_2020_Eur.J.Med.Chem__112915
PubMedSearch : Wang_2020_Eur.J.Med.Chem__112915
PubMedID: 33139110

Title : Ajmalicine and Reserpine: Indole Alkaloids as Multi-Target Directed Ligands Towards Factors Implicated in Alzheimer's Disease - Kashyap_2020_Molecules_25_
Author(s) : Kashyap P , Kalaiselvan V , Kumar R , Kumar S
Ref : Molecules , 25 : , 2020
Abstract : Alzheimer's disease (AD) is a multifactorial disorder characterized by exponential loss of memory and cognitive deficit involving several disease modifying targets (amyloid beta, beta-secretase, monoaminoxidase-B, and cholinesterase). The present study explores multi-target directed ligand approach using secondary metabolite reserpine (RES) and ajmalicine (AJM) obtained from Rauwolfia serpentina roots. Novel LCMS and HPLC methods were developed for identification and quantification of reserpine and ajmalicine. In vitro enzyme inhibition assays were performed to evaluate anti-cholinesterase, beta-site amyloid cleaving enzyme (BACE-1) inhibition and monoamine oxidase-B (MAO-B) inhibition, further analyzed with in silico analysis. Anti-amyloidogenic potential was studied using anti-aggregation studies along with TEM and circular dichroism (CD) analysis. In vitro neuroprotective potential against Abeta toxicity and anti-oxidative stress was demonstrated using PC12 cell cultures. Reserpine is a more potent dual cholinesterase inhibitor than ajmalicine (IC50 values of 1.7 muM (AChE) and 2.8 muM (BuChE)). The anti-aggregation activity of reserpine (68%) was more than ajmalicine (56%). Both compounds demonstrated neuroprotective activity against Abeta42 (92%) and H2O2 (93%) induced toxicity in PC12 cells against controls. Phytocompounds also inhibited MAO-B and BACE-1 enzymes in concentration dependent manner. Molecular docking studies indicated the strong binding of compounds to the catalytic site of targets. This novel study demonstrated that reserpine and ajmalicine as a multi-target directed ligand that have disease modifying potential for amelioration of AD.
ESTHER : Kashyap_2020_Molecules_25_
PubMedSearch : Kashyap_2020_Molecules_25_
PubMedID: 32244635

Title : Cloning, Characterization, and Structural Modeling of an Extremophilic Bacterial Lipase Isolated from Saline Habitats of the Thar Desert - Verma_2020_Appl.Biochem.Biotechnol__
Author(s) : Verma S , Kumar R , Kumar P , Sharma D , Gahlot H , Sharma PK , Meghwanshi GK
Ref : Appl Biochem Biotechnol , : , 2020
Abstract : Lipases have a characteristic folding pattern of alpha/beta-hydrolase with mostly parallel beta-sheets, flanked on both sides by alpha-helixes in the structure. The active site is formed by a catalytic triad (serine, aspartic/glutamic acid, and histidine), which is highly conserved. In this study, we have used an integrated experimental and computational approach to identify the extremophilic microbial lipases from the saline habitats of the Thar Desert of Rajasthan. Lipase-producing bacteria were screened and a few samples showed significant lipase activity in both quantitative and qualitative experiments. 16S rRNA sequence analysis of the isolate F1 showed that its sequence is quite similar to that of Bacillus licheniformis and Bacillus haynesii, indicating that this isolate belongs to a new subspecies of Bacillus. The isolate F7 showed maximum sequence identity with Bacillus tequilensis strain 10b. The isolate F7 sequence analysis provided a clear testimony that it can be a new strain of Bacillus tequilensis. The F7 lipase exhibited optimal activity at 60 degrees C and pH 9. Structural modeling of the F7 lipase revealed that it has a highly conserved alpha/beta hydrolase fold at the sequence and structural level except for the N-terminal region. Interestingly, residue Glu128 was different from the template structure and showed the hydrogen bonding between the side chain of Glu128 and side chains of Asn35 and Gln152 amino acids. Besides, this amino acid also showed salt bridge interaction between Glu128--Lys101. These interactions may be assisting in preserving the stability and activity of lipase at high temperatures and in alkaline pH conditions. The information gathered from this investigation will guide in the rational designing of new more potential extremophilic lipase.
ESTHER : Verma_2020_Appl.Biochem.Biotechnol__
PubMedSearch : Verma_2020_Appl.Biochem.Biotechnol__
PubMedID: 32424739
Gene_locus related to this paper: 9baci-F7lip

Title : A Broad Temperature Active Lipase Purified From a Psychrotrophic Bacterium of Sikkim Himalaya With Potential Application in Detergent Formulation - Kumar_2020_Front.Bioeng.Biotechnol_8_642
Author(s) : Kumar A , Mukhia S , Kumar N , Acharya V , Kumar S , Kumar R
Ref : Front Bioeng Biotechnol , 8 :642 , 2020
Abstract : Bacterial lipases with activity spanning over a broad temperature and substrate range have several industrial applications. An efficient enzyme-producing bacterium Chryseobacterium polytrichastri ERMR1:04, previously reported from Sikkim Himalaya, was explored for purification and characterization of cold-adapted lipase. Optimum lipase production was observed in 1% (v/v) rice bran oil, pH 7 at 20degC. Size exclusion and hydrophobic interaction chromatography purified the enzyme up to 21.3-fold predicting it to be a hexameric protein of 250 kDa, with 39.8 kDa monomeric unit. MALDI-TOF-MS analysis of the purified lipase showed maximum similarity with alpha/beta hydrolase (lipase superfamily). Biochemical characterization of the purified enzyme revealed optimum pH (8.0), temperature (37degC) and activity over a temperature range of 5-65degC. The tested metals (except Cu(2+) and Fe(2+)) enhanced the enzyme activity and it was tolerant to 5% (v/v) methanol and isopropanol. The Km and Vmax values were determined as 0.104 mM and 3.58 U/mg, respectively for p-nitrophenyl palmitate. Bioinformatics analysis also supported in vitro findings by predicting enzyme's broad temperature and substrate specificity. The compatibility of the purified lipase with regular commercial detergents, coupled with its versatile temperature and substrate range, renders the given enzyme a promising biocatalyst for potential detergent formulations.
ESTHER : Kumar_2020_Front.Bioeng.Biotechnol_8_642
PubMedSearch : Kumar_2020_Front.Bioeng.Biotechnol_8_642
PubMedID: 32671041

Title : A comprehensive review on ethnomedicine, phytochemistry, pharmacology, and toxicity of Tephrosia purpurea (L.) Pers - Rao_2020_Phytother.Res__
Author(s) : Rao AS , Yadav SS , Singh P , Nandal A , Singh N , Ganaie SA , Yadav N , Kumar R , Bhandoria MS , Bansal P
Ref : Phytother Res , : , 2020
Abstract : Tephrosia purpurea (L.) Pers. is a well-known plant in Ayurveda and named "Sarwa wranvishapaka" for its property to heal wounds. Traditionally, it is practiced for impotency, asthma, dyspepsia, hemorrhoids, syphilis gonorrhea, rheumatism, enlargement of kidney and spleen. It is an important component of herbal preparations like Tephroli and Yakrifti used to cure liver disorders. Various phytocompounds including pongamol, purpurin, purpurenone, tephrosin, bulnesol, tephrostachin, beta-sitosterol, and so on have been reported. Modern pharmacological studies have shown that the plant have wound healing, antileishmanial, anticarcinogenic, antimicrobial, antioxidant, hepatoprotective, antifertility, antispermatogenic, anti-diarrheal, diuretic, and insecticidal properties. Acetylcholinesterase inhibitory action reported from this plant aids its utilization for the development of drugs for Alzheimer's and dementia neurological disorders. Among the known active compounds of T. purpurea, tephrostachin is responsible for antiplasmodial activity, tephrosin, pongaglabol, and semiglabrin exerts antiulcer activity while quercetin, rutin, beta-sitosterol, and lupeol are mainly responsible for its anti-inflammatory and anti-cancer properties. From different toxicological studies, concentrations up to 2,000 mg/kg were considered safe. The present review comprehensively summarizes the ethnomedicine, phytochemistry, pharmacology, and toxicology of T. purpurea. Further research on elucidation of the structure-function relationship among active compounds, understanding of multi-target network pharmacology and clinical applications will intensify its therapeutic potential.
ESTHER : Rao_2020_Phytother.Res__
PubMedSearch : Rao_2020_Phytother.Res__
PubMedID: 32147928

Title : Structural and functional insights about unique extremophilic bacterial lipolytic enzyme from metagenome source - Kaur_2020_Int.J.Biol.Macromol__
Author(s) : Kaur R , Kumar R , Verma S , Kumar A , Rajesh C , Sharma PK
Ref : Int J Biol Macromol , : , 2020
Abstract : In the present investigation, a lipid hydrolyzing gene RPK01was cloned from metagenome source of hot spring. Expression and purification of recombinant protein revealed a protein band of ~24 KDa on 12% SDS-PAGE and is well corroborated with the deduced molecular weight calculated from its amino acid sequence. The purified protein displayed high activity towards short chain fatty acids and was found to be completely stable at 30 degrees C till 3h, and retained ~40% activity at 50 degrees C and 60 degrees C temperature till 3h. Additionally, the pH stability assay showed its functionality in broad range pH, with maximum stability observed at pH2.0, it decreases from pH4.0 to pH12.0 and has retained ~ 40% activity in these pHs. Both circular dichroism and intrinsic Trp fluorescence studies revealed conformational stability of protein structure in wide range of temperature and pH. Enzyme activity enhances in presence of non-ionic surfactants like Tween 20 and TritonX-100. Further, inhibitors of the active site residues including PMSF and DEPC alone were unable to inhibit enzyme activity, while cumulative presence of calcium and inhibitors reduces enzyme activity to 90% indicating conformational changes in the protein. Molecular simulation dynamics analysis revealed a calcium binding site near the lid helix (Asn75-Ile80).
ESTHER : Kaur_2020_Int.J.Biol.Macromol__
PubMedSearch : Kaur_2020_Int.J.Biol.Macromol__
PubMedID: 32088224
Gene_locus related to this paper: bacce-BC4862

Title : Comparison of Chemical Composition and Biological Activities of Eight Selaginella Species - Krizkovska_2020_Pharmaceuticals.(Basel)_14_
Author(s) : Krizkovska B , Kumar R , Rehorova K , Sykora D , Dobiasova S , Kucerova D , Tan MC , Linis V , Oyong G , Ruml T , Lipov J , Viktorova J
Ref : Pharmaceuticals (Basel) , 14 : , 2020
Abstract : Selaginella P. Beauv. is a group of vascular plants in the family Selaginellaceae Willk., found worldwide and numbering more than 700 species, with some used as foods and medicines. The aim of this paper was to compare methanolic (MeOH) and dichloromethane (DCM) extracts of eight Selaginella species on the basis of their composition and biological activities. Six of these Selaginella species are underinvestigated. Using ultra-high performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) analysis, we identified a total of 193 compounds among the tested Selaginella species, with flavonoids predominating. MeOH extracts recovered more constituents that were detected, including selaginellins, the occurrence of which is only typical for this plant genus. Of all the tested species, Selaginellaapoda contained the highest number of identified selaginellins. The majority of the compounds were identified in S. apoda, the fewest compounds in Selaginellacupressina. All the tested species demonstrated antioxidant activity using oxygen radical absorption capacity (ORAC) assay, which showed that MeOH extracts had higher antioxidant capacity, with the half maximal effective concentration (EC(50)) ranging from 12 +/- 1 (Selaginellamyosuroides) to 124 +/- 2 (Selaginellacupressina) mg/L. The antioxidant capacity was presumed to be correlated with the content of flavonoids, (neo)lignans, and selaginellins. Inhibition of acetylcholinesterase (AChE) was mostly discerned in DCM extracts and was only exhibited in S. myosuroides, S. cupressina, Selaginellabiformis, and S. apoda extracts with the half maximal inhibitory concentration (IC(50)) in the range of 19 +/- 3 to 62 +/- 1 mg/L. Substantial cytotoxicity against cancer cell lines was demonstrated by the MeOH extract of S. apoda, where the ratio of the IC(50) HEK (human embryonic kidney) to IC(50) HepG2 (hepatocellular carcinoma) was 7.9 +/- 0.2. MeOH extracts inhibited the production of nitrate oxide and cytokines in a dose-dependent manner. Notably, S. biformis halved the production of NO, tumor necrosis factor (TNF)-alpha, and interleukin (IL)-6 at the following concentrations: 105 +/- 9, 11 +/- 1, and 10 +/- 1 mg/L, respectively. Our data confirmed that extracts from Selaginella species exhibited cytotoxicity against cancer cell lines and AChE inhibition. The activity observed in S. apoda was the most promising and is worth further exploration.
ESTHER : Krizkovska_2020_Pharmaceuticals.(Basel)_14_
PubMedSearch : Krizkovska_2020_Pharmaceuticals.(Basel)_14_
PubMedID: 33375355

Title : Identification of new members of alkaliphilic lipases in archaea and metagenome database using reconstruction of ancestral sequences - Verma_2019_3.Biotech_9_165
Author(s) : Verma S , Kumar R , Meghwanshi GK
Ref : 3 Biotech , 9 :165 , 2019
Abstract : The application of bioinformatics in lipase research has the potential to discover robust members from different genomic/metagenomic databses. In this study, we explored the diversity and distribution of alkaliphilic lipases in archaea domain and metagenome data sets through phylogenetic survey. Reconstructed ancestral sequence of alkaphilic lipase was used to search the homologous alkaliphilic lipases among the archaea and metagenome public databases. Our investigation revealed a total 21 unique sequences of new alkaliphilic lipases in the archaeal and environmental metagenomic protein databases that shared significant sequence similarity to the bacterial alkaliphilic lipases. Most of the identified new members of alkaliphilic lipases belong to class Haloarchaea. The searched list of homologs also comprised of one characterized lipase from alkalohyperthermophilic Archaeoglobus fulgidus. All the newly identified alkaliphilic lipase members showed conserved pentapeptide [X-His-Ser-X-Gly] motif, a key feature of lipase family. Furthermore, detailed analysis of all these new sequences showed homology either with thermostable or alkalophilic lipases. The reconstructed ancestral sequence-based searches increased the sensitivity and efficacies to detect remotely homologous sequences. We hypothesize that this study can enrich our current knowledge on lipases in designing more potential thermo-alkaliphilic lipases for industrial applications.
ESTHER : Verma_2019_3.Biotech_9_165
PubMedSearch : Verma_2019_3.Biotech_9_165
PubMedID: 30997302

Title : Investigation of novel chemical scaffolds targeting prolyl oligopeptidase for neurological therapeutics - Kumar_2019_J.Mol.Graph.Model_88_92
Author(s) : Kumar R , Parameswaran S , Bavi R , Baek A , Son M , Rampogu S , Park C , Lee G , Zeb A , Parate S , Rana RM , Lee KW
Ref : J Mol Graph Model , 88 :92 , 2019
Abstract : Prolyl oligopeptidase (POP) is a potential therapeutic target for treatment of several neurological disorders and alpha-synucleinopathies including Parkinson's disease. Most of the known POP inhibitors failed in the clinical trials due to poor pharmacokinetic properties and blood-brain impermeability. Therefore, a training set of 30 structurally diverse compounds with a wide range of inhibitory activity against POP was used to generate a quantitative pharmacophore model, Hypo 3, to identify potential POP inhibitors with desirable drug-like properties. Validations through test set, cost analysis, and Fisher's randomization methods proved that Hypo 3 accurately predicted the known inhibitors among inactive compounds. Hypo 3 was employed as 3D query for virtual screening on an in-house drug-like chemical database containing compounds with good brain permeability and ADMET parameters. Database screening with Hypo 3 resulted in 99 compounds that were narrowed down to 21 compounds through molecular docking. Among them, five compounds were identified in our earlier studies, while two compounds showed in vitro POP inhibition. The current study proposed new 16 virtually screened compounds as potential inhibitors against POP that possess Gold docking score in the range of 64.61-75.74 and Chemscore of -32.25 to -38.35. Furthermore, the top scoring four hit compounds were subjected to molecular dynamics simulations to reveal their appropriate binding modes and assessing binding free energies. The hit compounds interacted with POP effectively via hydrogen bonds with important active site residues along with hydrophobic interactions. Moreover, the hit compounds had key inter-molecular interactions and better binding free energies as compared to the reference inhibitor. A potential new hydrogen bond interaction was discovered between Hit 2 with the Arg252 residue of POP. To conclude, we propose four hit compounds with new structural scaffolds against POP for the lead development of POP-based therapeutics for neurological disorders.
ESTHER : Kumar_2019_J.Mol.Graph.Model_88_92
PubMedSearch : Kumar_2019_J.Mol.Graph.Model_88_92
PubMedID: 30665156

Title : Engineering lipases for temperature adaptation: Structure function correlation - Kumar_2019_Biochim.Biophys.Acta.Proteins.Proteom_1867_140261
Author(s) : Kumar R , Goomber S , Kaur J
Ref : Biochimica & Biophysica Acta Proteins Proteom , 1867 :140261 , 2019
Abstract : Bacillus lipases are industrially attractive enzymes due to their broad substrate specificity and optimum alkaline pH. However, narrow temperature range of action and low thermostability restrain their optimal use and thus, necessitate attention. Several laboratories are engaged in protein engineering of Bacillus lipases to generate variants with improved attributes for decades using techniques such as directed evolution or rational design. This review summarizes the effect of mutations on the conformational changes through in silico modeling and their manifestation with respect to various biochemical parameters. Various studies have been put together to develop a perspective on the molecular basis of biocatalysis of lipases holding industrial importance.
ESTHER : Kumar_2019_Biochim.Biophys.Acta.Proteins.Proteom_1867_140261
PubMedSearch : Kumar_2019_Biochim.Biophys.Acta.Proteins.Proteom_1867_140261
PubMedID: 31401312

Title : Molecular markers and their application in the monitoring of acaricide resistance in Rhipicephalus microplus - Kumar_2019_Exp.Appl.Acarol_78_149
Author(s) : Kumar R
Ref : Exp Appl Acarol , 78 :149 , 2019
Abstract : Monitoring acaricide resistance and understanding the underlying mechanisms are critically important in developing strategies for resistance management and tick control. Identification of single nucleotide polymorphisms in the acaricide-resistant associated gene of Rhipicephalus microplus has enabled the development of molecular markers for detection and monitoring of resistance against different types of acaricide. There are many molecular markers developed for resistance monitoring, including mutations on target genes such as sodium channel, acetylcholinesterase, carboxylesterase, beta-adrenergic octopamine receptor, octopamine-tyramine etc. Molecular genotyping through molecular markers can detect the presence of resistance-associated genes in a tick population before it reaches high frequency. This review aims to provide an update on the various molecular markers discovered to date from different regions of the world.
ESTHER : Kumar_2019_Exp.Appl.Acarol_78_149
PubMedSearch : Kumar_2019_Exp.Appl.Acarol_78_149
PubMedID: 31190248

Title : Soluble Abeta42 Acts as Allosteric Activator of the Core Cholinergic Enzyme Choline Acetyltransferase - Kumar_2018_Front.Mol.Neurosci_11_327
Author(s) : Kumar A , Lana E , Kumar R , Lithner CU , Darreh-Shori T
Ref : Front Mol Neurosci , 11 :327 , 2018
Abstract : Two major questions in the field of Alzheimer-type dementia remain elusive. One is the native function of amyloid-beta (Abeta) peptides and the other is an early deficit in the central cholinergic network. Nevertheless, recent evidence suggests that Abeta peptides are involved in the regulation of acetylcholine (ACh) homeostasis either by allosteric activation of ACh-degrading cholinesterases or by inhibiting the high-affinity choline uptake transporter. In the current study, we report that Abeta peptides, in particular Abeta42, allosterically enhances the catalytic rate of the core-cholinergic enzyme choline acetyltransferase (ChAT), responsible for biosynthesis of ACh. Detailed in vitro enzyme kinetic analysis indicated that both soluble Abeta40 and Abeta42 enhanced the catalytic efficiency of ChAT by approximately 21% and 26% at physiological concentration ranges found in human cerebrospinal fluid (CSF). Further analyses indicated that activation of ChAT by Abeta was highly specific. Intriguingly, Abeta42 exhibited an EC50 of activation potency at 10-fold lower concentrations compared to Abeta40. The activation was persistent even in the presence of a physiological Abeta 40/42 mixture ratio, expected in human CSF. In conclusion, we report for the first time that Abeta42 peptide acts as allosteric enhancers of ACh-biosynthesizing enzyme ChAT. Together with two previous observations, this points to a complex molecular cross-talk between Abeta and the enzymatic machinery involved in maintaining cellular, synaptic and extra-synaptic ACh homeostasis, warranting further investigation.
ESTHER : Kumar_2018_Front.Mol.Neurosci_11_327
PubMedSearch : Kumar_2018_Front.Mol.Neurosci_11_327
PubMedID: 30271321

Title : Comparison of three different extracts of Centella asiatica for anti-amnesic, antioxidant and anticholinergic activities: in vitro and in vivo study - Arora_2018_Biomed.Pharmacother_105_1344
Author(s) : Arora R , Kumar R , Agarwal A , Reeta KH , Gupta YK
Ref : Biomed Pharmacother , 105 :1344 , 2018
Abstract : Centella asiatica (CA) has been used by Ayurvedic medical practitioners in India for almost 3000 years. The neuropharmacological properties of CA and its constituents have been studied extensively. Anti-oxidant, free radical scavenging and cholinergic modulatory activities are the reported mechanisms of action for its efficacy in memory disorders. Its medicinal values are mainly attributed to the presence of several triterpenes, namely asiatic acid, madecassic acid, asiaticoside, and madecassoside. The present study was aimed to investigate the role of these triterpenes content in CA extract on the antioxidant, cholinesterase modulation and anti-amnesic properties. The fractions of CA extract enriched for (CAE-EF) and depleted/freed of (CAE-FF) triterpenes contents were compared with methanolic extract (CAE). Both in vitro and in vivo methods for evaluation of antioxidant and anticholinergic activities were used. In vitro, free radical scavenging assays (ABTS, DPPH, NO, NORAC, and ORAC) and cholinesterase (AChE and BuChE) inhibition assays were used. For evaluation of anti-amnesic effect, scopolamine induced amnesia in rats, as the acute model of memory loss was used. Following behavioural assessments (MWM, PA, EPM), biomarkers of oxidative stress (reduced GSH, MDA and SOD activity) and cholinesterase (AChE and BuChE) status were also estimated in cerebral cortex and hippocampus of rat brain. The methanolic extract (CAE) was found to perform best among all three fractions for in vitro free radical scavenging, cholinesterase inhibition, improvement of scopolamine-induced amnesia and also in vivo antioxidant effect and cholinesterase inhibitory activities. Interestingly triterpenes free fraction (CAE-FF) showed better antioxidant activity than triterpenes enriched fraction (CAE-EF) along with comparable anti-amnesic effect. This indicates that triterpenes are not solely responsible for antioxidant activity, cholinesterase inhibitory and anti-amnesic effect of CA.
ESTHER : Arora_2018_Biomed.Pharmacother_105_1344
PubMedSearch : Arora_2018_Biomed.Pharmacother_105_1344
PubMedID: 30021372

Title : Molecular mechanism of synthetic pyrethroid and organophosphate resistance in field isolates of Rhipicephalus microplus tick collected from a northern state of India - Nagar_2018_Exp.Appl.Acarol_75_319
Author(s) : Nagar G , Sharma AK , Kumar S , Saravanan BC , Kumar R , Gupta S , Ghosh S
Ref : Exp Appl Acarol , 75 :319 , 2018
Abstract : The frequently used chemical control method to manage Rhipicephalus microplus is limited by the emergence of resistance populations. Understanding of resistance mechanisms is essential to develop strategy for sustainable management. The present study was focused on working out the molecular mechanisms of resistance against synthetic pyrethroids (SPs) and organophosphates (OPs) in field isolates of R. microplus collected from six districts of Uttar Pradesh, India. Adult immersion test with discriminating concentrations (AIT-DC) was used to determine resistance status of isolates to SPs (deltamethrin, cypermethrin) and OPs (diazinon, coumaphos). All the six isolates were found resistant to SPs with resistance factor (RF) of 2.9-58.6 and to one of the OP compounds, diazinon having RF of 3.5-13.7 but susceptible to coumaphos (RF < 1.4). Three R. microplus genes, viz. para-sodium channel domain II S4-5 linker, carboxylesterase (372 bp) and acetylcholinesterase 2 (1692 bp) were sequenced and compared with respective sequences of reference susceptible IVRI-I, reference OP resistant population (IVRI-III), IVRI-IV and multi-acaricide resistant population (IVRI-V) of R. microplus. A C190A mutation in the domain II S4-5 linker region of sodium channel gene leading to L64I amino acid substitution was detected in all six isolates. The G1120A mutation in the carboxylesterase gene could not be detected in any isolate. Five nucleotide substitutions viz., G138A, G889A, T1090A, C1234T and G1403A were identified in the acetylcholinesterase 2 gene leading to four amino acid substitutions. The findings of the study corroborate the role of mutation in sodium channel and acetylcholinesterase 2 genes in SP and OP resistance in this part of India.
ESTHER : Nagar_2018_Exp.Appl.Acarol_75_319
PubMedSearch : Nagar_2018_Exp.Appl.Acarol_75_319
PubMedID: 29846851
Gene_locus related to this paper: boomi-ACHE2

Title : Serum butyrylcholinesterase and zinc in breast cancer - Kumar_2017_J.Cancer.Res.Ther_13_367
Author(s) : Kumar R , Razab S , Prabhu K , Ray S , Prakash B
Ref : J Cancer Research Ther , 13 :367 , 2017
Abstract : CONTEXT: Even though, a large number of serological, molecular markers have been proposed for breast cancer screening, most of them lack specificity, sensitivity, prognostic value, and cost effectiveness. Butyrylcholinesterase (BChE) and its genes are aberrantly expressed in a variety of human cancers. It has-been linked to tumorigenesis, cell proliferation, and cell differentiation. Zinc (Zn) is a cofactor for superoxide dismutase, an enzyme that protects cellular components against free radical-induced damage and carcinogenesis. Therefore, the aim of present study was to estimate and compare serum BChE and serum Zn levels in healthy controls and biopsy proven breast cancer patients before definitive therapy. AIMS: To estimate and compare serum BChE and serum Zn levels in healthy controls and biopsy proven breast cancer patients before definitive therapy. SETTINGS AND DESIGN: Serum BChE and Zn were estimated in 46 newly diagnosed (preoperative) female patients with breast cancer and 50 healthy female volunteers. SUBJECTS AND
METHODS: Serum BChE and Zn were estimated by spectrophotometric method. STATISTICAL ANALYSIS USED: Data was expressed as median and inter quartile range. Comparisons between different stages of cancer were done using Kruskal-Wallis test.
RESULTS: There was a significant increase in serum BChE and Zn in breast cancer patients compared to controls (P < 0.001). Serum BChE showed a significant increase and Zn was significantly decreased in different stages of breast cancer.
CONCLUSIONS: Both BChE and Zn are inexpensive and can easily be analyzed and may play a role in the management of breast cancer.
ESTHER : Kumar_2017_J.Cancer.Res.Ther_13_367
PubMedSearch : Kumar_2017_J.Cancer.Res.Ther_13_367
PubMedID: 28643762

Title : Thirty-degree shift in optimum temperature of a thermophilic lipase by a single-point mutation: effect of serine to threonine mutation on structural flexibility - Sharma_2017_Mol.Cell.Biochem_430_21
Author(s) : Sharma M , Kumar R , Singh R , Kaur J
Ref : Molecular & Cellular Biochemistry , 430 :21 , 2017
Abstract : In order to understand the molecular basis of cold adaptation, we have used directed evolution to transform a thermophilic lipase LipR1 into its psychrophilic counterpart. A single round of random mutagenesis followed by screening for improved variants yielded a mutant with single-point mutation LipR1M1 (S130T), with optimum activity at 20 degrees C. Its activity at 50 degrees C is only 20% as compared to wild type (100%). It showed catalytic rate constant (k cat) 3 times higher and a catalytic efficiency (k cat/K m) 4 times that of wild type. Circular dichroism and fluorescence studies also supported our observation of mutant structural flexibility. Structure analysis using homology models showed that Threonine 130 is exposed to solvent and has lost H-bond interaction with neighboring amino acid, thereby increasing flexibility of this lipase structure.
ESTHER : Sharma_2017_Mol.Cell.Biochem_430_21
PubMedSearch : Sharma_2017_Mol.Cell.Biochem_430_21
PubMedID: 28190170

Title : Enantiomeric separation of pharmaceutically important drug intermediates using a Metagenomic lipase and optimization of its large scale production - Kumar_2017_Int.J.Biol.Macromol_95_995
Author(s) : Kumar R , Banoth L , Banerjee UC , Kaur J
Ref : Int J Biol Macromol , 95 :995 , 2017
Abstract : In the present study, efficient enzymatic methods were developed using a recombinant metagenomic lipase (LipR1) for the synthesis of corresponding esters by the transesterification of five different pharmaceutically important secondary alcohols. The recombinant lipase (specific activity=87m6U/mg) showed maximum conversion in presence of ionic liquid with Naphthyl-ethanol (eeP=99%), Indanol and Methyl-4 pyridine methanol (eeS of 98% and 99%) respectively in 1h. Vinyl acetate was found as suitable acyl donor in transesterification reactions. It was interesting to observe that maximum eeP of 85% was observed in just 15min with 1-indanol. As this enzyme demonstrated pharmaceutical applications, attempts were made to scale up the enzyme production on a pilot scale in a 5litre bioreactor. Different physical parameters affecting enzyme production and biomass concentration such as agitation rate, aeration rate and inoculum concentration were evaluated. Maximum lipase activity of 8463U/ml was obtained at 7h of cultivation at 1 lpm, 300rpm and 1.5% inoculum.
ESTHER : Kumar_2017_Int.J.Biol.Macromol_95_995
PubMedSearch : Kumar_2017_Int.J.Biol.Macromol_95_995
PubMedID: 27984150

Title : New compounds identified through in silico approaches reduce the alpha-synuclein expression by inhibiting prolyl oligopeptidase in vitro - Kumar_2017_Sci.Rep_7_10827
Author(s) : Kumar R , Bavi R , Jo MG , Arulalapperumal V , Baek A , Rampogu S , Kim MO , Lee KW
Ref : Sci Rep , 7 :10827 , 2017
Abstract : Prolyl oligopeptidase (POP) is a serine protease that is responsible for the maturation and degradation of short neuropeptides and peptide hormones. The inhibition of POP has been demonstrated in the treatment of alpha-synucleinopathies and several neurological conditions. Therefore, ligand-based and structure-based pharmacophore models were generated and validated in order to identify potent POP inhibitors. Pharmacophore-based and docking-based virtual screening of a drug-like database resulted in 20 compounds. The in vitro POP assays indicated that the top scoring compounds obtained from virtual screening, Hit 1 and Hit 2 inhibit POP activity at a wide range of concentrations from 0.1 to 10 microM. Moreover, treatment of the hit compounds significantly reduced the alpha-synuclein expression in SH-SY5Y human neuroblastoma cells, that is implicated in Parkinson's disease. Binding modes of Hit 1 and Hit 2 compounds were explored through molecular dynamics simulations. A detailed investigation of the binding interactions revealed that the hit compounds exhibited hydrogen bond interactions with important active site residues and greater electrostatic and hydrophobic interactions compared to those of the reference inhibitors. Finally, our findings indicated the potential of the identified compounds for the treatment of synucleinopathies and CNS related disorders.
ESTHER : Kumar_2017_Sci.Rep_7_10827
PubMedSearch : Kumar_2017_Sci.Rep_7_10827
PubMedID: 28883518

Title : Characterization and establishment of a reference deltamethrin and cypermethrin resistant tick line (IVRI-IV) of Rhipicephalus (Boophilus) microplus - Ghosh_2017_Pestic.Biochem.Physiol_138_66
Author(s) : Ghosh S , Gupta S , Ajith Kumar KG , Sharma AK , Kumar S , Nagar G , Kumar R , Paul S , Fular A , Chigure G , Nandi A , Manjunathachar HV , Mohammad A , Verma MR , Saravanan BC , Ray D
Ref : Pestic Biochem Physiol , 138 :66 , 2017
Abstract : The problem of ticks and tick borne diseases is a global threat and growing reports of resistance to commonly used insecticides further aggravated the condition and demands for country specific resistance monitoring tools and possible solutions of the problem. Establishment of standard reference is prerequisite for development of monitoring tools. For studying possible role of different mechanisms involved in development of resistance in Rhipicephalus (Boophilus) microplus population and to develop newer drug to manage the problem of resistance, a deltamethrin exposed and selected tick colony, referred to as IVRI-IV, was characterized using reference susceptible IVRI-I tick line as control. The RF values of IVRI-IV ticks against deltamethrin, cypermethrin and diazinon were determined as 194.0, 26.6, 2.86, respectively, against adults. The esterase enzyme ratios of 2.60 and 5.83 was observed using alpha-naphthyl and beta-naphthyl acetate while glutathione S-transferase (GST) ratio was 3.77. Comparative analysis of IVRI-I and IVRI-IV carboxylesterase gene sequences revealed 13 synonymous and 5 non synonymous mutations, reported for the first time. The C190A mutation in the domain II S4-5 linker region of sodium channel gene leading to leucine to isoleucine (L64I) amino acid substitution was also detected in the IVRI-IV population. In the present study, monitorable indicators for the maintenance of the reference IVRI-IV colony, the first established deltamethrin and cypermethrin resistant tick line of India, were identified.
ESTHER : Ghosh_2017_Pestic.Biochem.Physiol_138_66
PubMedSearch : Ghosh_2017_Pestic.Biochem.Physiol_138_66
PubMedID: 28456306

Title : Amyloid-beta peptides act as allosteric modulators of cholinergic signalling through formation of soluble BAbetaACs - Kumar_2016_Brain_139_174
Author(s) : Kumar R , Nordberg A , Darreh-Shori T
Ref : Brain , 139 :174 , 2016
Abstract : Amyloid-beta peptides, through highly sophisticated enzymatic machinery, are universally produced and released in an action potential synchronized manner into the interstitial fluids in the brain. Yet no native functions are attributed to amyloid-beta. The amyloid-beta hypothesis ascribes just neurotoxicity properties through build-up of soluble homomeric amyloid-beta oligomers or fibrillar deposits. Apolipoprotein-epsilon4 (APOE4) allele is the only confirmed genetic risk factor of sporadic Alzheimer's disease; once more it is unclear how it increases the risk of Alzheimer's disease. Similarly, central cholinergic signalling is affected selectively and early in the Alzheimer's disease brain, again why cholinergic neurons show this sensitivity is still unclear. However, the three main known Alzheimer's disease risk factors, advancing age, female gender and APOE4, have been linked to a high apolipoprotein-E and accumulation of the acetylcholine degrading enzyme, butyrylcholinesterase in cerebrospinal fluids of patients. Furthermore, numerous reports indicate that amyloid-beta interacts with butyrylcholinesterase and apolipoprotein-E. We have proposed that this interaction leads to formation of soluble ultrareactive acetylcholine-hydrolyzing complexes termed BAbetaACs, to adjust at demand both synaptic and extracellular acetylcholine signalling. This hypothesis predicted presence of acetylcholine-synthesizing enzyme, choline acetyltransferase in extracellular fluids to allow maintenance of equilibrium between breakdown and synthesis of acetylcholine through continuous in situ syntheses. A recent proof-of-concept study led to the discovery of this enzyme in the human extracellular fluids. We report here that apolipoprotein-E, in particular epsilon4 isoprotein acts as one of the strongest endogenous anti-amyloid-beta fibrillization agents reported in the literature. At biological concentrations, apolipoprotein-E prevented amyloid-beta fibrillization for at least 65 h. We show that amyloid-beta interacts readily in an apolipoprotein-facilitated manner with butyrylcholinesterase, forming highly stable and soluble complexes, BAbetaACs, which can be separated in their native states by sucrose density gradient technique. Enzymological analyses further evinced that amyloid-beta concentration dependently increased the acetylcholine-hydrolyzing capacity of cholinesterases. In silico biomolecular analysis further deciphered the allosteric amino acid fingerprint of the amyloid-beta-cholinesterase molecular interaction in formation of BAbetaACs. In the case of butyrylcholinesterase, the results indicated that amyloid-beta interacts with a putative activation site at the mouth of its catalytic tunnel, most likely leading to increased acetylcholine influx into the catalytic site, and thereby increasing the intrinsic catalytic rate of butyrylcholinesterase. In conclusion, at least one of the native physiological functions of amyloid-beta is allosteric modulation of the intrinsic catalytic efficiency of cholinesterases, and thereby regulation of synaptic and extrasynaptic cholinergic signalling. High apolipoprotein-E may pathologically alter the biodynamics of this amyloid-beta function.
ESTHER : Kumar_2016_Brain_139_174
PubMedSearch : Kumar_2016_Brain_139_174
PubMedID: 26525916

Title : Novel ligands of Choline Acetyltransferase designed by in silico molecular docking, hologram QSAR and lead optimization - Kumar_2016_Sci.Rep_6_31247
Author(s) : Kumar R , Langstrom B , Darreh-Shori T
Ref : Sci Rep , 6 :31247 , 2016
Abstract : Recent reports have brought back the acetylcholine synthesizing enzyme, choline acetyltransferase in the mainstream research in dementia and the cholinergic anti-inflammatory pathway. Here we report, a specific strategy for the design of novel ChAT ligands based on molecular docking, Hologram Quantitative Structure Activity Relationship (HQSAR) and lead optimization. Molecular docking was performed on a series of ChAT inhibitors to decipher the molecular fingerprint of their interaction with the active site of ChAT. Then robust statistical fragment HQSAR models were developed. A library of novel ligands was generated based on the pharmacophoric and shape similarity scoring function, and evaluated in silico for their molecular interactions with ChAT. Ten of the top scoring invented compounds are reported here. We confirmed the activity of alpha-NETA, the only commercially available ChAT inhibitor, and one of the seed compounds in our model, using a new simple colorimetric ChAT assay (IC50 ~ 88 nM). In contrast, alpha-NETA exhibited an IC50 of ~30 muM for the ACh-degrading cholinesterases. In conclusion, the overall results may provide useful insight for discovering novel ChAT ligands and potential positron emission tomography tracers as in vivo functional biomarkers of the health of central cholinergic system in neurodegenerative disorders, such as Alzheimer's disease.
ESTHER : Kumar_2016_Sci.Rep_6_31247
PubMedSearch : Kumar_2016_Sci.Rep_6_31247
PubMedID: 27507101

Title : Point mutation Gln121-Arg increased temperature optima of Bacillus lipase (1.4 subfamily) by fifteen degrees - Goomber_2016_Int.J.Biol.Macromol_88_507
Author(s) : Goomber S , Kumar R , Singh R , Mishra N , Kaur J
Ref : Int J Biol Macromol , 88 :507 , 2016
Abstract : Small molecular weight Bacillus lipases are industrially attractive because of its alkaline optimum pH, broad substrate specificity and production in high yield by overexpression both in Escherichia coli and Bacillus subtilis. Its major limitation of being mesophilic in nature is constantly targeted by laboratory evolution studies. Herein metagenomically isolated Bacillus LipJ was randomly evolved by error prone PCR and library of variants were screened for enhanced thermostability. Point mutant Gln121Arg was extensively characterized and it showed dramatic shift of Temp. opt to 50 degrees C compared to 37 degrees C for parent enzyme. Thermostability studies at 45 degrees C and 50 degrees C determined six fold increase in half life for point variant Gln121Arg compared to LipJ. Circular dichroism (CD) and tryptophan fluorescence study established enhanced thermostability of Gln121Arg. Specific activity of point variant Gln121Arg was comparable to wild type with increased substrate affinity (Km reduced). Reduced kcat for variant Gln121Arg infer that kinetic and catalytic efficiency of mutant was compromised. Structural implications by homolog modelling predicted Gln121 to be placed within longest loop of the structure at surface. Localization of loop due to additional polar interactions by Arg121 to protein core defines molecular basis of enhanced thermostability of random point variant Gln121Arg.
ESTHER : Goomber_2016_Int.J.Biol.Macromol_88_507
PubMedSearch : Goomber_2016_Int.J.Biol.Macromol_88_507
PubMedID: 27083848

Title : Survey of acaricides resistance status of Rhipiciphalus (Boophilus) microplus collected from selected places of Bihar, an eastern state of India - Ghosh_2015_Ticks.Tick.Borne.Dis_6_668
Author(s) : Ghosh S , Kumar R , Nagar G , Kumar S , Sharma AK , Srivastava A , Ajith Kumar KG , Saravanan BC
Ref : Ticks Tick Borne Dis , 6 :668 , 2015
Abstract : Monitoring acaricide resistance in field ticks and use of suitable managemental practices are essential for controlling tick populations infesting animals. In the present study, the acaricide resistance status in Rhipicephalus (Boophilus) microplus ticks infesting cattle and buffaloes of five districts located in the eastern Indian state, Bihar were characterized using three data sets (AIT, Biochemical assays and gene sequences). Adult immersion test (AIT) was adopted using seven field isolates and their resistance factor (RF) was determined. Six isolates (DNP, MUZ, BEG, VSH, DRB and SUL) were found resistant to both deltamethrin and diazinon and except VSH all were resistant to cypermethrin. One isolate (PTN) was susceptible with a RF below 1.5. To understand the possible mode of resistance development, targeted enzymes and gene sequences of the para sodium channel and achetylcholinesterase 2 (AChE2) were analyzed. The esterase, monooxygenase and glutathione-S-transferase (GST) activity of reference susceptible IVRI-I line was determined as 2.47+/-0.007nmol/min/mg protein, 0.089+/-0.0016nmol/mg of protein and 0.0439+/-0.0003nmol/mg/min respectively, which increased significantly in the resistant field isolates. However, except esterases, the fold increase of monooxygenase (1.14-2.27 times) and GST (0.82-1.53 times) activities were not very high. A cytosine (C) to adenine (A) nucleotide substitution (CTC to ATC) at position 190 in domain II S4-5 linker region was detected only in one isolate (SUL) having RF of 34.9 and in the reference deltamethrin resistant line (IVRI-IV). However, the T2134A mutation was not detected in domain IIIS6 transmembrane segment of resistant isolates and also in reference IVRI-IV line despite of varying degree of resistance. The flumethrin specific G215T and the recently identified T170C mutations were also absent in domain II sequences under study. Four novel amino acid substitutions in AChE2 gene of field isolates and in organophosphate (OP) resistant reference IVRI-III line were identified which can possibly have a role in resistance development.
ESTHER : Ghosh_2015_Ticks.Tick.Borne.Dis_6_668
PubMedSearch : Ghosh_2015_Ticks.Tick.Borne.Dis_6_668
PubMedID: 26117183
Gene_locus related to this paper: boomi-ACHE2

Title : Insights into controlling role of substitution mutation, E315G on thermostability of a lipase cloned from metagenome of hot spring soil - Sharma_2014_3.Biotech_4_189
Author(s) : Sharma PK , Kumar R , Garg P , Kaur J
Ref : 3 Biotech , 4 :189 , 2014
Abstract : Rational mutagenesis was performed (at the vicinity of the active site residues D317 and H358 of a mature polypeptide) to investigate the role of amino acids in the thermostability/activity of a lipase enzyme. The single variant enzyme created with E315G (lip M2) mutation near one of the active site residue (D317) found to be an important residue in controlling the thermal stability, the variant with E315G mutation demonstrated biochemical properties similar to that of native lipase. However, we found that this mutation strongly affected the activity and stability of the lip M1 mutant, reported in our previous study (Sharma et al. in Gene 491:264-271, 2012b). The dual mutant with E315G/N355K mutation in the Wt showed small increase in the protein thermostability compared to the native lipase, however, the thermostability of the mutant lip M1 was reduced several fold. Presumably, E315G (lip M2) mutation reverted the thermostability evolved by N355K (lip M1). The native and variant enzymes also displayed large variation in enzyme kinetics and their preference for pNP-esters (substrates). We further generated 3D models and studied the loop modelling of the WT and variants. Interestingly, loop region Leu314-Asn321 showed structural flexibility on introducing E315G mutation in the native lipase. On the other hand, lysine in mutant N355K exhibited side chain conformational changes in the loop Thr353-His358 which resulted in its H-bonding with Glu284. In addition, replacing glutamic acid by glycine at 315 position in lip M3 distorted the electrostatic interactions between Glu315 and Lys355 in the flexible loop region Leu314-Asn321.
ESTHER : Sharma_2014_3.Biotech_4_189
PubMedSearch : Sharma_2014_3.Biotech_4_189
PubMedID: 28324449

Title : Trigger factor assisted folding of the recombinant epoxide hydrolases identified from C. pelagibacter and S. nassauensis - Saini_2014_Protein.Expr.Purif_104C_71
Author(s) : Saini P , Wani SI , Kumar R , Chhabra R , Chimni SS , Sareen D
Ref : Protein Expr Purif , 104C :71 , 2014
Abstract : Epoxide hydrolases (EHs), are enantioselective enzymes as they catalyze the kinetic resolution of racemic epoxides into the corresponding enantiopure vicinal diols, which are useful precursors in the synthesis of chiral pharmaceutical compounds. Here, we have identified and cloned two putative epoxide hydrolase genes (cpeh and sneh) from marine bacteria, Candidatus pelagibacter ubique and terrestrial bacteria, Stackebrandtia nassauensis, respectively and overexpressed them in pET28a vector in Escherichia coli BL21(DE3). The CPEH protein (42kDa) was found to be overexpressed as inactive inclusion bodies while SNEH protein (40kDa) was found to form soluble aggregates. In this study, the recombinant CPEH was successfully transformed from insoluble aggregates to the soluble and functionally active form, using pCold TF vector, though with low EH activity. To prevent the soluble aggregate formation of SNEH, it was co-expressed with GroEL/ES chaperone and was also fused with trigger factor (TF) chaperone at its N-terminus. The TF chaperone-assisted correct folding of SNEH led to a purified active EH with a specific activity of 3.85mumol/min/mg. The pure enzyme was further used to biocatalyze the hydrolysis of 10mM benzyl glycidyl ether (BGE) and alpha-methyl styrene oxide (MSO) with an enantiomeric excess of the product (eep) of 86% and 73% in 30 and 15min, respectively. In conclusion, this is the first report about the heterologous expression of epoxide hydrolases using TF as a molecular chaperone in pCold TF expression vector, resulting in remarkable increase in the solubility and activity of the otherwise improperly folded recombinant epoxide hydrolases.
ESTHER : Saini_2014_Protein.Expr.Purif_104C_71
PubMedSearch : Saini_2014_Protein.Expr.Purif_104C_71
PubMedID: 25229949

Title : Docking based virtual screening and molecular dynamics study to identify potential monoacylglycerol lipase inhibitors - Afzal_2014_Bioorg.Med.Chem.Lett_24_3986
Author(s) : Afzal O , Kumar S , Kumar R , Firoz A , Jaggi M , Bawa S
Ref : Bioorganic & Medicinal Chemistry Lett , 24 :3986 , 2014
Abstract : Monoacylglycerol lipase (MAGL) is one of the key enzymes of the endocannabinoid system (ECS). It hydrolyzes one of the major endocannabinoid, 2-arachidonoylglycerol (2-AG), an endogenous full agonist at G protein coupled cannabinoid receptors CB1 and CB2. Numerous studies showed that MGL inhibitors are potentially useful for the treatment of pain, inflammation, cancer and CNS disorders. These provocative findings suggested that pharmacological inhibition of MAGL function may confer significant therapeutic benefits. In this study, we presented hybrid ligand and structure-based approaches to obtain a novel set of virtual leads as MAGL inhibitors. The constraints used in this study, were Glide score, binding free energy estimates and ADME properties to screen the ZINC database, containing approximately 21 million compounds. A total of seven virtual hits were obtained, which showed significant binding affinity towards MAGL protein. Ligand, ZINC24092691 was employed in complex form with the protein MAGL, for molecular dynamics simulation study, because of its excellent glide score, binding free energy and ADME properties. The RMSD of ZINC24092691 was observed to stay at 0.1nm (1A) in most of the trajectories, which further confirmed its ability to inhibit the protein MAGL. The hits were then evaluated for their ability to inhibit human MAGL. The compound ZINC24092691 displayed the noteworthy inhibitory activity reducing MAGL activity to 21.15% at 100nM concentration, with an IC50 value of 10nM.
ESTHER : Afzal_2014_Bioorg.Med.Chem.Lett_24_3986
PubMedSearch : Afzal_2014_Bioorg.Med.Chem.Lett_24_3986
PubMedID: 25011912

Title : Effect of acyl chain length on selective biocatalytic deacylation on O-aryl glycosides and separation of anomers - Aggarwal_2014_Bioorg.Chem_53_83
Author(s) : Aggarwal N , Arya A , Mathur D , Singh S , Tyagi A , Kumar R , Rana N , Singh R , Prasad AK
Ref : Bioorg Chem , 53 :83 , 2014
Abstract : It has been demonstrated that Lipozyme TL IM (Thermomyces lanuginosus lipase immobilised on silica) can selectively deacylate the ester function involving the C-5' hydroxyl group of alpha-anomers over the other acyl functions of anomeric mixture of peracylated O-aryl alpha,beta-D-ribofuranoside. The analysis of results of biocatalytic deacylation reaction revealed that the reaction time decreases with the increase in the acyl chain length from C1 to C4. The unique selectivity of Lipozyme TL IM has been harnessed for the separation of anomeric mixture of peracylated O-aryl alpha,beta-D-ribofuranosides, The lipase mediated selective deacylation methodology has been used for the synthesis of O-aryl alpha-D-ribofuranosides and O-aryl beta-D-ribofuranosides in pure forms, which can be used as chromogenic substrate for the detection of pathogenic microbial parasites containing glycosidases.
ESTHER : Aggarwal_2014_Bioorg.Chem_53_83
PubMedSearch : Aggarwal_2014_Bioorg.Chem_53_83
PubMedID: 24632507

Title : Combinatorial reshaping of a lipase structure for thermostability: additive role of surface stabilizing single point mutations - Kumar_2014_Biochem.Biophys.Res.Commun_447_626
Author(s) : Kumar R , Singh R , Kaur J
Ref : Biochemical & Biophysical Research Communications , 447 :626 , 2014
Abstract : Thermostable lipases are of high priority for industrial applications. In the present study, targeted improvement of the thermostability of a lipase from metagenomic origin was examined by using a combinatorial protein engineering approach exploring additive effects of single amino acid substitutions. A variant (LipR5) was generated after combination of two thermostabilizing mutations (R214C & N355K). Thermostability of the variant enzyme was analyzed by half-life measurement and circular dichroism (CD). To assess whether catalytic properties were affected by mutation, the optimal reaction conditions were determined. The protein LipR5, displayed optimum activity at 50 degrees C and pH 8.0. It showed two fold enhancement in thermostability (at 60 degrees C) as compared to LipR3 (R214C) and nearly 168 fold enhancement as compared to parent enzyme (LipR1). Circular dichroism and fluorescence study suggest that the protein structure had become more rigid and stable to denaturation. Study of 3D model suggested that Lys355 was involved in formation of a Hydrogen bond with OE1 of Glu284. Lys355 was also making salt bridge with OE2 of Glu284.
ESTHER : Kumar_2014_Biochem.Biophys.Res.Commun_447_626
PubMedSearch : Kumar_2014_Biochem.Biophys.Res.Commun_447_626
PubMedID: 24751523

Title : Draft Genome Sequence of Sphingobium lactosutens Strain DS20T, Isolated from a Hexachlorocyclohexane Dumpsite - Kumar_2013_Genome.Announc_1_e00753
Author(s) : Kumar R , Dwivedi V , Negi V , Khurana JP , Lal R
Ref : Genome Announc , 1 : , 2013
Abstract : Sphingobium lactosutens DS20(T) has been isolated from the hexachlorocyclohexane (HCH) dumpsite in Lucknow, India, but does not degrade any of the HCH isomers. Here, we present the ~5.36-Mb draft genome sequence of strain DS20(T), which consists of 110 contigs and 5,288 coding sequences, with a G+C content of 63.1%.
ESTHER : Kumar_2013_Genome.Announc_1_e00753
PubMedSearch : Kumar_2013_Genome.Announc_1_e00753
PubMedID: 24051323
Gene_locus related to this paper: 9sphn-q1n750 , 9sphn-t0hf11 , 9sphn-t0him9 , 9sphn-t0i493

Title : Draft Genome Sequence of Sphingobium sp. Strain HDIPO4, an Avid Degrader of Hexachlorocyclohexane - Mukherjee_2013_Genome.Announc_1_e00749
Author(s) : Mukherjee U , Kumar R , Mahato NK , Khurana JP , Lal R
Ref : Genome Announc , 1 : , 2013
Abstract : Sphingobium sp. strain HDIPO4 was isolated from a hexachlorocyclohexane (HCH) dumpsite and degraded HCH isomers rapidly. The draft genome sequence of HDIPO4 (~4.7 Mbp) contains 143 contigs and 4,646 coding sequences with a G+C content of 65%.
ESTHER : Mukherjee_2013_Genome.Announc_1_e00749
PubMedSearch : Mukherjee_2013_Genome.Announc_1_e00749
PubMedID: 24051321
Gene_locus related to this paper: sphju-d4z7y1 , sphju-d4z363 , sphpi-linb

Title : Collybistin activation by GTP-TC10 enhances postsynaptic gephyrin clustering and hippocampal GABAergic neurotransmission - Mayer_2013_Proc.Natl.Acad.Sci.U.S.A_110_20795
Author(s) : Mayer S , Kumar R , Jaiswal M , Soykan T , Ahmadian MR , Brose N , Betz H , Rhee JS , Papadopoulos T
Ref : Proc Natl Acad Sci U S A , 110 :20795 , 2013
Abstract : In many brain regions, gephyrin and GABAA receptor clustering at developing inhibitory synapses depends on the guanine nucleotide exchange factor collybistin (Cb). The vast majority of Cb splice variants contain an autoinhibitory src homology 3 domain, and several synaptic proteins are known to bind to this SH3 domain and to thereby activate gephyrin clustering. However, many functional GABAergic synapses form independently of the known Cb-activating proteins, indicating that additional Cb activators must exist. Here we show that the small Rho-like GTPase TC10 stimulates Cb-dependent gephyrin clustering by binding in its active, GTP-bound state to the pleckstrin homology domain of Cb. Overexpression of a constitutively active TC10 variant in neurons causes an increase in the density of synaptic gephyrin clusters and mean miniature inhibitory postsynaptic current amplitudes, whereas a dominant negative TC10 variant has opposite effects. The enhancement of Cb-induced gephyrin clustering by GTP-TC10 does not depend on the guanine nucleotide exchange activity of Cb but involves an interaction that resembles reported interactions of other small GTPases with their effectors. Our data indicate that GTP-TC10 activates the major src homology 3 domain-containing Cb variants by relieving autoinhibition and thus define an alternative GTPase-driven signaling pathway in the genesis of inhibitory synapses.
ESTHER : Mayer_2013_Proc.Natl.Acad.Sci.U.S.A_110_20795
PubMedSearch : Mayer_2013_Proc.Natl.Acad.Sci.U.S.A_110_20795
PubMedID: 24297911

Title : Characterization and evolution of a metagenome-derived lipase towards enhanced enzyme activity and thermostability - Kumar_2013_Mol.Cell.Biochem_373_149
Author(s) : Kumar R , Sharma M , Singh R , Kaur J
Ref : Molecular & Cellular Biochemistry , 373 :149 , 2013
Abstract : In the present investigation, we used directed evolution approach to engineer a lipase from metagenomic origin. A variant S311C, was generated, characterized in detail and compared with wild type. Wild type and variant lipases were overexpressed and purified to homogeneity. The temperature optima of the purified lipases (Variant and wild type) were almost same, and found to be 45 and 50 degrees C, respectively. The variant protein was highly thermostable (54 times) as compared with the wild type at 60 degrees C. The variant displayed very high kinetic efficiency over the wild type protein. Analysis of the homology models of wild type and variant lipase showed that the substitution is on the surface of the protein. This substitution, along with hydrophobic residues in near vicinity may be involved in formation of strong hydrophobic channel leading to active site. This study identifies the role of hydrophobic interactions in protein stability along with enhancement of enzyme activity.
ESTHER : Kumar_2013_Mol.Cell.Biochem_373_149
PubMedSearch : Kumar_2013_Mol.Cell.Biochem_373_149
PubMedID: 23104399

Title : Organochlorine pesticide, endosulfan induced cellular and organismal response in Drosophila melanogaster - Sharma_2012_J.Hazard.Mater_221-222_275
Author(s) : Sharma A , Mishra M , Shukla AK , Kumar R , Abdin MZ , Chowdhuri DK
Ref : J Hazard Mater , 221-222 :275 , 2012
Abstract : The effect of endosulfan (0.02-2.0mugmL(-1)) to Drosophila melanogaster (Oregon R(+)) at the cellular and organismal levels was examined. Third instar larvae of D. melanogaster and the strains transgenic for hsp70, hsp83 and hsp26 were exposed to endosulfan through food for 12-48h to examine the heat shock proteins (hsps), reactive oxygen species (ROS) generation, anti-oxidant stress markers and xenobiotic metabolism enzymes. We observed a concentration- and time-dependent significant induction of only small hsps (hsp23>hsp22) in the exposed organism in concurrence with a significant induction of ROS generation, oxidative stress and xenobiotic metabolism markers. Sub-organismal response was to be propagated towards organismal response, i.e., delay in the emergence of flies and decreased locomotor behaviour. Organisms with diminished locomotion also exhibited significantly lowered acetylcholinesterase activity. A significant positive correlation observed among ROS generation and different cellular endpoints (small hsps, oxidative stress markers, cytochrome P450 activities) in the exposed organism indicate a modulatory role of ROS in endosulfan-mediated cellular toxicity. The study thus suggests that the adverse effects of endosulfan in exposed Drosophila are manifested both at cellular and organismal levels and recommends Drosophila as an alternative animal model for screening the risk caused by environmental chemicals.
ESTHER : Sharma_2012_J.Hazard.Mater_221-222_275
PubMedSearch : Sharma_2012_J.Hazard.Mater_221-222_275
PubMedID: 22579458

Title : Engineering of a metagenome derived lipase toward thermal tolerance: effect of asparagine to lysine mutation on the protein surface - Sharma_2012_Gene_491_264
Author(s) : Sharma PK , Kumar R , Mohammad O , Singh R , Kaur J
Ref : Gene , 491 :264 , 2012
Abstract : A highly thermostable mutant lipase was generated and characterized. Mutant enzyme demonstrated 144 fold enhanced thermostability over the wild type enzyme at 60 degrees C. Interestingly, the overall catalytic efficiency (k(cat/)K(m)) of mutant was also enhanced (~20 folds). Circular dichroism spectroscopy, studied as function of temperature, demonstrated that the mutant lipase retained its secondary structure up to 70-80 degrees C, whereas wild type protein structure was completely distorted above 35 degrees C. Additionally, the intrinsic tryptophan fluorescence (a probe for the tertiary structure) also displayed difference in the conformation of two enzymes during temperature dependent unfolding. Furthermore, mutation N355K resulted in extensive H-bonding (Lys355 HZ1OE2 Glu284) with a distance 2.44 A. In contrast to this, Wt enzyme has not shown such H-bonding interaction.
ESTHER : Sharma_2012_Gene_491_264
PubMedSearch : Sharma_2012_Gene_491_264
PubMedID: 22001407

Title : Identification of variables and value optimization for optimum lipase production by Bacillus pumilus RK31 using statistical methodology - Kumar_2011_N.Biotechnol_28_65
Author(s) : Kumar R , Mahajan S , Kumar A , Singh D
Ref : N Biotechnol , 28 :65 , 2011
Abstract : In an effort to optimize the medium components, the statistical methodology was applied to achieve the optimum lipase production under shake flask conditions. The study was conducted in three steps on newly isolated Bacillus pumilus RK 31. In the first step, 12 different variables viz., Glucose, Olive oil, Yeast extract, Peptone, Tween 80, KH(2)PO(4), MgSO(4), NaNO(3), CaCl(2), Temperature, pH and Inoculum size were used to identify the most significant variables affecting lipase production using Plackett-Burman statistical design. Variance analysis showed that Olive oil, Tween 80 and KH(2)PO(4) played significant role in lipase production. In the second step, the values of the above-identified three variables were optimized by central composite design using three-level-three-factor approach. The optimum values of Olive oil, Tween 80 and KH(2)PO(4) were found to be 10.0ml/l, 5.0ml/l and 8.0g/l, respectively. KH(2)PO(4) was found to be responsible for maximum lipase production of 5.59IU/ml, experimental and 5.03IU/ml, predicted. In the third step, the optimum predicted values of the three factors and lipase production were verified by experimental approach. The amount of lipase produced in the designated medium was in agreement with that of predicted values by statistical method.
ESTHER : Kumar_2011_N.Biotechnol_28_65
PubMedSearch : Kumar_2011_N.Biotechnol_28_65
PubMedID: 20601261

Title : Cloning and characterization of an epoxide hydrolase from Cupriavidus metallidurans-CH34 - Kumar_2011_Protein.Expr.Purif_79_49
Author(s) : Kumar R , Wani SI , Chauhan NS , Sharma R , Sareen D
Ref : Protein Expr Purif , 79 :49 , 2011
Abstract : A putative epoxide hydrolase-encoding gene was identified from the genome sequence of Cupriavidus metallidurans CH34. The gene was cloned and overexpressed in Escherichia coli with His(6)-tag at its N-terminus. The epoxide hydrolase (CMEH) was purified to near homogeneity and was found to be a homodimer, with subunit molecular weight of 36 kDa. The CMEH had broad substrate specificity as it could hydrolyze 13 epoxides, out of 15 substrates tested. CMEH had high specific activity with 1,2-epoxyoctane, 1,2-epoxyhexane, styrene oxide (SO) and was also found to be active with meso-epoxides. The enzyme had optimum pH and temperature of 7.5 and 37 degrees C respectively, with racemic SO. Biotransformation of 80 mM SO with recombinant whole E. coli cells expressing CMEH led to 56% ee(P) of (R)-diol with 77.23% conversion in 30 min. The enzyme could hydrolyze (R)-SO, approximately 2-fold faster than (S)-SO, though it accepted both (R)- and (S)-SO with similar affinity as K(m)(R) and K(m)(S) of CMEH were 2.05+/-0.42 and 2.11+/-0.16 mM, respectively. However, the k(cat)(R) and k(cat)(S) for the two enantiomers of SO were 4.80 and 3.34 s(-1), respectively. The wide substrate spectrum exhibited by CMEH combined with the fast conversion rate makes it a robust biocatalyst for industrial use. Regioselectivity studies with enantiopure (R)- and (S)-SO revealed that with slightly altered regioselectivity, CMEH has a high potential to synthesize an enantiopure (R)-PED, through an enantioconvergent hydrolytic process.
ESTHER : Kumar_2011_Protein.Expr.Purif_79_49
PubMedSearch : Kumar_2011_Protein.Expr.Purif_79_49
PubMedID: 21515382

Title : Genotoxicity assessment of acute exposure of chlorpyrifos to freshwater fish Channa punctatus (Bloch) using micronucleus assay and alkaline single-cell gel electrophoresis - Ali_2008_Chemosphere_71_1823
Author(s) : Ali D , Nagpure NS , Kumar S , Kumar R , Kushwaha B
Ref : Chemosphere , 71 :1823 , 2008
Abstract : Chlorpyrifos (O,O-diethyl O-3,5,6-trichloro-2-pyridylphosphorothioate) is one of the organophosphate pesticides widely used in agricultural practices throughout world and irreversible inhibitor of cholinesterase in all animal species. Limited efforts have been made to study acute genotoxic effects of chlorpyrifos (CPF) in different tissues of fish using genotoxic biomarkers. Therefore, the present investigation was aimed to study the induction of DNA damage by CPF in freshwater teleost fish Channapunctatus using micronucleus assay (MN assay) and alkaline single-cell gel electrophoresis (comet assay). The value of LC(50) - 96 h of CPF was determined as 811.98 microgl(-1) for C. punctatus, in a semi-static system and on the basis of LC(50) value three acute concentrations viz., 203, 406 and 609 microgl(-1) were determined. The fishes were exposed to the different concentrations of CPF for 96 h and samplings were done at regular intervals for assessment of the MN frequencies and DNA damage. In general, significant effects (P<0.01) from both concentrations and time of exposure were observed in exposed fishes. It was found that the micronucleus induction was highest on 96 h at all concentrations in the peripheral blood. Similar trend was observed for the DNA damage measured in terms of the percentage of tail DNA in the lymphocyte and gill cells. This study explored the combined use of micronucleus assay and comet assay for in vivo laboratory studies using fresh water fish for screening the genotoxic potential of xenobiotics.
ESTHER : Ali_2008_Chemosphere_71_1823
PubMedSearch : Ali_2008_Chemosphere_71_1823
PubMedID: 18359502

Title : Deacylation studies on furanose triesters using an immobilized lipase: synthesis of a key precursor for bicyclonucleosides - Prasad_2007_Chem.Commun.(Camb)__2616
Author(s) : Prasad AK , Kalra N , Yadav Y , Kumar R , Sharma SK , Patkar S , Lange L , Wengel J , Parmar VS
Ref : Chem Commun (Camb) , :2616 , 2007
Abstract : Lipozyme TL IM immobilized on silica catalyses the deacylation of 4-C-acyloxymethyl-3,5-di-O-acyl-1,2-O-(1-methylethylidene)-beta-L-threo-pentofuranose to form 3,5-di-O-acyl-4-C-hydroxymethyl-1,2-O-(1-methylethylidene)-alpha-d-xylo-pentofuranose in a highly selective and efficient manner.
ESTHER : Prasad_2007_Chem.Commun.(Camb)__2616
PubMedSearch : Prasad_2007_Chem.Commun.(Camb)__2616
PubMedID: 17579756

Title : Acute toxicity bioassays of mercuric chloride and malathion on air-breathing fish Channa punctatus (Bloch) - Pandey_2005_Ecotoxicol.Environ.Saf_61_114
Author(s) : Pandey S , Kumar R , Sharma S , Nagpure NS , Srivastava SK , Verma MS
Ref : Ecotoxicology & Environmental Safety , 61 :114 , 2005
Abstract : Acute toxicity tests (96 h) were conducted in flow-through systems to determine the lethal toxicity of a heavy metal compound, mercuric chloride, and an organophosphorus pesticide, malathion, to air-breathing teleost fish, Channa punctatus (Bloch) and to study their behavior. The 96-h LC50 values were determined, as well as safe levels. The results indicate that mercuric chloride is more toxic than malathion to the fish species under study. Dose- and dose-time-dependent increases in mortality rate were also observed in response to both test chemicals.
ESTHER : Pandey_2005_Ecotoxicol.Environ.Saf_61_114
PubMedSearch : Pandey_2005_Ecotoxicol.Environ.Saf_61_114
PubMedID: 15814317

Title : Magnitude of pesticidal contamination in winter vegetables from Hisar, Haryana - Kumari_2003_Environ.Monit.Assess_87_311
Author(s) : Kumari B , Kumar R , Madan VK , Singh R , Singh J , Kathpal TS
Ref : Environ Monit Assess , 87 :311 , 2003
Abstract : Monitoring of 80 winter vegetable samples during 1997-1998 for pesticidal contamination was carried out on GC-ECD and GC-NPD systems with capillary columns following multiresidue analytical technique. The tested samples were found 100% contaminated with low but measurable amounts of pesticide residues. Among the four major chemical groups, residue levels of organophosphorous insecticides were highest followed by carbamates, synthetic pyrethroids and organochlorines. About 32% of the samples showed contamination with organophosphorous and carbamate insecticides above their respective MRL values. On the basis of observations made in these studies, it is suggested that more extensive monitoring studies covering all vegetable crops from different agro-climatic regions of the state be carried out to know exact level of pesticidal contamination, which may serve as basis for future policy on chemical use.
ESTHER : Kumari_2003_Environ.Monit.Assess_87_311
PubMedSearch : Kumari_2003_Environ.Monit.Assess_87_311
PubMedID: 12952358

Title : Inhibition of human cholinesterases by drugs used to treat Alzheimer disease - Darvesh_2003_Alzheimer.Dis.Assoc.Disord_17_117
Author(s) : Darvesh S , Walsh R , Kumar R , Caines A , Roberts S , Magee D , Rockwood K , Martin E
Ref : Alzheimer Disease & Associated Disorders , 17 :117 , 2003
Abstract : Current approaches to the treatment of cognitive and behavioral symptoms of Alzheimer disease emphasize the use of cholinesterase inhibitors. The kinetic effects of the cholinesterase inhibitors donepezil, galantamine, metrifonate, physostigmine, rivastigmine, and tetrahydroaminoacridine were examined with respect to their action on the esterase and aryl acylamidase activities of human acetylcholinesterase (AChE) and human butyrylcholinesterase (BuChE). Each of these drugs inhibited both AChE and BuChE, but to different degrees. Inhibition of BuChE by these compounds was approximately the same, or better, when acetylthiocholine, the analog of the neurotransmitter acetylcholine, was used as the substrate, instead of butyrylthiocholine. In addition, for these drugs, the inhibition of aryl acylamidase activity paralleled that observed for inhibition of esterase activity of AChE and BuChE. Given that drugs that are currently in use for the treatment of Alzheimer disease inhibit both AChE and BuChE, the development of drugs targeted toward the exclusive inhibition of one or the other cholinesterase may be important for understanding the relative importance of inhibition of BuChE and AChE in the treatment of this disease.
ESTHER : Darvesh_2003_Alzheimer.Dis.Assoc.Disord_17_117
PubMedSearch : Darvesh_2003_Alzheimer.Dis.Assoc.Disord_17_117
PubMedID: 12794390

Title : Biocatalytic route to well-defined macromers built around a sugar core - Kumar_2002_J.Am.Chem.Soc_124_1850
Author(s) : Kumar R , Gross RA
Ref : Journal of the American Chemical Society , 124 :1850 , 2002
Abstract : By using 4-C-hydroxymethyl-alpha-D-pentofuranose as the sugar core and lipase-catalyzed transformations, a macromer was constructed with exceptional control of substituent placement around the carbohydrate core. The key synthetic transformations performed were as follows: (1) selective lipase-catalyzed acrylation along with prochiral selection of 4-C-hydroxymethyl-1,2-O-isopropylidene-alpha-D-pentofuranose (diastereomeric excess up to 93%); (2) the ring-opening of epsilon-caprolactone, epsilon-CL, from the remaining primary hydroxyl group to give an acryl-sugar capped macromer (M(n) = 11 300, M(w)/M(n) = 1.36, initiator efficiency 50-55%, <5% water initiated PCL chains); (3) selective lipase-catalyzed esterification of the terminal hydroxyl of oligo(epsilon-CL) chains; (4) hydrolysis of the 1,2-O-isopropylidene group at the sugar core without any substantial loss in macromer molecular weight; and (5) homopolymerization of the corresponding macromer. In principle, the method developed is flexible so that it can be used to generate a wide array of unusual macromers and heteroarm stars. In the absence of biocatalytic transformation, such structural control would be extremely difficult or currently impossible to obtain.
ESTHER : Kumar_2002_J.Am.Chem.Soc_124_1850
PubMedSearch : Kumar_2002_J.Am.Chem.Soc_124_1850
PubMedID: 11866587

Title : Butyrylcholinesterase-Mediated enhancement of the enzymatic activity of trypsin - Darvesh_2001_Cell.Mol.Neurobiol_21_285
Author(s) : Darvesh S , Kumar R , Roberts S , Walsh R , Martin E
Ref : Cellular Molecular Neurobiology , 21 :285 , 2001
Abstract : 1. Acetylcholinesterase (AChE, EC and butyrylcholinesterase (BuChE, EC are enzymes that catalyze the hydrolysis of esters of choline. 2. Both AChE and BuChE have been shown to copurify with peptidases. 3. BuChE has also been shown to copurify with other proteins such as transferrin, with which it forms a stable complex. In addition, BuChE is found in association with beta-amyloid protein in Alzheimer brain tissues. 4. Since BuChE copurifies with peptidases, we hypothesized that BuChE interacts with these enzymes and that this association had an influence on their catalytic activities. One of the peptidases that copurifies with cholinesterases has specificity similar to trypsin, hence, this enzyme was used as a model to test this hypothesis. 5. Purified BuChE causes a concentration-dependent enhancement of the catalytic activity of trypsin while trypsin does not influence the catalytic activity of BuChE. 6. We suggest that, in addition to its esterase activity, BuChE may assume a regulatory role by interacting with other proteins.
ESTHER : Darvesh_2001_Cell.Mol.Neurobiol_21_285
PubMedSearch : Darvesh_2001_Cell.Mol.Neurobiol_21_285
PubMedID: 11569538

Title : Simultaneous determination of some organophosphorus pesticides by high performance liquid chromatography - Kumar_1989_Biomed.Chromatogr_3_272
Author(s) : Kumar R
Ref : Biomedical Chromatography , 3 :272 , 1989
Abstract : An HPLC method for the simultaneous detection of six organophosphorus pesticides (Dimethoate, Ethion, Malathion, Phorate, Phosalone and Parathion) on a Zorbex ODS column using methanol + water (80:20) as solvent is described.
ESTHER : Kumar_1989_Biomed.Chromatogr_3_272
PubMedSearch : Kumar_1989_Biomed.Chromatogr_3_272
PubMedID: 2620148

Title : Effects of nicotine and d-amphetamine on intracranial self-stimulation in a shuttle box test in rats - Clarke_1984_Psychopharmacology.(Berl)_84_109
Author(s) : Clarke PB , Kumar R
Ref : Psychopharmacology (Berl) , 84 :109 , 1984
Abstract : Rats were permitted to turn on and off electrical stimulation of the medial forebrain bundle, by alternating between two photobeams running along opposite walls of a shuttle box. Entry into one beam (the "ON" beam) triggered the delivery of a succession of short, regularly occurring (1 Hz) pulse trains, which could be terminated by breaking the other ("OFF" beam). The two beams were frequently reversed. When this occurred, the rat was given a free period of 10 s in which to reorient, and brain stimulation reward was then assessed by the amount of time spent receiving brain stimulation (SST) within a fixed interval of time. SST increased with increasing current intensity. After training, subjects were tested for 10 consecutive days, alternately with saline and nicotine bitartrate (0.4 mg/kg SC base), and received a constant daily dose of the drug (0.4 mg/kg). Initially, nicotine visibly impaired motor performance for several minutes after injection, which may at least partly explain the observed reduction of SST; both effects waned across successive nicotine tests. Later in each 78 min session, nicotine consistently increased SST over a range of current, and drugged subjects entered the photobeams more frequently even when electrical stimulation was unavailable. d-Amphetamine sulphate (0.25, 0.75 mg/kg SC salt), given 15 min before testing, also increased SST and stimulated responding. The possible effects of motor impairment or activation on SST are discussed, and it is concluded that nicotine and d-amphetamine may have enhanced the rewarding properties of medial forebrain bundle stimulation.
ESTHER : Clarke_1984_Psychopharmacology.(Berl)_84_109
PubMedSearch : Clarke_1984_Psychopharmacology.(Berl)_84_109
PubMedID: 6436877

Title : Characterization of the locomotor stimulant action of nicotine in tolerant rats - Clarke_1983_Br.J.Pharmacol_80_587
Author(s) : Clarke PB , Kumar R
Ref : British Journal of Pharmacology , 80 :587 , 1983
Abstract : Tests of locomotor activity (photocell cages) were used to investigate the development of tolerance to nicotine in rats. Repeated exposure to the apparatus did not influence the rate at which tolerance was acquired. Comparisons of (+)-nicotine (0.4-1.6 mg kg-1, s.c.) and (-)-nicotine (0.1-0.4 mg kg-1, s.c.) in tolerant rats showed that the (-)-isomer was at least ten times more potent in stimulating motor activity. Subcutaneous pretreatment with mecamylamine (1.0 mg kg-1) completely prevented the locomotor stimulant action of nicotine in tolerant rats, whereas chlorisondamine (0.01 or 0.1 mg kg-1 s.c.) only partially reduced it. When mecamylamine was given after an injection of nicotine, the locomotor stimulant action of nicotine was blocked, and nicotine actually reduced activity. A single intraventricular dose of chlorisondamine (2 micrograms) blocked the stimulant actions of nicotine for the duration of the experiment (23-24 days).
ESTHER : Clarke_1983_Br.J.Pharmacol_80_587
PubMedSearch : Clarke_1983_Br.J.Pharmacol_80_587
PubMedID: 6640208

Title : The effects of nicotine on locomotor activity in non-tolerant and tolerant rats - Clarke_1983_Br.J.Pharmacol_78_329
Author(s) : Clarke PB , Kumar R
Ref : British Journal of Pharmacology , 78 :329 , 1983
Abstract : 1--Rats were tested for locomotor activity in photocell cages, for 80 min starting immediately after subcutaneous injection of (-)-nicotine bitartrate or 0.9% w/v NaCl solution (saline). In non-tolerant subjects, nicotine (0.1 to 0.4 mg/kg base) depressed activity and induced ataxia in the first 20 min, but increased activity later in the session; these actions were dose-dependent. 2--Tolerance was studied by comparing rats given nicotine (0.4 mg/kg s.c.) every day with control rats given saline instead. Each week, every subject was tested once with nicotine (0.4 mg/kg) and once with saline. With daily or even weekly injections of nicotine, the initial depressant action of the drug was replaced by a dose-dependent stimulant action which occurred throughout the session. In these tolerant animals, little ataxia was seen except when a larger dose of 0.8 mg/kg was given. Tolerance to the depressant action of nicotine persisted for at least 3 weeks. 3--In non-tolerant subjects, mecamylamine (0.5, 1.0 mg/kg s.c.) prevented the initial depressant action of nicotine (0.4 mg/kg). In tolerant rats, the locomotor stimulant action of nicotine (0.4 mg/kg) was prevented by mecamylamine (0.1, 0.32, 1.0 mg/kg s.c.) in a dose-related way; the quaternary ganglion blocker, hexamethonium (0.2, 1.0, 5.0 mg/kg s.c.) had little or no such effect. Neither mecamylamine nor hexamethonium altered activity when given alone. 4--It is suggested that a few treatments with nicotine can unmask a stimulant action of the drug, probably of central origin, which possibly reflects a stimulation of nicotine receptors.
ESTHER : Clarke_1983_Br.J.Pharmacol_78_329
PubMedSearch : Clarke_1983_Br.J.Pharmacol_78_329
PubMedID: 6131718

Title : Nicotine does not improve discrimination of brain stimulation reward by rats - Clarke_1983_Psychopharmacology.(Berl)_79_271
Author(s) : Clarke PB , Kumar R
Ref : Psychopharmacology (Berl) , 79 :271 , 1983
Abstract : Rats were trained to shuttle between two selected ("ON") arms of a Y maze, to obtain electrical stimulation of the medial forebrain bundle. Each shuttle response was rewarded with a brief pulse train. Repetitive entries into the same "ON" arm were not rewarded, nor were entries made into the third ("OFF") arm. Every 67s, stimulation was made available from a different pair of arms. Test sessions lasted for 80 min, beginning immediately after SC injection. Undrugged subjects responded faster, and with a greater proportion of rewarded responses, the higher the stimulation current. In non-tolerant rats, nicotine (0-0.4 mg/kg) depressed responding and induced ataxia shortly after injection; from 40 min, nicotine increased low rates of responding but decreased high rates. All these effects were dose-dependent. Mecamylamine (2.0 mg/kg) prevented the initial depressant action. With repeated daily injections of nicotine (0.4 mg/kg), a marked stimulant action emerged which replaced the initial depressant action, and this was dose-dependent. However, responding was increased by nicotine even when brain stimulation was not available ("time-out"). In contrast, an additional "rate-free" index based on discrimination showed that nicotine did not augment the rewarding properties of the brain stimulation.
ESTHER : Clarke_1983_Psychopharmacology.(Berl)_79_271
PubMedSearch : Clarke_1983_Psychopharmacology.(Berl)_79_271
PubMedID: 6405438