Lum KM

References (11)

Title : Chemoproteomic identification of a DPP4 homolog in Bacteroides thetaiotaomicron - Keller_2023_Nat.Chem.Biol__
Author(s) : Keller LJ , Nguyen TH , Liu LJ , Hurysz BM , Lakemeyer M , Guerra M , Gelsinger DJ , Chanin R , Ngo N , Lum KM , Faucher F , Ipock P , Niphakis MJ , Bhatt AS , O'Donoghue AJ , Huang KC , Bogyo M
Ref : Nat Chemical Biology , : , 2023
Abstract : Serine hydrolases have important roles in signaling and human metabolism, yet little is known about their functions in gut commensal bacteria. Using bioinformatics and chemoproteomics, we identify serine hydrolases in the gut commensal Bacteroides thetaiotaomicron that are specific to the Bacteroidetes phylum. Two are predicted homologs of the human dipeptidyl peptidase 4 (hDPP4), a key enzyme that regulates insulin signaling. Our functional studies reveal that BT4193 is a true homolog of hDPP4 that can be inhibited by FDA-approved type 2 diabetes medications targeting hDPP4, while the other is a misannotated proline-specific triaminopeptidase. We demonstrate that BT4193 is important for envelope integrity and that loss of BT4193 reduces B. thetaiotaomicron fitness during in vitro growth within a diverse community. However, neither function is dependent on BT4193 proteolytic activity, suggesting a scaffolding or signaling function for this bacterial protease.
ESTHER : Keller_2023_Nat.Chem.Biol__
PubMedSearch : Keller_2023_Nat.Chem.Biol__
PubMedID: 37349583

Title : Chemoproteomics-Enabled Identification of 4-Oxo-beta-Lactams as Inhibitors of Dipeptidyl Peptidases 8 and 9 - Carvalho_2022_Angew.Chem.Int.Ed.Engl_61_e202210498
Author(s) : Carvalho LAR , Ross B , Fehr L , Bolgi O , Wohrle S , Lum KM , Podlesainski D , Vieira AC , Kiefersauer R , Felix R , Rodrigues T , Lucas SD , Gross O , Geiss-Friedlander R , Cravatt BF , Huber R , Kaiser M , Moreira R
Ref : Angew Chem Int Ed Engl , : , 2022
Abstract : Dipeptidyl peptidases 8 and 9 (DPP8/9) have gathered interest as drug targets due to their important roles in biological processes like immunity and tumorigenesis. Elucidation of their distinct individual functions remains an ongoing task and could benefit from the availability of novel, chemically diverse and selective chemical tools. Here, we report the activity-based protein profiling (ABPP)-mediated discovery of 4-oxo-beta-lactams as potent, non-substrate-like nanomolar DPP8/9 inhibitors. X-ray crystallographic structures revealed different ligand binding modes for DPP8 and DPP9, including an unprecedented targeting of an extended S2' (eS2') subsite in DPP8. Biological assays confirmed inhibition at both target and cellular levels. Altogether, our integrated chemical proteomics and structure-guided small molecule design approach led to novel DPP8/9 inhibitors with alternative molecular inhibition mechanisms, delivering the highest selectivity index reported to date.
ESTHER : Carvalho_2022_Angew.Chem.Int.Ed.Engl_61_e202210498
PubMedSearch : Carvalho_2022_Angew.Chem.Int.Ed.Engl_61_e202210498
PubMedID: 36089535
Gene_locus related to this paper: human-DPP8 , human-DPP9

Title : ABHD17 regulation of plasma membrane palmitoylation and N-Ras-dependent cancer growth - Remsberg_2021_Nat.Chem.Biol__
Author(s) : Remsberg JR , Suciu RM , Zambetti NA , Hanigan TW , Firestone AJ , Inguva A , Long A , Ngo N , Lum KM , Henry CL , Richardson SK , Predovic M , Huang B , Dix MM , Howell AR , Niphakis MJ , Shannon K , Cravatt BF
Ref : Nat Chemical Biology , : , 2021
Abstract : Multiple Ras proteins, including N-Ras, depend on a palmitoylation/depalmitoylation cycle to regulate their subcellular trafficking and oncogenicity. General lipase inhibitors such as Palmostatin M (Palm M) block N-Ras depalmitoylation, but lack specificity and target several enzymes displaying depalmitoylase activity. Here, we describe ABD957, a potent and selective covalent inhibitor of the ABHD17 family of depalmitoylases, and show that this compound impairs N-Ras depalmitoylation in human acute myeloid leukemia (AML) cells. ABD957 produced partial effects on N-Ras palmitoylation compared with Palm M, but was much more selective across the proteome, reflecting a plasma membrane-delineated action on dynamically palmitoylated proteins. Finally, ABD957 impaired N-Ras signaling and the growth of NRAS-mutant AML cells in a manner that synergizes with MAP kinase kinase (MEK) inhibition. Our findings uncover a surprisingly restricted role for ABHD17 enzymes as regulators of the N-Ras palmitoylation cycle and suggest that ABHD17 inhibitors may have value as targeted therapies for NRAS-mutant cancers.
ESTHER : Remsberg_2021_Nat.Chem.Biol__
PubMedSearch : Remsberg_2021_Nat.Chem.Biol__
PubMedID: 33927411
Gene_locus related to this paper: human-ABHD17A , human-ABHD17B , human-ABHD17C

Title : Toxoplasma gondii serine hydrolases regulate parasite lipid mobilization during growth and replication within the host - Onguka_2021_Cell.Chem.Biol__
Author(s) : Onguka O , Babin BM , Lakemeyer M , Foe IT , Amara N , Terrell SM , Lum KM , Cieplak P , Niphakis MJ , Long JZ , Bogyo M
Ref : Cell Chemical Biology , : , 2021
Abstract : The intracellular protozoan parasite Toxoplasma gondii must scavenge cholesterol and other lipids from the host to facilitate intracellular growth and replication. Enzymes responsible for neutral lipid synthesis have been identified but there is no evidence for enzymes that catalyze lipolysis of cholesterol esters and esterified lipids. Here, we characterize several T. gondii serine hydrolases with esterase and thioesterase activities that were previously thought to be depalmitoylating enzymes. We find they do not cleave palmitoyl thiol esters but rather hydrolyze short-chain lipid esters. Deletion of one of the hydrolases results in alterations in levels of multiple lipids species. We also identify small-molecule inhibitors of these hydrolases and show that treatment of parasites results in phenotypic defects reminiscent of parasites exposed to excess cholesterol or oleic acid. Together, these data characterize enzymes necessary for processing lipids critical for infection and highlight the potential for targeting parasite hydrolases for therapeutic applications.
ESTHER : Onguka_2021_Cell.Chem.Biol__
PubMedSearch : Onguka_2021_Cell.Chem.Biol__
PubMedID: 34043961
Gene_locus related to this paper: toxgo-TgASH3 , toxgo-TgASH2 , toxgo-s4ug63 , toxgo-a0a125yz56

Title : 3-Oxo-beta-sultam as a Sulfonylating Chemotype for Inhibition of Serine Hydrolases and Activity-Based Protein Profiling - Carvalho_2020_ACS.Chem.Biol_15_878
Author(s) : Carvalho LAR , Almeida VT , Brito JA , Lum KM , Oliveira TF , Guedes RC , Goncalves LM , Lucas SD , Cravatt BF , Archer M , Moreira R
Ref : ACS Chemical Biology , 15 :878 , 2020
Abstract : 3-Oxo-beta-sultams are four-membered ring ambident electrophiles that can react with nucleophiles either at the carbonyl carbon or at the sulfonyl sulfur atoms, and that have been reported to inhibit serine hydrolases via acylation of the active-site serine residue. We have developed a panel of 3-oxo-beta-sultam inhibitors and show, through crystallographic data, that they are regioselective sulfonylating electrophiles, covalently binding to the catalytic serine of human and porcine elastases through the sulfur atom. Application of 3-oxo-beta-sultam-derived activity-based probes in a human proteome revealed their potential to label disease-related serine hydrolases and proteasome subunits. Activity-based protein profiling applications of 3-oxo-beta-sultams should open up new opportunities to investigate these classes of enzymes in complex proteomes and expand the toolbox of available sulfur-based covalent protein modifiers in chemical biology.
ESTHER : Carvalho_2020_ACS.Chem.Biol_15_878
PubMedSearch : Carvalho_2020_ACS.Chem.Biol_15_878
PubMedID: 32176480

Title : AIG1 and ADTRP are endogenous hydrolases of fatty acid esters of hydroxy fatty acids (FAHFAs) in mice - Erikci_2020_J.Biol.Chem_295_5891
Author(s) : Erikci Ertunc M , Kok BP , Parsons WH , Wang JG , Tan D , Donaldson CJ , Pinto AFM , Vaughan JM , Ngo N , Lum KM , Henry CL , Coppola AR , Niphakis MJ , Cravatt BF , Saez E , Saghatelian A
Ref : Journal of Biological Chemistry , 295 :5891 , 2020
Abstract : Fatty acid esters of hydroxy fatty acids (FAHFAs) are a newly discovered class of signaling lipids with anti-inflammatory and anti-diabetic properties. However, the endogenous regulation of FAHFAs remains a pressing but unanswered question. Here, using MS-based FAHFA hydrolysis assays, LC-MS-based lipidomics analyses, and activity-based protein profiling, we found that androgen-induced gene 1 (AIG1) and androgen-dependent TFPI-regulating protein (ADTRP), two threonine hydrolases, control FAHFA levels in vivo in both genetic and pharmacologic mouse models. Tissues from mice lacking ADTRP (Adtrp-KO), or both AIG1 and ADTRP (DKO) had higher concentrations of FAHFAs particularly isomers with the ester bond at the 9(th) carbon due to decreased FAHFA hydrolysis activity. The levels of other lipid classes were unaltered indicating that AIG1 and ADTRP specifically hydrolyze FAHFAs. Complementing these genetic studies, we also identified a dual AIG1/ADTRP inhibitor, ABD-110207, which is active in vivo Acute treatment of WT mice with ABD-110207 resulted in elevated FAHFA levels, further supporting the notion that AIG1 and ADTRP activity control endogenous FAHFA levels. However, loss of AIG1/ADTRP did not mimic the changes associated with pharmacologically administered FAHFAs on extent of upregulation of FAHFA levels, glucose tolerance, or insulin sensitivity in mice, indicating that therapeutic strategies should weigh more on FAHFA administration. Together, these findings identify AIG1 and ADTRP as the first endogenous FAHFA hydrolases identified and provide critical genetic and chemical tools for further characterization of these enzymes and endogenous FAHFAs to unravel their physiological functions and roles in health and disease.
ESTHER : Erikci_2020_J.Biol.Chem_295_5891
PubMedSearch : Erikci_2020_J.Biol.Chem_295_5891
PubMedID: 32152231

Title : Single-Cell Profiling and SCOPE-Seq Reveal Lineage Dynamics of Adult Ventricular-Subventricular Zone Neurogenesis and NOTUM as a Key Regulator - Mizrak_2020_Cell.Rep_31_107805
Author(s) : Mizrak D , Bayin NS , Yuan J , Liu Z , Suciu RM , Niphakis MJ , Ngo N , Lum KM , Cravatt BF , Joyner AL , Sims PA
Ref : Cell Rep , 31 :107805 , 2020
Abstract : In the adult ventricular-subventricular zone (V-SVZ), neural stem cells (NSCs) generate new olfactory bulb (OB) neurons and glia throughout life. To map adult neuronal lineage progression, we profiled >56,000 V-SVZ and OB cells by single-cell RNA sequencing (scRNA-seq). Our analyses reveal the molecular diversity of OB neurons, including fate-mapped neurons, lineage progression dynamics, and an NSC intermediate enriched for Notum, which encodes a secreted WNT antagonist. SCOPE-seq technology, which links live-cell imaging with scRNA-seq, uncovers cell-size transitions during NSC differentiation and preferential NOTUM binding to proliferating neuronal precursors. Consistently, application of NOTUM protein in slice cultures and pharmacological inhibition of NOTUM in slice cultures and in vivo demonstrated that NOTUM negatively regulates V-SVZ proliferation. Timely, context-dependent neurogenesis demands adaptive signaling among neighboring progenitors. Our findings highlight a critical regulatory state during NSC activation marked by NOTUM, which attenuates WNT-stimulated proliferation in NSC progeny.
ESTHER : Mizrak_2020_Cell.Rep_31_107805
PubMedSearch : Mizrak_2020_Cell.Rep_31_107805
PubMedID: 32579931
Gene_locus related to this paper: human-NOTUM

Title : Pharmacological convergence reveals a lipid pathway that regulates C. elegans lifespan - Chen_2019_Nat.Chem.Biol_15_453
Author(s) : Chen AL , Lum KM , Lara-Gonzalez P , Ogasawara D , Cognetta AB, 3rd , To A , Parsons WH , Simon GM , Desai A , Petrascheck M , Bar-Peled L , Cravatt BF
Ref : Nat Chemical Biology , 15 :453 , 2019
Abstract : Phenotypic screening has identified small-molecule modulators of aging, but the mechanism of compound action often remains opaque due to the complexities of mapping protein targets in whole organisms. Here, we combine a library of covalent inhibitors with activity-based protein profiling to coordinately discover bioactive compounds and protein targets that extend lifespan in Caenorhabditis elegans. We identify JZL184-an inhibitor of the mammalian endocannabinoid (eCB) hydrolase monoacylglycerol lipase (MAGL or MGLL)-as a potent inducer of longevity, a result that was initially perplexing as C. elegans does not possess an MAGL ortholog. We instead identify FAAH-4 as a principal target of JZL184 and show that this enzyme, despite lacking homology with MAGL, performs the equivalent metabolic function of degrading eCB-related monoacylglycerides in C. elegans. Small-molecule phenotypic screening thus illuminates pure pharmacological connections marking convergent metabolic functions in distantly related organisms, implicating the FAAH-4/monoacylglyceride pathway as a regulator of lifespan in C. elegans.
ESTHER : Chen_2019_Nat.Chem.Biol_15_453
PubMedSearch : Chen_2019_Nat.Chem.Biol_15_453
PubMedID: 30911178

Title : Multicomponent mapping of boron chemotypes furnishes selective enzyme inhibitors - Tan_2017_Nat.Commun_8_1760
Author(s) : Tan J , Cognetta AB, 3rd , Diaz DB , Lum KM , Adachi S , Kundu S , Cravatt BF , Yudin AK
Ref : Nat Commun , 8 :1760 , 2017
Abstract : Heteroatom-rich organoboron compounds have attracted attention as modulators of enzyme function. Driven by the unmet need to develop chemoselective access to boron chemotypes, we report herein the synthesis of alpha- and beta-aminocyano(MIDA)boronates from borylated carbonyl compounds. Activity-based protein profiling of the resulting beta-aminoboronic acids furnishes selective and cell-active inhibitors of the (ox)lipid-metabolizing enzyme alpha/beta-hydrolase domain 3 (ABHD3). The most potent compound displays nanomolar in vitro and in situ IC50 values and fully inhibits ABHD3 activity in human cells with no detectable cross-reactivity against other serine hydrolases. These findings demonstrate that synthetic methods that enhance the heteroatom diversity of boron-containing molecules within a limited set of scaffolds accelerate the discovery of chemical probes of human enzymes.
ESTHER : Tan_2017_Nat.Commun_8_1760
PubMedSearch : Tan_2017_Nat.Commun_8_1760
PubMedID: 29170371
Gene_locus related to this paper: human-ABHD3 , mouse-abhd3

Title : Chemical Proteomic Profiling of Human Methyltransferases - Horning_2016_J.Am.Chem.Soc_138_13335
Author(s) : Horning BD , Suciu RM , Ghadiri DA , Ulanovskaya OA , Matthews ML , Lum KM , Backus KM , Brown SJ , Rosen H , Cravatt BF
Ref : Journal of the American Chemical Society , 138 :13335 , 2016
Abstract : Methylation is a fundamental mechanism used in Nature to modify the structure and function of biomolecules, including proteins, DNA, RNA, and metabolites. Methyl groups are predominantly installed into biomolecules by a large and diverse class of S-adenosyl methionine (SAM)-dependent methyltransferases (MTs), of which there are approximately 200 known or putative members in the human proteome. Deregulated MT activity contributes to numerous diseases, including cancer, and several MT inhibitors are in clinical development. Nonetheless, a large fraction of the human MT family remains poorly characterized, underscoring the need for new technologies to characterize MTs and their inhibitors in native biological systems. Here, we describe a suite of S-adenosyl homocysteine (SAH) photoreactive probes and their application in chemical proteomic experiments to profile and enrich a large number of MTs (>50) from human cancer cell lysates with remarkable specificity over other classes of proteins. We further demonstrate that the SAH probes can enrich MT-associated proteins and be used to screen for and assess the selectivity of MT inhibitors, leading to the discovery of a covalent inhibitor of nicotinamide N-methyltransferase (NNMT), an enzyme implicated in cancer and metabolic disorders. The chemical proteomics probes and methods for their utilization reported herein should prove of value for the functional characterization of MTs, MT complexes, and MT inhibitors in mammalian biology and disease.
ESTHER : Horning_2016_J.Am.Chem.Soc_138_13335
PubMedSearch : Horning_2016_J.Am.Chem.Soc_138_13335
PubMedID: 27689866

Title : Highly selective inhibitors of monoacylglycerol lipase bearing a reactive group that is bioisosteric with endocannabinoid substrates - Chang_2012_Chem.Biol_19_579
Author(s) : Chang JW , Niphakis MJ , Lum KM , Cognetta AB, 3rd , Wang C , Matthews ML , Niessen S , Buczynski MW , Parsons LH , Cravatt BF
Ref : Chemical Biology , 19 :579 , 2012
Abstract : The endocannabinoids 2-arachidonoyl glycerol (2-AG) and N-arachidonoyl ethanolamine (anandamide) are principally degraded by monoacylglycerol lipase (MAGL) and fatty acid amide hydrolase (FAAH), respectively. The recent discovery of O-aryl carbamates such as JZL184 as selective MAGL inhibitors has enabled functional investigation of 2-AG signaling pathways in vivo. Nonetheless, JZL184 and other reported MAGL inhibitors still display low-level cross-reactivity with FAAH and peripheral carboxylesterases, which can complicate their use in certain biological studies. Here, we report a distinct class of O-hexafluoroisopropyl (HFIP) carbamates that inhibits MAGL in vitro and in vivo with excellent potency and greatly improved selectivity, including showing no detectable cross-reactivity with FAAH. These findings designate HFIP carbamates as a versatile chemotype for inhibiting MAGL and should encourage the pursuit of other serine hydrolase inhibitors that bear reactive groups resembling the structures of natural substrates.
ESTHER : Chang_2012_Chem.Biol_19_579
PubMedSearch : Chang_2012_Chem.Biol_19_579
PubMedID: 22542104
Gene_locus related to this paper: human-MGLL