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Author Report for: Zhai J

Title: Static Binding and Dynamic Transporting-Based Design of Specific Ring-Chain-Ring Acetylcholinesterase Inhibitor: From Galantamine to Natural Product
Zhang Z, Lv J, Wang Y, Yu H, Guo B, Zhai J, Wang C, Zhao Y, Fan F, Luo W
Ref: Chemistry, :e202203363, 2023 : PubMed
Abstract


ESTHER: Zhang_2023_Chemistry__e202203363
PubMedSearch: Zhang 2023 Chemistry e202203363
PubMedID: 36826395

Abstract

Acetylcholinesterase (AChE) is a key target for the current symptomatic treatment of Alzheimer's disease, and galantamine is a clinical anticholinesterase drug with transiently acting characteristic and good selectivity for AChE. The present theoretical-experimental work improves the drug's residence time without reducing inhibition effect, thus provides crucial breakthrough for modifying the inhibitor of AChE with better-kinetic behavior. The static binding and dynamic delivery properties acquired from atomic view reveal that the galantamine simply occupies catalytic anionic site, and its release from AChE needs only ~ 8.6 kcal/mol. Both of them may cause the short residence time of galantamine. The hotspots and most favorable transport mechanism are identified, and the hydrogen bond and aromatic stacking interactions are observed to play crucial roles for galantamine binding and release in AChE. The typical peripheral anionic site arisen at the delivery process would provide another key occupation to enhance the anti-release ability for inhibitors. The compound with "specific-ring-chain-ring" framework with detail beneficial modify scheme is summarized, which may improve the residence time of inhibitor in AChE. The thermodynamic and dynamic properties of galantamine derivatives are also studied. Based on dictamnine, a natural alkaloid, two novel eligible derivatives are designed, synthesized and evaluated, which verifies our prediction. Multiple computational approaches and experiment combination probably provide a train of thought from static and dynamic view to modify or design appropriate inhibitor on the basis of specific binding and transportation features.



        

Title: The Medicago genome provides insight into the evolution of rhizobial symbioses
Young ND, Debelle F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J and Roe BA <114 more author(s)> Young ND, Debelle F, Oldroyd GE, Geurts R, Cannon SB, Udvardi MK, Benedito VA, Mayer KF, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook DR, Meyers BC, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, Mudge J, Bharti AK, Murray JD, Naoumkina MA, Rosen B, Silverstein KA, Tang H, Rombauts S, Zhao PX, Zhou P, Barbe V, Bardou P, Bechner M, Bellec A, Berger A, Berges H, Bidwell S, Bisseling T, Choisne N, Couloux A, Denny R, Deshpande S, Dai X, Doyle JJ, Dudez AM, Farmer AD, Fouteau S, Franken C, Gibelin C, Gish J, Goldstein S, Gonzalez AJ, Green PJ, Hallab A, Hartog M, Hua A, Humphray SJ, Jeong DH, Jing Y, Jocker A, Kenton SM, Kim DJ, Klee K, Lai H, Lang C, Lin S, Macmil SL, Magdelenat G, Matthews L, McCorrison J, Monaghan EL, Mun JH, Najar FZ, Nicholson C, Noirot C, O'Bleness M, Paule CR, Poulain J, Prion F, Qin B, Qu C, Retzel EF, Riddle C, Sallet E, Samain S, Samson N, Sanders I, Saurat O, Scarpelli C, Schiex T, Segurens B, Severin AJ, Sherrier DJ, Shi R, Sims S, Singer SR, Sinharoy S, Sterck L, Viollet A, Wang BB, Wang K, Wang M, Wang X, Warfsmann J, Weissenbach J, White DD, White JD, Wiley GB, Wincker P, Xing Y, Yang L, Yao Z, Ying F, Zhai J, Zhou L, Zuber A, Denarie J, Dixon RA, May GD, Schwartz DC, Rogers J, Quetier F, Town CD, Roe BA (- 114)
Ref: Nature, 480:520, 2011 : PubMed
Abstract


ESTHER: Young_2011_Nature_480_520
PubMedSearch: Young 2011 Nature 480 520
PubMedID: 22089132
Gene_locus related to this paper: medtr-b7fki4, medtr-b7fmi1, medtr-g7itl1, medtr-g7iu67, medtr-g7izm0, medtr-g7j641, medtr-g7jtf8, medtr-g7jtg2, medtr-g7jtg4, medtr-g7kem3, medtr-g7kml3, medtr-g7ksx5, medtr-g7leb3, medtr-q1s5d8, medtr-q1s9m3, medtr-q1t171, medtr-g7k9e1, medtr-g7k9e3, medtr-g7k9e5, medtr-g7k9e8, medtr-g7k9e9, medtr-g7lbp2, medtr-g7lch3, medtr-g7ib94, medtr-g7ljk8, medtr-g7i6w5, medtr-g7kvg4, medtr-g7iam1, medtr-g7iam3, medtr-g7l754, medtr-g7jr41, medtr-g7l4f5, medtr-g7l755, medtr-a0a072vyl4, medtr-g7jwk8, medtr-a0a072vhg0, medtr-a0a072vrv9, medtr-g7kmk5, medtr-a0a072uuf6, medtr-a0a072urp3, medtr-g7zzc3, medtr-g7ie19, medtr-g7kst7, medtr-a0a072u5k5, medtr-a0a072v056, medtr-scp1

Abstract

Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing approximately 94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.



        

Title: Genome sequencing and analysis of the model grass Brachypodium distachyon.
Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokhsar D, Bevan MW, Barry K, Lucas S, Harmon-Smith M and Baxter I <127 more author(s)> Vogel JP, Garvin DF, Mockler TC, Schmutz J, Rokhsar D, Bevan MW, Barry K, Lucas S, Harmon-Smith M, Lail K, Tice H, Grimwood J, McKenzie N, Huo N, Gu YQ, Lazo GR, Anderson OD, You FM, Luo MC, Dvorak J, Wright J, Febrer M, Idziak D, Hasterok R, Lindquist E, Wang M, Fox SE, Priest HD, Filichkin SA, Givan SA, Bryant DW, Chang JH, Wu H, Wu W, Hsia AP, Schnable PS, Kalyanaraman A, Barbazuk B, Michael TP, Hazen SP, Bragg JN, Laudencia-Chingcuanco D, Weng Y, Haberer G, Spannagl M, Mayer K, Rattei T, Mitros T, Lee SJ, Rose JK, Mueller LA, York TL, Wicker T, Buchmann JP, Tanskanen J, Schulman AH, Gundlach H, Bevan M, de Oliveira AC, Maia Lda C, Belknap W, Jiang N, Lai J, Zhu L, Ma J, Sun C, Pritham E, Salse J, Murat F, Abrouk M, Bruggmann R, Messing J, Fahlgren N, Sullivan CM, Carrington JC, Chapman EJ, May GD, Zhai J, Ganssmann M, Gurazada SG, German M, Meyers BC, Green PJ, Tyler L, Wu J, Thomson J, Chen S, Scheller HV, Harholt J, Ulvskov P, Kimbrel JA, Bartley LE, Cao P, Jung KH, Sharma MK, Vega-Sanchez M, Ronald P, Dardick CD, De Bodt S, Verelst W, Inz D, Heese M, Schnittger A, Yang X, Kalluri UC, Tuskan GA, Hua Z, Vierstra RD, Cui Y, Ouyang S, Sun Q, Liu Z, Yilmaz A, Grotewold E, Sibout R, Hematy K, Mouille G, Hofte H, Michael T, Pelloux J, O'Connor D, Schnable J, Rowe S, Harmon F, Cass CL, Sedbrook JC, Byrne ME, Walsh S, Higgins J, Li P, Brutnell T, Unver T, Budak H, Belcram H, Charles M, Chalhoub B, Baxter I (- 127)
Ref: Nature, 463:763, 2010 : PubMed
Abstract


ESTHER: Vogel_2010_Nature_463_763
PubMedSearch: Vogel 2010 Nature 463 763
PubMedID: 20148030
Gene_locus related to this paper: bradi-i1grm0, bradi-i1gx82, bradi-i1hb80, bradi-i1hkv6, bradi-i1hpu6, bradi-i1i3e4, bradi-i1i9i0, bradi-i1i435, bradi-i1ix93, bradi-i1gsk6, bradi-i1hk44, bradi-i1hk45, bradi-i1hnk7, bradi-i1hsd5, bradi-i1huy4, bradi-i1huy9, bradi-i1huz0, bradi-i1gxx9, bradi-i1hl25, bradi-i1hcw7, bradi-i1hyv6, bradi-i1hyb5, bradi-i1hvr8, bradi-i1hmu2, bradi-i1hf05, bradi-i1gry7, bradi-i1hf06, bradi-i1i5z8, bradi-i1icy3, bradi-i1j1h3, bradi-i1h1e3, bradi-i1hvr9, bradi-a0a0q3r7i7, bradi-i1i377, bradi-i1hjg5, bradi-i1h3i9, bradi-i1gsg5, bradi-a0a0q3mph9, bradi-i1h682, bradi-a0a0q3lc91



        

Title: Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans
Song Y, Tong Z, Wang J, Wang L, Guo Z, Han Y, Zhang J, Pei D, Zhou D and Yang R <16 more author(s)> Song Y, Tong Z, Wang J, Wang L, Guo Z, Han Y, Zhang J, Pei D, Zhou D, Qin H, Pang X, Zhai J, Li M, Cui B, Qi Z, Jin L, Dai R, Chen F, Li S, Ye C, Du Z, Lin W, Yu J, Yang H, Huang P, Yang R (- 16)
Ref: DNA Research, 11:179, 2004 : PubMed
Abstract


ESTHER: Song_2004_DNA.Res_11_179
PubMedSearch: Song 2004 DNA.Res 11 179
PubMedID: 15368893
Gene_locus related to this paper: yerpe-BIOH, yerpe-IRP1, yerpe-PIP, yerpe-PLDB, yerpe-PTRB, yerpe-q8zey9, yerpe-Y0644, yerpe-y1616, yerpe-y3224, yerpe-YPLA, yerpe-YPO0180, yerpe-YPO0667, yerpe-YPO0773, yerpe-YPO0776, yerpe-YPO0986, yerpe-YPO1501, yerpe-YPO1997, yerpe-YPO2002, yerpe-YPO2336, yerpe-YPO2526, yerpe-YPO2638, yerpe-YPO2814

Abstract

Genomics provides an unprecedented opportunity to probe in minute detail into the genomes of the world's most deadly pathogenic bacteria- Yersinia pestis. Here we report the complete genome sequence of Y. pestis strain 91001, a human-avirulent strain isolated from the rodent Brandt's vole-Microtus brandti. The genome of strain 91001 consists of one chromosome and four plasmids (pPCP1, pCD1, pMT1 and pCRY). The 9609-bp pPCP1 plasmid of strain 91001 is almost identical to the counterparts from reference strains (CO92 and KIM). There are 98 genes in the 70,159-bp range of plasmid pCD1. The 106,642-bp plasmid pMT1 has slightly different architecture compared with the reference ones. pCRY is a novel plasmid discovered in this work. It is 21,742 bp long and harbors a cryptic type IV secretory system. The chromosome of 91001 is 4,595,065 bp in length. Among the 4037 predicted genes, 141 are possible pseudo-genes. Due to the rearrangements mediated by insertion elements, the structure of the 91001 chromosome shows dramatic differences compared with CO92 and KIM. Based on the analysis of plasmids and chromosome architectures, pseudogene distribution, nitrate reduction negative mechanism and gene comparison, we conclude that strain 91001 and other strains isolated from M. brandti might have evolved from ancestral Y. pestis in a different lineage. The large genome fragment deletions in the 91001 chromosome and some pseudogenes may contribute to its unique nonpathogenicity to humans and host-specificity.



        

Title: Genetics of metabolic variations between Yersinia pestis biovars and the proposal of a new biovar, microtus
Zhou D, Tong Z, Song Y, Han Y, Pei D, Pang X, Zhai J, Li M, Cui B and Yang R <7 more author(s)> Zhou D, Tong Z, Song Y, Han Y, Pei D, Pang X, Zhai J, Li M, Cui B, Qi Z, Jin L, Dai R, Du Z, Wang J, Guo Z, Huang P, Yang R (- 7)
Ref: Journal of Bacteriology, 186:5147, 2004 : PubMed
Abstract


ESTHER: Zhou_2004_J.Bacteriol_186_5147
PubMedSearch: Zhou 2004 J.Bacteriol 186 5147
PubMedID: 15262951
Gene_locus related to this paper: yerpe-YPLA

Abstract

Yersinia pestis has been historically divided into three biovars: antiqua, mediaevalis, and orientalis. On the basis of this study, strains from Microtus-related plague foci are proposed to constitute a new biovar, microtus. Based on the ability to ferment glycerol and arabinose and to reduce nitrate, Y. pestis strains can be assigned to one of four biovars: antiqua (glycerol positive, arabinose positive, and nitrate positive), mediaevalis (glycerol positive, arabinose positive, and nitrate negative), orientalis (glycerol negative, arabinose positive, and nitrate positive), and microtus (glycerol positive, arabinose negative, and nitrate negative). A 93-bp in-frame deletion in glpD gene results in the glycerol-negative characteristic of biovar orientalis strains. Two kinds of point mutations in the napA gene may cause the nitrate reduction-negative characteristic in biovars mediaevalis and microtus, respectively. A 122-bp frameshift deletion in the araC gene may lead to the arabinose-negative phenotype of biovar microtus strains. Biovar microtus strains have a unique genomic profile of gene loss and pseudogene distribution, which most likely accounts for the human attenuation of this new biovar. Focused, hypothesis-based investigations on these specific genes will help delineate the determinants that enable this deadly pathogen to be virulent to humans and give insight into the evolution of Y. pestis and plague pathogenesis. Moreover, there may be the implications for development of biovar microtus strains as a potential vaccine.