51
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Han S, Mei L, Quach T, Porter C, Trevaskis N. Lipophilic Conjugates of Drugs: A Tool to Improve Drug Pharmacokinetic and Therapeutic Profiles. Pharm Res 2021; 38:1497-1518. [PMID: 34463935 DOI: 10.1007/s11095-021-03093-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/05/2021] [Indexed: 01/19/2023]
Abstract
Lipophilic conjugates (LCs) of small molecule drugs have been used widely in clinical and pre-clinical studies to achieve a number of pharmacokinetic and therapeutic benefits. For example, lipophilic derivatives of drugs are employed in several long acting injectable products to provide sustained drug exposure for hormone replacement therapy and to treat conditions such as neuropsychiatric diseases. LCs can also be used to modulate drug metabolism, and to enhance drug permeation across membranes, either by increasing lipophilicity to enhance passive diffusion or by increasing protein-mediated active transport. Furthermore, such conjugation strategies have been employed to promote drug association with endogenous macromolecular carriers (e.g. albumin and lipoproteins), and this in turn results in altered drug distribution and pharmacokinetic profiles, where the changes can be 'general' (e.g. prolonged plasma half-life) or 'specific' (e.g. enhanced delivery to specific tissues in parallel with the macromolecular carriers). Another utility of LCs is to enhance the encapsulation of drugs within engineered nanoscale drug delivery systems, in order to best take advantage of the targeting and pharmacokinetic benefits of nanomedicines. The current review provides a summary of the mechanisms by which lipophilic conjugates, including in combination with delivery vehicles, can be used to control drug delivery, distribution and therapeutic profiles. The article is structured into sections which highlight a specific benefit of LCs and then demonstrate this benefit with case studies. The review attempts to provide a toolbox to assist researchers to design and optimise drug candidates, including consideration of drug-formulation compatibility.
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Affiliation(s)
- Sifei Han
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
- Suzhou Institute of Drug Innovation, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Suzhou, Jiangsu, 215123, China.
| | - Lianghe Mei
- Suzhou Institute of Drug Innovation, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Suzhou, Jiangsu, 215123, China
| | - Tim Quach
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
- PureTech Health, 6 Tide Street, Boston, MA, 02210, USA
| | - Chris Porter
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Natalie Trevaskis
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
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52
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Hatmal MM, Abuyaman O, Taha M. Docking-generated multiple ligand poses for bootstrapping bioactivity classifying Machine Learning: Repurposing covalent inhibitors for COVID-19-related TMPRSS2 as case study. Comput Struct Biotechnol J 2021; 19:4790-4824. [PMID: 34426763 PMCID: PMC8373588 DOI: 10.1016/j.csbj.2021.08.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/03/2021] [Accepted: 08/16/2021] [Indexed: 01/10/2023] Open
Abstract
In the present work we introduce the use of multiple docked poses for bootstrapping machine learning-based QSAR modelling. Ligand-receptor contact fingerprints are implemented as descriptor variables. We implemented this method for the discovery of potential inhibitors of the serine protease enzyme TMPRSS2 involved the infectivity of coronaviruses. Several machine learners were scanned, however, Xgboost, support vector machines (SVM) and random forests (RF) were the best with testing set accuracies reaching 90%. Three potential hits were identified upon using the method to scan known untested FDA approved drugs against TMPRSS2. Subsequent molecular dynamics simulation and covalent docking supported the results of the new computational approach.
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Affiliation(s)
- Ma'mon M. Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, PO Box 330127, Zarqa 13133, Jordan
| | - Omar Abuyaman
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, PO Box 330127, Zarqa 13133, Jordan
| | - Mutasem Taha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman 11942, Jordan
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53
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Liu M, Xu B, Ma Y, Shang L, Ye S, Wang Y. Reversible covalent inhibitors suppress enterovirus 71 infection by targeting the 3C protease. Antiviral Res 2021; 192:105102. [PMID: 34082057 DOI: 10.1016/j.antiviral.2021.105102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/27/2021] [Accepted: 05/26/2021] [Indexed: 12/25/2022]
Abstract
As one of the principal etiological agents of hand, foot, and mouth disease (HFMD), enterovirus 71 (EV71) is associated with severe neurological complications or fatal diseases, while without effective medications thus far. Here we applied dually activated Michael acceptor to develop a series of reversible covalent compounds for EV71 3C protease (3Cpro), a promising antiviral drug target that plays an essential role during viral replication by cleaving the precursor polyprotein, inhibiting host protein synthesis, and evading innate immunity. Among them, cyanoacrylate and Boc-protected cyanoarylamide derivatives (SLQ-4 and SLQ-5) showed effective antiviral activity against EV71. The two inhibitors exhibited broad antiviral effects, acting on RD, 293T, and Vero cell lines, as well as on EV71 A, B, C, CVA16, and CVB3 viral strains. We further determined the binding pockets between the two inhibitors and 3Cpro based on docking studies. These results, together with our previous studies, provide evidence to elucidate the mechanism of action of these two reversible covalent inhibitors and contribute to the development of clinically effective medicines to treat EV71 infections.
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Affiliation(s)
- Meijun Liu
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Binghong Xu
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, 300072, China
| | - Yuying Ma
- College of Pharmacy, Nankai University, Tianjin, 300350, China; Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Luqing Shang
- College of Pharmacy, Nankai University, Tianjin, 300350, China
| | - Sheng Ye
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, 300072, China.
| | - Yaxin Wang
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, 300072, China.
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54
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Ikeda S, Sugiyama H, Tokuhara H, Murakami M, Nakamura M, Oguro Y, Aida J, Morishita N, Sogabe S, Dougan DR, Gay SC, Qin L, Arimura N, Takahashi Y, Sasaki M, Kamada Y, Aoyama K, Kimoto K, Kamata M. Design and Synthesis of Novel Spiro Derivatives as Potent and Reversible Monoacylglycerol Lipase (MAGL) Inhibitors: Bioisosteric Transformation from 3-Oxo-3,4-dihydro-2 H-benzo[ b][1,4]oxazin-6-yl Moiety. J Med Chem 2021; 64:11014-11044. [PMID: 34328319 DOI: 10.1021/acs.jmedchem.1c00432] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The therapeutic potential of monoacylglycerol lipase (MAGL) inhibitors in central nervous system-related diseases has attracted attention worldwide. However, the availability of reversible-type inhibitor is still limited to clarify the pharmacological effect. Herein, we report the discovery of novel spiro chemical series as potent and reversible MAGL inhibitors with a different binding mode to MAGL using Arg57 and His121. Starting from hit compound 1 and its co-crystal structure with MAGL, structure-based drug discovery (SBDD) approach enabled us to generate various spiro scaffolds like 2a (azetidine-lactam), 2b (cyclobutane-lactam), and 2d (cyclobutane-carbamate) as novel bioisosteres of 3-oxo-3,4-dihydro-2H-benzo[b][1,4]oxazin-6-yl moiety in 1 with higher lipophilic ligand efficiency (LLE). Optimization of the left hand side afforded 4f as a promising reversible MAGL inhibitor, which showed potent in vitro MAGL inhibitory activity (IC50 6.2 nM), good oral absorption, blood-brain barrier penetration, and significant pharmacodynamic changes (2-arachidonoylglycerol increase and arachidonic acid decrease) at 0.3-10 mg/kg, po. in mice.
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Affiliation(s)
- Shuhei Ikeda
- Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Hideyuki Sugiyama
- Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Hidekazu Tokuhara
- Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masataka Murakami
- Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Minoru Nakamura
- Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yuya Oguro
- Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Jumpei Aida
- Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Nao Morishita
- Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoshi Sogabe
- Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Douglas R Dougan
- Structural Biology and Biophysics, Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Sean C Gay
- Structural Biology and Biophysics, Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Ling Qin
- Structural Biology and Biophysics, Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Naoto Arimura
- Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yasuko Takahashi
- Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masako Sasaki
- Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yusuke Kamada
- Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kazunobu Aoyama
- Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kouya Kimoto
- Pharmaceutical Sciences, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Makoto Kamata
- Research, Takeda Pharmaceutical Co., Ltd., 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa 251-8555, Japan
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55
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Parsons WH, Rutland NT, Crainic JA, Cardozo JM, Chow AS, Andrews CL, Sheehan BK. Development of succinimide-based inhibitors for the mitochondrial rhomboid protease PARL. Bioorg Med Chem Lett 2021; 49:128290. [PMID: 34311087 DOI: 10.1016/j.bmcl.2021.128290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/16/2021] [Accepted: 07/20/2021] [Indexed: 01/26/2023]
Abstract
While the biochemistry of rhomboid proteases has been extensively studied since their discovery two decades ago, efforts to define the physiological roles of these enzymes are ongoing and would benefit from chemical probes that can be used to manipulate the functions of these proteins in their native settings. Here, we describe the use of activity-based protein profiling (ABPP) technology to conduct a targeted screen for small-molecule inhibitors of the mitochondrial rhomboid protease PARL, which plays a critical role in regulating mitophagy and cell death. We synthesized a series of succinimide-containing sulfonyl esters and sulfonamides and discovered that these compounds serve as inhibitors of PARL with the most potent sulfonamides having submicromolar affinity for the enzyme. A counterscreen against the bacterial rhomboid protease GlpG demonstrates that several of these compounds display selectivity for PARL over GlpG by as much as two orders of magnitude. Both the sulfonyl ester and sulfonamide scaffolds exhibit reversible binding and are able to engage PARL in mammalian cells. Collectively, our findings provide encouraging precedent for the development of PARL-selective inhibitors and establish N-[(arylsulfonyl)oxy]succinimides and N-arylsulfonylsuccinimides as new molecular scaffolds for inhibiting members of the rhomboid protease family.
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Affiliation(s)
- William H Parsons
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States.
| | - Nicholas T Rutland
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Jennifer A Crainic
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Joaquin M Cardozo
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Alyssa S Chow
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Charlotte L Andrews
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
| | - Brendan K Sheehan
- Department of Chemistry and Biochemistry, Oberlin College, Room A263, Science Center, 119 Woodland St., Oberlin, OH 44074, United States
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56
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Toroitich EK, Ciancone AM, Hahm HS, Brodowski SM, Libby AH, Hsu KL. Discovery of a Cell-Active SuTEx Ligand of Prostaglandin Reductase 2. Chembiochem 2021; 22:2134-2139. [PMID: 33861519 PMCID: PMC8206015 DOI: 10.1002/cbic.202000879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/13/2021] [Indexed: 11/09/2022]
Abstract
Sulfonyl-triazoles have emerged as a new reactive group for covalent modification of tyrosine sites on proteins through sulfur-triazole exchange (SuTEx) chemistry. The extent to which this sulfur electrophile can be tuned for developing ligands with cellular activity remains largely underexplored. Here, we performed fragment-based ligand discovery in live cells to identify SuTEx compounds capable of liganding tyrosine sites on diverse protein targets. We verified our quantitative chemical proteomic findings by demonstrating concentration-dependent activity of SuTEx ligands, but not inactive counterparts, against recombinant protein targets directly in live cells. Our structure-activity relationship studies identified the SuTEx ligand HHS-0701 as a cell-active inhibitor capable of blocking prostaglandin reductase 2 (PTGR2) biochemical activity.
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Affiliation(s)
- Emmanuel K. Toroitich
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Anthony M. Ciancone
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Heung Sik Hahm
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Skylar M. Brodowski
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Adam H. Libby
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
- University of Virginia Cancer Center, University of Virginia, Charlottesville, VA 22903, USA
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia, 22908, United States
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States
- University of Virginia Cancer Center, University of Virginia, Charlottesville, VA 22903, USA
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57
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Rudolph S, Dahlhaus H, Hanekamp W, Albers C, Barth M, Michels G, Friedrich D, Lehr M. Aryl N-[ω-(6-Fluoroindol-1-yl)alkyl]carbamates as Inhibitors of Fatty Acid Amide Hydrolase, Monoacylglycerol Lipase, and Butyrylcholinesterase: Structure-Activity Relationships and Hydrolytic Stability. ACS OMEGA 2021; 6:13466-13483. [PMID: 34056494 PMCID: PMC8158844 DOI: 10.1021/acsomega.1c01699] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/29/2021] [Indexed: 05/02/2023]
Abstract
A series of aryl N-[ω-(6-fluoroindol-1-yl)alkyl]carbamates with alkyl spacers of varying lengths between the indole and the carbamate group and with differently substituted aryl moieties at the carbamate oxygen were synthesized and tested for inhibition of the pharmacologically interesting serine hydrolases fatty acid amide hydrolase (FAAH), monoacylglycerol lipase (MAGL), butyrylcholinesterase (BuChE), and acetylcholinesterase (AChE). Furthermore, the chemical stability in an aqueous solution and the metabolic stability toward esterases in porcine liver homogenate and porcine blood plasma were determined. While most of the synthesized derivatives were potent inhibitors of FAAH, a considerable inhibition of MAGL and BuChE was elicited only by compounds with a high carbamate reactivity, as evidenced by a significant hydrolysis of these compounds in an aqueous solution. However, the high inhibitory potency of some compounds toward MAGL and BuChE, especially that of the ortho-carboxyphenyl derivative 37, could not be explained by chemical reactivity alone. Several of the carbamates studied possessed varying degrees of stability toward esterases from liver and blood plasma. In some cases, marked inactivation by the pseudo-esterase activity of plasma albumin was observed. Mass spectrometric studies showed that such carbamates formed covalent bonds with albumin at several sites.
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Affiliation(s)
- Stefan Rudolph
- Institute
of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstrasse 48, 48149 Münster, Germany
| | - Helmut Dahlhaus
- Institute
of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstrasse 48, 48149 Münster, Germany
| | - Walburga Hanekamp
- Institute
of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstrasse 48, 48149 Münster, Germany
| | - Christian Albers
- Bruker
Daltonik GmbH, Fahrenheitstrasse
4, 28359 Bremen, Germany
| | - Maximilian Barth
- Institute
of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstrasse 48, 48149 Münster, Germany
| | - Giulia Michels
- Institute
of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstrasse 48, 48149 Münster, Germany
| | - Denise Friedrich
- Institute
of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstrasse 48, 48149 Münster, Germany
| | - Matthias Lehr
- Institute
of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstrasse 48, 48149 Münster, Germany
- . Tel: +49251 83 33331. Fax: +49251 83 32144
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58
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Long DH, Townsend CA. Acyl Donor Stringency and Dehydroaminoacyl Intermediates in β-Lactam Formation by a Non-ribosomal Peptide Synthetase. ACS Chem Biol 2021; 16:806-812. [PMID: 33847484 DOI: 10.1021/acschembio.1c00117] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Condensation (C) domains in non-ribosomal peptide synthetases catalyze peptide elongation steps whereby activated amino acid or peptidyl acyl donors are coupled with specific amino acid acceptors. In the biosynthesis of the β-lactam antibiotic nocardicin A, an unusual C domain converts a seryl tetrapeptide into its pentapeptide product containing an integrated β-lactam ring. While indirect evidence for the intermediacy of a dehydroalanyl species has been reported, here we describe observation of the elusive enzyme-bound dehydroamino acyl intermediate generated from the corresponding allo-threonyl tetrapeptide and partitioned into pentapeptide products containing either a dehydrobutyrine residue or an embedded β-lactam. Contrary to trends in the literature where condensation domains have been deemed flexible as to acyl donor structure, this β-lactam synthesizing domain is highly discriminating. The observation of dehydrobutyrine formation links this C domain to related clades associated with natural products containing dehydroamino acid and d-configured residues, suggesting a common mechanistic link.
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Affiliation(s)
- Darcie H. Long
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Craig A. Townsend
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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59
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Mastracchio A, Lai C, Digiammarino E, Ready DB, Lasko LM, Bromberg KD, McClellan WJ, Montgomery D, Manaves V, Shaw B, Algire M, Patterson MJ, Sun CC, Rosenberg S, Lai A, Michaelides MR. Discovery of a Potent and Selective Covalent p300/CBP Inhibitor. ACS Med Chem Lett 2021; 12:726-731. [PMID: 34055218 DOI: 10.1021/acsmedchemlett.0c00654] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/02/2021] [Indexed: 01/10/2023] Open
Abstract
Aberrant gene activation driven by the histone acetyltransferases p300 and CREB binding protein (CBP) has been linked to several diseases, including cancers. Because of this, many efforts have been aimed toward the targeting of the closely related paralogues, p300 and CBP, but these endeavors have been exclusively directed toward noncovalent inhibitors. X-ray crystallography of A-485 revealed that both p300 and CBP possess a cysteine (C1450) near the active site, thus rendering covalent inhibition an attractive chemical approach. Herein we report the development of compound 2, an acrylamide-based inhibitor of p300/CBP that forms a covalent adduct with C1450. We demonstrated using mass spectrometry that compound 2 selectively targets C1450, and we also validated covalent binding using kinetics experiments and cellular washout studies. The discovery of covalent inhibitor 2 gives us a unique tool for the study of p300/CBP biology.
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Affiliation(s)
- Anthony Mastracchio
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Chunqiu Lai
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Enrico Digiammarino
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Damien B. Ready
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Loren M. Lasko
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Kenneth D. Bromberg
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - William J. McClellan
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Debra Montgomery
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Vlasios Manaves
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Bailin Shaw
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Mikkel Algire
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Melanie J. Patterson
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Chaohong C. Sun
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Saul Rosenberg
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Albert Lai
- AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
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60
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Kumar K, Mhetre A, Ratnaparkhi GS, Kamat SS. A Superfamily-wide Activity Atlas of Serine Hydrolases in Drosophila melanogaster. Biochemistry 2021; 60:1312-1324. [PMID: 33827210 PMCID: PMC7610703 DOI: 10.1021/acs.biochem.1c00171] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The serine hydrolase (SH) superfamily is, perhaps, one of the largest functional enzyme classes in all forms of life and consists of proteases, peptidases, lipases, and carboxylesterases as representative members. Consistent with the name of this superfamily, all members, without any exception to date, use a nucleophilic serine residue in the enzyme active site to perform hydrolytic-type reactions via a two-step ping-pong mechanism involving a covalent enzyme intermediate. Given the highly conserved catalytic mechanism, this superfamily has served as a classical prototype in the development of several platforms of chemical proteomics techniques, activity-based protein profiling (ABPP), to globally interrogate the functions of its different members in various native, yet complex, biological settings. While ABPP-based proteome-wide activity atlases for SH activities are available in numerous organisms, including humans, to the best of our knowledge, such an analysis for this superfamily is lacking in any insect model. To address this, we initially report a bioinformatics analysis toward the identification and categorization of nonredundant SHs in Drosophila melanogaster. Following up on this in silico analysis, leveraging discovery chemoproteomics, we identify and globally map the full complement of SH activities during various developmental stages and in different adult tissues of Drosophila. Finally, as a proof of concept of the utility of this activity atlas, we highlight sexual dimorphism in SH activities across different tissues in adult D. melanogaster, and we propose new research directions, resources, and tools that this study can provide to the fly community.
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Affiliation(s)
- Kundan Kumar
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, India 411008
| | - Amol Mhetre
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, India 411008
| | - Girish S. Ratnaparkhi
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, India 411008
| | - Siddhesh S. Kamat
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, India 411008
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61
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Bayle E, Svensson F, Atkinson BN, Steadman D, Willis NJ, Woodward HL, Whiting P, Vincent JP, Fish PV. Carboxylesterase Notum Is a Druggable Target to Modulate Wnt Signaling. J Med Chem 2021; 64:4289-4311. [PMID: 33783220 PMCID: PMC8172013 DOI: 10.1021/acs.jmedchem.0c01974] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Indexed: 12/12/2022]
Abstract
Regulation of the Wnt signaling pathway is critically important for a number of cellular processes in both development and adult mammalian biology. This Perspective will provide a summary of current and emerging therapeutic opportunities in modulating Wnt signaling, especially through inhibition of Notum carboxylesterase activity. Notum was recently shown to act as a negative regulator of Wnt signaling through the removal of an essential palmitoleate group. Inhibition of Notum activity may represent a new approach to treat disease where aberrant Notum activity has been identified as the underlying cause. Reliable screening technologies are available to identify inhibitors of Notum, and structural studies are accelerating the discovery of new inhibitors. A selection of these hits have been optimized to give fit-for-purpose small molecule inhibitors of Notum. Three noteworthy examples are LP-922056 (26), ABC99 (27), and ARUK3001185 (28), which are complementary chemical tools for exploring the role of Notum in Wnt signaling.
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Affiliation(s)
- Elliott
D. Bayle
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Fredrik Svensson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Benjamin N. Atkinson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - David Steadman
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Nicky J. Willis
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Hannah L. Woodward
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Paul Whiting
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Jean-Paul Vincent
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Paul V. Fish
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
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62
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Borne AL, Brulet JW, Yuan K, Hsu KL. Development and biological applications of sulfur-triazole exchange (SuTEx) chemistry. RSC Chem Biol 2021; 2:322-337. [PMID: 34095850 PMCID: PMC8174820 DOI: 10.1039/d0cb00180e] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/05/2021] [Indexed: 12/27/2022] Open
Abstract
Sulfur electrophiles constitute an important class of covalent small molecules that have found widespread applications in synthetic chemistry and chemical biology. Various electrophilic scaffolds, including sulfonyl fluorides and arylfluorosulfates as recent examples, have been applied for protein bioconjugation to probe ligand sites amenable for chemical proteomics and drug discovery. In this review, we describe the development of sulfonyl-triazoles as a new class of electrophiles for sulfur-triazole exchange (SuTEx) chemistry. SuTEx achieves covalent reaction with protein sites through irreversible modification of a residue with an adduct group (AG) upon departure of a leaving group (LG). A principal differentiator of SuTEx from other chemotypes is the selection of a triazole heterocycle as the LG, which introduces additional capabilities for tuning the sulfur electrophile. We describe the opportunities afforded by modifications to the LG and AG alone or in tandem to facilitate nucleophilic substitution reactions at the SO2 center in cell lysates and live cells. As a result of these features, SuTEx serves as an efficient platform for developing chemical probes with tunable bioactivity to study novel nucleophilic sites on established and poorly annotated protein targets. Here, we highlight a suite of biological applications for the SuTEx electrophile and discuss future goals for this enabling covalent chemistry.
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Affiliation(s)
- Adam L. Borne
- Department of Pharmacology, University of Virginia School of MedicineCharlottesvilleVirginia 22908USA
| | - Jeffrey W. Brulet
- Department of Chemistry, University of VirginiaMcCormick Road, P.O. Box 400319CharlottesvilleVirginia 22904USA+1-434-297-4864
| | - Kun Yuan
- Department of Chemistry, University of VirginiaMcCormick Road, P.O. Box 400319CharlottesvilleVirginia 22904USA+1-434-297-4864
| | - Ku-Lung Hsu
- Department of Pharmacology, University of Virginia School of MedicineCharlottesvilleVirginia 22908USA
- Department of Chemistry, University of VirginiaMcCormick Road, P.O. Box 400319CharlottesvilleVirginia 22904USA+1-434-297-4864
- University of Virginia Cancer Center, University of VirginiaCharlottesvilleVA 22903USA
- Department of Molecular Physiology and Biological Physics, University of VirginiaCharlottesvilleVirginia 22908USA
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63
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Dutra JK, Foley TL, Huang Z, Fisher EL, Lachapelle EA, Mahapatra S, Ogilvie K, Butler TW, Bellenger J, Devraj Majmudar J, Am Ende CW. Fluorophosphonates on-Demand: A General and Simplified Approach toward Fluorophosphonate Synthesis. Chembiochem 2021; 22:1769-1774. [PMID: 33491295 DOI: 10.1002/cbic.202000852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/23/2021] [Indexed: 11/08/2022]
Abstract
Herein, we report a general and simplified synthesis of fluorophosphonates directly from p-nitrophenylphosphonates. This FP on-demand reaction is mediated by a commercially available polymer-supported fluoride reagent that produces a variety (25 examples) of fluorophosphonates in high yields while only requiring reagent filtration for pure fluorophosphonate isolation. This reaction protocol facilitates the rapid profiling of serine hydrolases with diverse and novel sets of activated phosphonates with differential proteome reactivity. Moreover, slight modification of the procedure into a reaction-to-assay format has enabled additional screening efficiency.
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Affiliation(s)
- Jason K Dutra
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | - Timothy L Foley
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | - Zhen Huang
- Pfizer Worldwide Research and Development, 1 Portland St, Cambridge, MA 02139, USA
| | - Ethan L Fisher
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | - Erik A Lachapelle
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | - Subham Mahapatra
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | - Kevin Ogilvie
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | - Todd W Butler
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | - Justin Bellenger
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
| | | | - Christopher W Am Ende
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, USA
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64
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Silveira RL, Knott BC, Pereira CS, Crowley MF, Skaf MS, Beckham GT. Transition Path Sampling Study of the Feruloyl Esterase Mechanism. J Phys Chem B 2021; 125:2018-2030. [PMID: 33616402 DOI: 10.1021/acs.jpcb.0c09725] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Serine hydrolases cleave peptide and ester bonds and are ubiquitous in nature, with applications in biotechnology, in materials, and as drug targets. The serine hydrolase two-step mechanism employs a serine-histidine-aspartate/glutamate catalytic triad, where the histidine residue acts as a base to activate poor nucleophiles (a serine residue or a water molecule) and as an acid to allow the dissociation of poor leaving groups. This mechanism has been the subject of debate regarding how histidine shuttles the proton from the nucleophile to the leaving group. To elucidate the reaction mechanism of serine hydrolases, we employ quantum mechanics/molecular mechanics-based transition path sampling to obtain the reaction coordinate using the Aspergillus niger feruloyl esterase A (AnFaeA) as a model enzyme. The optimal reaction coordinates include terms involving nucleophilic attack on the carbonyl carbon and proton transfer to, and dissociation of, the leaving group. During the reaction, the histidine residue undergoes a reorientation on the time scale of hundreds of femtoseconds that supports the "moving histidine" mechanism, thus calling into question the "ring flip" mechanism. We find a concerted mechanism, where the transition state coincides with the tetrahedral intermediate with the histidine residue pointed between the nucleophile and the leaving group. Moreover, motions of the catalytic aspartate toward the histidine occur concertedly with proton abstraction by the catalytic histidine and help stabilize the transition state, thus partially explaining how serine hydrolases enable poor nucleophiles to attack the substrate carbonyl carbon. Rate calculations indicate that the second step (deacylation) is rate-determining, with a calculated rate constant of 66 s-1. Overall, these results reveal the pivotal role of active-site dynamics in the catalytic mechanism of AnFaeA, which is likely similar in other serine hydrolases.
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Affiliation(s)
- Rodrigo L Silveira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States.,Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, Sao Paulo 13084-862, Brazil.,Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil
| | - Brandon C Knott
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Caroline S Pereira
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States.,Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, Sao Paulo 13084-862, Brazil
| | - Michael F Crowley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Munir S Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas, Campinas, Sao Paulo 13084-862, Brazil
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
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65
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Dwyer BG, Wang C, Abegg D, Racioppo B, Qiu N, Zhao Z, Pechalrieu D, Shuster A, Hoch DG, Adibekian A. Chemoproteomics-Enabled De Novo Discovery of Photoswitchable Carboxylesterase Inhibitors for Optically Controlled Drug Metabolism. Angew Chem Int Ed Engl 2021; 60:3071-3079. [PMID: 33035395 DOI: 10.1002/anie.202011163] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/07/2020] [Indexed: 12/28/2022]
Abstract
Herein, we report arylazopyrazole ureas and sulfones as a novel class of photoswitchable serine hydrolase inhibitors and present a chemoproteomic platform for rapid discovery of optically controlled serine hydrolase targets in complex proteomes. Specifically, we identify highly potent and selective photoswitchable inhibitors of the drug-metabolizing enzymes carboxylesterases 1 and 2 and demonstrate their pharmacological application by optically controlling the metabolism of the immunosuppressant drug mycophenolate mofetil. Collectively, this proof-of-concept study provides a first example of photopharmacological tools to optically control drug metabolism by modulating the activity of a metabolizing enzyme. Our arylazopyrazole ureas and sulfones offer synthetically accessible scaffolds that can be expanded to identify specific photoswitchable inhibitors for other serine hydrolases, including lipases, peptidases, and proteases. Our chemoproteomic platform can be applied to other photoswitches and scaffolds to achieve optical control over diverse protein classes.
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Affiliation(s)
- Brendan G Dwyer
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Chao Wang
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA.,Current address: Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Daniel Abegg
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Brittney Racioppo
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Nan Qiu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Zhensheng Zhao
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Dany Pechalrieu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Anton Shuster
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Dominic G Hoch
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA.,Current address: Laboratory of Organic Chemistry, ETH Zürich, 8093, Zürich, Switzerland
| | - Alexander Adibekian
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL, 33458, USA
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66
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Gogliettino M, Cocca E, Sandomenico A, Gratino L, Iaccarino E, Calvanese L, Rossi M, Palmieri G. Selective inhibition of acylpeptide hydrolase in SAOS-2 osteosarcoma cells: is this enzyme a viable anticancer target? Mol Biol Rep 2021; 48:1505-1519. [PMID: 33471263 DOI: 10.1007/s11033-020-06129-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 12/24/2020] [Indexed: 12/28/2022]
Abstract
Serine hydrolases play crucial roles in many physiological and pathophysiological processes and a panel of these enzymes are targets of approved drugs. Despite this, most of the human serine hydrolases remain poorly characterized with respect to their biological functions and substrates and only a limited number of in vivo active inhibitors have been so far identified. Acylpeptide hydrolase (APEH) is a member of the prolyl-oligopeptidase class, with a unique substrate specificity, that has been suggested to have a potential oncogenic role. In this study, a set of peptides was rationally designed from the lead compound SsCEI 4 and in vitro screened for APEH inhibition. Out of these molecules, a dodecapeptide named Ala 3 showed the best inhibitory effects and it was chosen as a candidate for investigating the anti-cancer effects induced by inhibition of APEH in SAOS-2 cell lines. The results clearly demonstrated that Ala 3 markedly reduced cell viability via deregulation of the APEH-proteasome system. Furthermore, flow cytometric analysis revealed that Ala 3 anti-proliferative effects were closely related to the activation of a caspase-dependent apoptotic pathway. Our findings provide further evidence that APEH can play a crucial role in the pathogenesis of cancer, shedding new light on the great potential of this enzyme as an attractive target for the diagnosis and the quest for selective cancer therapies.
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Affiliation(s)
- Marta Gogliettino
- Institute of Biosciences and BioResources, National Research Council (CNR-IBBR), 80131, Napoli, Italy
| | - Ennio Cocca
- Institute of Biosciences and BioResources, National Research Council (CNR-IBBR), 80131, Napoli, Italy
| | - Annamaria Sandomenico
- Institute of Biostructure and Bioimaging, National Research Council (CNR-IBB), 80134, Napoli, Italy
| | - Lorena Gratino
- Institute of Biosciences and BioResources, National Research Council (CNR-IBBR), 80131, Napoli, Italy
| | - Emanuela Iaccarino
- Institute of Biostructure and Bioimaging, National Research Council (CNR-IBB), 80134, Napoli, Italy
| | - Luisa Calvanese
- Institute of Biostructure and Bioimaging, National Research Council (CNR-IBB), 80134, Napoli, Italy
| | - Mosè Rossi
- Institute of Biosciences and BioResources, National Research Council (CNR-IBBR), 80131, Napoli, Italy
| | - Gianna Palmieri
- Institute of Biosciences and BioResources, National Research Council (CNR-IBBR), 80131, Napoli, Italy.
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67
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Filip R, Desrochers GF, Lefebvre DM, Reed A, Singaravelu R, Cravatt BF, Pezacki JP. Profiling of MicroRNA Targets Using Activity-Based Protein Profiling: Linking Enzyme Activity to MicroRNA-185 Function. Cell Chem Biol 2021; 28:202-212.e6. [PMID: 33450181 DOI: 10.1016/j.chembiol.2020.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 11/06/2020] [Accepted: 12/18/2020] [Indexed: 02/08/2023]
Abstract
MicroRNAs (miRNAs) act as cellular signal transducers through repression of protein translation. Elucidating targets using bioinformatics and traditional quantitation methods is often insufficient to uncover global miRNA function. Herein, alteration of protein function caused by miRNA-185 (miR-185), an immunometabolic miRNA, was determined using activity-based protein profiling, transcriptomics, and lipidomics. Fluorophosphonate-based activity-based protein profiling of miR-185-induced changes to human liver cells revealed that exclusively metabolic serine hydrolase enzymes were regulated in activity, some with roles in lipid and endocannabinoid metabolism. Lipidomic analysis linked enzymatic changes to levels of cellular lipid species, such as components of very-low-density lipoprotein particles. Additionally, inhibition of one miR-185 target, monoglyceride lipase, led to decreased hepatitis C virus levels in an infectious model. Overall, the approaches used here were able to identify key functional changes in serine hydrolases caused by miR-185 that are targetable pharmacologically, such that a small molecule inhibitor can recapitulate the miRNA phenotype.
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Affiliation(s)
- Roxana Filip
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Geneviève F Desrochers
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - David M Lefebvre
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Alex Reed
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ragunath Singaravelu
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada.
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68
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Ha J, Park H, Park J, Park SB. Recent advances in identifying protein targets in drug discovery. Cell Chem Biol 2020; 28:394-423. [PMID: 33357463 DOI: 10.1016/j.chembiol.2020.12.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/11/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
Phenotype-based screening has emerged as an alternative route for discovering new chemical entities toward first-in-class therapeutics. However, clarifying their mode of action has been a significant bottleneck for drug discovery. For target protein identification, conventionally bioactive small molecules are conjugated onto solid supports and then applied to isolate target proteins from whole proteome. This approach requires a high binding affinity between bioactive small molecules and their target proteins. Besides, the binding affinity can be significantly hampered after structural modifications of bioactive molecules with linkers. To overcome these limitations, two major strategies have recently been pursued: (1) the covalent conjugation between small molecules and target proteins using photoactivatable moieties or electrophiles, and (2) label-free target identification through monitoring target engagement by tracking the thermal, proteolytic, or chemical stability of target proteins. This review focuses on recent advancements in target identification from covalent capturing to label-free strategies.
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Affiliation(s)
- Jaeyoung Ha
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea
| | - Hankum Park
- CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jongmin Park
- Department of Chemistry, Kangwon National University, Chuncheon 24341, Korea.
| | - Seung Bum Park
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 08826, Korea; CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea.
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69
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Dwyer BG, Wang C, Abegg D, Racioppo B, Qiu N, Zhao Z, Pechalrieu D, Shuster A, Hoch DG, Adibekian A. Chemoproteomics‐Enabled De Novo Discovery of Photoswitchable Carboxylesterase Inhibitors for Optically Controlled Drug Metabolism. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Brendan G. Dwyer
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Chao Wang
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
- Current address: Department of Molecular Medicine The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Daniel Abegg
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Brittney Racioppo
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Nan Qiu
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Zhensheng Zhao
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Dany Pechalrieu
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Anton Shuster
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Dominic G. Hoch
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
- Current address: Laboratory of Organic Chemistry ETH Zürich 8093 Zürich Switzerland
| | - Alexander Adibekian
- Department of Chemistry The Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
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70
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Vanhoutte R, van de Plassche MAT, Verhelst SHL. Rapid Solid-Phase Construction of Serine Hydrolase Probes Results in Selective Activity-Based Probes for Acyl Protein Thioesterases-1/2. J Med Chem 2020; 63:11845-11853. [PMID: 32990443 DOI: 10.1021/acs.jmedchem.0c01043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Serine hydrolases (SHs) are a large, diverse family of enzymes that play various biomedically important roles. Their study has been substantially advanced by activity-based protein profiling, which makes use of covalent chemical probes for labeling the active site and detection by various methodologies. However, highly selective probes for individual SHs are scarce because probe synthesis usually takes place by time-consuming solution phase chemistry. We here report a general solid-phase synthesis toward SH chemical probes, which will speed up probe library synthesis. It involves the construction of a recognition element ending in a secondary amine followed by capping with different electrophiles. We illustrate the power of this approach by the discovery of selective chemical probes for the depalmitoylating enzymes APT-1/2. Overall, this study reports new methodologies to synthesize SH probes, while providing new reagents to study protein depalmitoylation.
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Affiliation(s)
- Roeland Vanhoutte
- Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, KU Leuven, Herestr. 49, 3000 Leuven, Belgium
| | - Merel A T van de Plassche
- Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, KU Leuven, Herestr. 49, 3000 Leuven, Belgium
| | - Steven H L Verhelst
- Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, KU Leuven, Herestr. 49, 3000 Leuven, Belgium.,Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
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71
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Druggable Targets in Endocannabinoid Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1274:177-201. [PMID: 32894511 DOI: 10.1007/978-3-030-50621-6_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cannabis and cannabinoid-based extracts have long been utilized for their perceived therapeutic value, and support for the legalization of cannabis for medicinal purposes continues to increase worldwide. Since the discovery of Δ9-tetrahydrocannabinol (THC) as the primary psychoactive component of cannabis over 50 years ago, substantial effort has been directed toward detection of endogenous mediators of cannabinoid activity. The discovery of anandamide and 2-arachidonoylglycerol as two endogenous lipid mediators of cannabinoid-like effects (endocannabinoids) has inspired exponential growth in our understanding of this essential pathway, as well as the pathological conditions that result from dysregulated endocannabinoid signaling. This review examines current knowledge of the endocannabinoid system including metabolic enzymes involved in biosynthesis and degradation and their receptors, and evaluates potential druggable targets for therapeutic intervention.
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72
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Li L, Chen F. Effects of mrpigG on Development and Secondary Metabolism of Monascus ruber M7. J Fungi (Basel) 2020; 6:jof6030156. [PMID: 32872515 PMCID: PMC7558996 DOI: 10.3390/jof6030156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022] Open
Abstract
Monascus pigments (MPs) have been used as food colorants for several centuries in Asian countries and are now used throughout the world via Asian catering. The MP biosynthetic pathway has been well-illustrated, but the functions of a few genes, including mrpigG, in the MP gene cluster are still unclear. In the current study, in order to investigate the function of mrpigG in M. ruber M7, gene deletion (ΔmrpigG), complementation (ΔmrpigG::mrpigG) and overexpression (M7::PtrpC-mrpigG) mutants were successfully obtained. The morphologies and biomasses, as well as the MP and citrinin production, of these mutants were analyzed. The results revealed that the disruption, complementation and overexpression of mrpigG showed no apparent defects in morphology, biomass or citrinin production (except MP production) in ΔmrpigG compared with M. ruber M7. Although the MP profiles of ΔmrpigG and M. ruber M7 were almost the same-with both having four yellow pigments, two orange pigments (OPs) and two red pigments (RPs)-their yields were decreased in ΔmrpigG to a certain extent. Particularly, the content of rubropunctatin (an OP) and its derivative rubropunctamine (an RP) in ΔmrpigG, both of which have a five-carbon side chain, accounted for 57.7%, and 22.3% of those in M. ruber M7. On the other hand, monascorubrin (an OP) and its derivative monascorubramine (an RP), both of which have a seven-carbon side chain, were increased by 1.15 and 2.55 times, respectively, in ΔmrpigG compared with M. ruber M7. These results suggest that the MrPigG protein may preferentially catalyze the biosynthesis of MPs with a five-carbon side chain.
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Affiliation(s)
- Li Li
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan 430070, China;
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Fusheng Chen
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Huazhong Agricultural University, Wuhan 430070, China;
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence:
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73
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Faucher F, Bennett JM, Bogyo M, Lovell S. Strategies for Tuning the Selectivity of Chemical Probes that Target Serine Hydrolases. Cell Chem Biol 2020; 27:937-952. [PMID: 32726586 PMCID: PMC7484133 DOI: 10.1016/j.chembiol.2020.07.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 02/08/2023]
Abstract
Serine hydrolases comprise a large family of enzymes that have diverse roles in key cellular processes, such as lipid metabolism, cell signaling, and regulation of post-translation modifications of proteins. They are also therapeutic targets for multiple human pathologies, including viral infection, diabetes, hypertension, and Alzheimer disease; however, few have well-defined substrates and biological functions. Activity-based probes (ABPs) have been used as effective tools to both profile activity and screen for selective inhibitors of serine hydrolases. One broad-spectrum ABP containing a fluorophosphonate electrophile has been used extensively to advance our understanding of diverse serine hydrolases. Due to the success of this single reagent, several robust chemistries have been developed to further diversify and tune the selectivity of ABPs used to target serine hydrolases. In this review, we highlight approaches to identify selective serine hydrolase ABPs and suggest new synthetic methodologies that could be applied to further advance probe development.
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Affiliation(s)
- Franco Faucher
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - John M Bennett
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Scott Lovell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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74
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Dolui AK, Vijayaraj P. A solvent-free delipidation method for functional validation of lipases. 3 Biotech 2020; 10:343. [PMID: 32714738 DOI: 10.1007/s13205-020-02338-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 07/12/2020] [Indexed: 10/23/2022] Open
Abstract
Extracting protein in its active form is critical for its functional characterization, and lipid removal is an essential step in the protein extraction process for further downstream applications. In the present study, we revisited the delipidation protocol and developed a rapid, solvent-free delipidation method using activated silica. The delipidated samples showed improved optical clarity and a significant reduction of endogenous lipids. The functional integrity of the lipases present in the delipidated sample was validated by in vitro enzyme assay using physiological substrate which includes neutral lipid as well as phospholipid. The accessibility of active site of the extracted enzymes was demonstrated by activity-based protein profiling (ABPP), a functional chemoproteomic approach. Detection of serine hydrolases using ABPP probe labeling was enhanced upon delipidation. Further, the total polyphenol content was significantly reduced, which helps to enhance the protein enrichment and small-molecule inhibitor screening by ABPP. Collectively, these results suggest that the present solvent-free delipidation approach is efficient and highly compatible with the functional characterization of the enzymes, particularly lipid hydrolases.
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75
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Field SD, Lee W, Dutra JK, Serneo FSF, Oyer J, Xu H, Johnson DS, am Ende CW, Seneviratne U. Fluorophosphonate‐Based Degrader Identifies Degradable Serine Hydrolases by Quantitative Proteomics. Chembiochem 2020; 21:2916-2920. [DOI: 10.1002/cbic.202000253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/25/2020] [Indexed: 01/26/2023]
Affiliation(s)
- S. Denise Field
- Pfizer Worldwide Research and Development 1 Portland St Cambridge MA 02139 USA
| | - Wankyu Lee
- Pfizer Worldwide Research and Development 1 Portland St Cambridge MA 02139 USA
| | - Jason K. Dutra
- Pfizer Worldwide Research and Development Eastern Point Road Groton CT 06340 USA
| | - Finley Scott F. Serneo
- Pfizer Worldwide Research and Development 10770 Science Center Drive San Diego CA 92121 USA
| | - Jon Oyer
- Pfizer Worldwide Research and Development 10770 Science Center Drive San Diego CA 92121 USA
| | - Hua Xu
- Pfizer Worldwide Research and Development 1 Portland St Cambridge MA 02139 USA
| | - Douglas S. Johnson
- Pfizer Worldwide Research and Development 1 Portland St Cambridge MA 02139 USA
| | | | - Uthpala Seneviratne
- Pfizer Worldwide Research and Development 1 Portland St Cambridge MA 02139 USA
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76
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Discovery of potent thrombin inhibitors from a protease-focused DNA-encoded chemical library. Proc Natl Acad Sci U S A 2020; 117:16782-16789. [PMID: 32641511 PMCID: PMC7382296 DOI: 10.1073/pnas.2005447117] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
To rapidly identify small-molecule lead compounds to target healthcare-associated proteases, we constructed a unique 9.8-million-membered protease-focused DNA-encoded chemical library. Affinity selection of this library with a healthcare-relevant protease (i.e., thrombin, a key protein necessary for blood coagulation) revealed potent inhibitors in the first screening attempt. Our results emphasize the utility of a structurally focused DNA-encoded chemical library approach to rapidly uncover hits for healthcare targets (e.g., proteases) where no drug exists (e.g., male contraception) and for emerging diseases (e.g., coronavirus disease 2019). DNA-encoded chemical libraries are collections of compounds individually coupled to unique DNA tags serving as amplifiable identification barcodes. By bridging split-and-pool combinatorial synthesis with the ligation of unique encoding DNA oligomers, million- to billion-member libraries can be synthesized for use in hundreds of healthcare target screens. Although structural diversity and desirable molecular property ranges generally guide DNA-encoded chemical library design, recent reports have highlighted the utility of focused DNA-encoded chemical libraries that are structurally biased for a class of protein targets. Herein, a protease-focused DNA-encoded chemical library was designed that utilizes chemotypes known to engage conserved catalytic protease residues. The three-cycle library features functional moieties such as guanidine, which interacts strongly with aspartate of the protease catalytic triad, as well as mild electrophiles such as sulfonamide, urea, and carbamate. We developed a DNA-compatible method for guanidinylation of amines and reduction of nitriles. Employing these optimized reactions, we constructed a 9.8-million-membered DNA-encoded chemical library. Affinity selection of the library with thrombin, a common protease, revealed a number of enriched features which ultimately led to the discovery of a 1 nM inhibitor of thrombin. Thus, structurally focused DNA-encoded chemical libraries have tremendous potential to find clinically useful high-affinity hits for the rapid discovery of drugs for targets (e.g., proteases) with essential functions in infectious diseases (e.g., severe acute respiratory syndrome coronavirus 2) and relevant healthcare conditions (e.g., male contraception).
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77
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Ranacyclin-NF, a Novel Bowman-Birk Type Protease Inhibitor from the Skin Secretion of the East Asian Frog, Pelophylax nigromaculatus. BIOLOGY 2020; 9:biology9070149. [PMID: 32630758 PMCID: PMC7407945 DOI: 10.3390/biology9070149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/19/2020] [Accepted: 06/29/2020] [Indexed: 01/10/2023]
Abstract
Serine protease inhibitors are found in plants, animals and microorganisms, where they play important roles in many physiological and pathological processes. Inhibitor scaffolds based on natural proteins and peptides have gradually become the focus of current research as they tend to bind to their targets with greater specificity than small molecules. In this report, a novel Bowman–Birk type inhibitor, named ranacyclin-NF (RNF), is described and was identified in the skin secretion of the East Asian frog, Pelophylax nigromaculatus. A synthetic replicate of the peptide was subjected to a series of functional assays. It displayed trypsin inhibitory activity with an inhibitory constant, Ki, of 447 nM and had negligible direct cytotoxicity. No observable direct antimicrobial activity was found but RNF improved the therapeutic potency of Gentamicin against Methicillin-resistant Staphylococcus aureus (MRSA). RNF shared significant sequence similarity to previously reported and related inhibitors from Odorrana grahami (ORB) and Rana esculenta (ranacyclin-T), both of which were found to be multi-functional. Two analogues of RNF, named ranacyclin-NF1 (RNF1) and ranacyclin-NF3L (RNF3L), were designed based on some features of ORB and ranacyclin-T to study structure–activity relationships. Structure–activity studies demonstrated that residues outside of the trypsin inhibitory loop (TIL) may be related to the efficacy of trypsin inhibitory activity.
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78
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Taabazuing CY, Griswold AR, Bachovchin DA. The NLRP1 and CARD8 inflammasomes. Immunol Rev 2020; 297:13-25. [PMID: 32558991 PMCID: PMC7483925 DOI: 10.1111/imr.12884] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/06/2020] [Accepted: 05/14/2020] [Indexed: 12/28/2022]
Abstract
Inflammasomes are multiprotein complexes that activate inflammatory cytokines and induce pyroptosis in response to intracellular danger-associated signals. NLRP1 and CARD8 are related germline-encoded pattern recognition receptors that form inflammasomes, but their activation mechanisms and biological purposes have not yet been fully established. Both NLRP1 and CARD8 undergo post-translational autoproteolysis to generate two non-covalently associated polypeptide chains. NLRP1 and CARD8 activators induce the proteasome-mediated destruction of the N-terminal fragment, liberating the C-terminal fragment to form an inflammasome. Here, we review the danger-associated stimuli that have been reported to activate NLRP1 and/or CARD8, including anthrax lethal toxin, Toxoplasma gondii, Shigella flexneri and the small molecule DPP8/9 inhibitor Val-boroPro, focusing on recent mechanistic insights and highlighting unresolved questions. In addition, we discuss the recently identified disease-associated mutations in NLRP1 and CARD8, the potential role that DPP9's protein structure plays in inflammasome regulation, and the emerging link between NLRP1 and metabolism. Finally, we summarize all of this latest research and consider the possible biological purposes of these enigmatic inflammasomes.
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Affiliation(s)
| | - Andrew R Griswold
- Weill Cornell, Rockefeller, Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA.,Pharmacology Program of the Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel A Bachovchin
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Pharmacology Program of the Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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79
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Navarrete M, Korkmaz B, Guarino C, Lesner A, Lao Y, Ho J, Nickerson P, Wilkins JA. Activity-based protein profiling guided identification of urine proteinase 3 activity in subclinical rejection after renal transplantation. Clin Proteomics 2020; 17:23. [PMID: 32549867 PMCID: PMC7296916 DOI: 10.1186/s12014-020-09284-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/19/2020] [Indexed: 03/04/2023] Open
Abstract
Background The pathophysiology of subclinical versus clinical rejection remains incompletely understood given their equivalent histological severity but discordant graft function. The goal was to evaluate serine hydrolase enzyme activities to explore if there were any underlying differences in activities during subclinical versus clinical rejection. Methods Serine hydrolase activity-based protein profiling (ABPP) was performed on the urines of a case control cohort of patients with biopsy confirmed subclinical or clinical transplant rejection. In-gel analysis and affinity purification with mass spectrometry were used to demonstrate and identify active serine hydrolase activity. An assay for proteinase 3 (PR3/PRTN3) was adapted for the quantitation of activity in urine. Results In-gel ABPP profiles suggested increased intensity and diversity of serine hydrolase activities in urine from patients undergoing subclinical versus clinical rejection. Serine hydrolases (n = 30) were identified by mass spectrometry in subclinical and clinical rejection patients with 4 non-overlapping candidates between the two groups (i.e. ABHD14B, LTF, PR3/PRTN3 and PRSS12). Western blot and the use of a specific inhibitor confirmed the presence of active PR3/PRTN3 in samples from patients undergoing subclinical rejection. Analysis of samples from normal donors or from several serial post-transplant urines indicated that although PR3/PRTN3 activity may be highly associated with low-grade subclinical inflammation, the enzyme activity was not restricted to this patient group. Conclusions There appear to be limited qualitative and quantitative differences in serine hydrolase activity in patients with subclinical versus clinical renal transplant rejection. The majority of enzymes identified were present in samples from both groups implying that in-gel quantitative differences may largely relate to the activity status of shared enzymes. However qualitative compositional differences were also observed indicating differential activities. The PR3/PRTN3 analyses indicate that the activity status of urine in transplant patients is dynamic possibly reflecting changes in the underlying processes in the transplant. These data suggest that differential serine hydrolase pathways may be active in subclinical versus clinical rejection which requires further exploration in larger patient cohorts. Although this study focused on PR3/PRTN3, this does not preclude the possibility that other enzymes may play critical roles in the rejection process.
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Affiliation(s)
- Mario Navarrete
- Manitoba Centre for Proteomics and Systems Biology, 799 John Buhler Research Centre, 715 McDermot Ave., Winnipeg, MB R3E3P4 Canada
| | - Brice Korkmaz
- INSERM, UMR 1100, "Centre d'Etude des Pathologies Respiratoires", Université de Tours, 37032 Tours, France
| | - Carla Guarino
- INSERM, UMR 1100, "Centre d'Etude des Pathologies Respiratoires", Université de Tours, 37032 Tours, France
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland
| | - Ying Lao
- Manitoba Centre for Proteomics and Systems Biology, 799 John Buhler Research Centre, 715 McDermot Ave., Winnipeg, MB R3E3P4 Canada
| | - Julie Ho
- Manitoba Centre for Proteomics and Systems Biology, 799 John Buhler Research Centre, 715 McDermot Ave., Winnipeg, MB R3E3P4 Canada.,Section Biomedical Proteomics, Dept. Internal Medicine, University of Manitoba, Winnipeg, MB Canada.,Section of Nephrology, Dept. Internal Medicine, University of Manitoba, Winnipeg, MB Canada.,Dept. Immunology, University of Manitoba, Winnipeg, MB Canada
| | - Peter Nickerson
- Manitoba Centre for Proteomics and Systems Biology, 799 John Buhler Research Centre, 715 McDermot Ave., Winnipeg, MB R3E3P4 Canada.,Section Biomedical Proteomics, Dept. Internal Medicine, University of Manitoba, Winnipeg, MB Canada.,Section of Nephrology, Dept. Internal Medicine, University of Manitoba, Winnipeg, MB Canada.,Dept. Immunology, University of Manitoba, Winnipeg, MB Canada
| | - John A Wilkins
- Manitoba Centre for Proteomics and Systems Biology, 799 John Buhler Research Centre, 715 McDermot Ave., Winnipeg, MB R3E3P4 Canada.,Section Biomedical Proteomics, Dept. Internal Medicine, University of Manitoba, Winnipeg, MB Canada
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80
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Vieyres G, Reichert I, Carpentier A, Vondran FWR, Pietschmann T. The ATGL lipase cooperates with ABHD5 to mobilize lipids for hepatitis C virus assembly. PLoS Pathog 2020; 16:e1008554. [PMID: 32542055 PMCID: PMC7316345 DOI: 10.1371/journal.ppat.1008554] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 06/25/2020] [Accepted: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
Lipid droplets are essential cellular organelles for storage of fatty acids and triglycerides. The hepatitis C virus (HCV) translocates several of its proteins onto their surface and uses them for production of infectious progeny. We recently reported that the lipid droplet-associated α/β hydrolase domain-containing protein 5 (ABHD5/CGI-58) participates in HCV assembly by mobilizing lipid droplet-associated lipids. However, ABHD5 itself has no lipase activity and it remained unclear how ABHD5 mediates lipolysis critical for HCV assembly. Here, we identify adipose triglyceride lipase (ATGL) as ABHD5 effector and new host factor involved in the hepatic lipid droplet degradation as well as in HCV and lipoprotein morphogenesis. Modulation of ATGL protein expression and lipase activity controlled lipid droplet lipolysis and virus production. ABHD4 is a paralog of ABHD5 unable to activate ATGL or support HCV assembly and lipid droplet lipolysis. Grafting ABHD5 residues critical for activation of ATGL onto ABHD4 restored the interaction between lipase and co-lipase and bestowed the pro-viral and lipolytic functions onto the engineered protein. Congruently, mutation of the predicted ABHD5 protein interface to ATGL ablated ABHD5 functions in lipid droplet lipolysis and HCV assembly. Interestingly, minor alleles of ABHD5 and ATGL associated with neutral lipid storage diseases in human, are also impaired in lipid droplet lipolysis and their pro-viral functions. Collectively, these results show that ABHD5 cooperates with ATGL to mobilize triglycerides for HCV infectious virus production. Moreover, viral manipulation of lipid droplet homeostasis via the ABHD5-ATGL axis, akin to natural genetic variation in these proteins, emerges as a possible mechanism by which chronic HCV infection causes liver steatosis.
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Affiliation(s)
- Gabrielle Vieyres
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research; a joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- * E-mail: (GV); (TP)
| | - Isabelle Reichert
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research; a joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Arnaud Carpentier
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research; a joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Florian W. R. Vondran
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany
- ReMediES, Department of General, Visceral and Transplant Surgery, Hannover Medical School, Hannover, Germany
| | - Thomas Pietschmann
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research; a joint venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany
- * E-mail: (GV); (TP)
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81
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Discovery of small-molecule enzyme activators by activity-based protein profiling. Nat Chem Biol 2020; 16:997-1005. [PMID: 32514184 PMCID: PMC7442688 DOI: 10.1038/s41589-020-0555-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 04/23/2020] [Indexed: 12/17/2022]
Abstract
Activity-based protein profiling (ABPP) has been used extensively to discover and optimize selective inhibitors of enzymes. Here, we show that ABPP can also be implemented to identify the converse – small-molecule enzyme activators. Using a kinetically controlled, fluorescence polarization-ABPP assay, we identify compounds that stimulate the activity of LYPLAL1 – a poorly characterized serine hydrolase with complex genetic links to human metabolic traits. We apply ABPP-guided medicinal chemistry to advance a lead into a selective LYPLAL1 activator suitable for use in vivo. Structural simulations coupled to mutational, biochemical, and biophysical analyses indicate that this compound increases LYPLAL1’s catalytic activity likely by enhancing the efficiency of the catalytic triad charge-relay system. Treatment with this LYPLAL1 activator confers beneficial effects in a mouse model of diet-induced obesity. These findings reveal a new mode of pharmacological regulation for this large enzyme family and suggest that ABPP may aid discovery of activators for additional enzyme classes.
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82
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Kathman SG, Boshart J, Jing H, Cravatt BF. Blockade of the Lysophosphatidylserine Lipase ABHD12 Potentiates Ferroptosis in Cancer Cells. ACS Chem Biol 2020; 15:871-877. [PMID: 32195565 DOI: 10.1021/acschembio.0c00086] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ferroptosis is a type of cell death caused by the pathogenic accumulation of lipid hydroperoxides. Pharmacological mechanisms to induce ferroptosis may provide a way to kill cancer cells that are resistant to other forms of cell death like apoptosis. Nonetheless, the proteins that regulate ferroptotic sensitivity in cancer cells remain incompletely understood. Here, we screened a panel of inhibitors of serine hydrolases-an enzyme class important for regulating lipid metabolism-for potentiation of ferroptosis in HT1080 fibrosarcoma cells. We found that DO264, a selective inhibitor of the lyso- and ox-phosphatidylserine (PS) lipase ABHD12, enhances ferroptotic death caused by RSL3, an inhibitor of the lipid peroxidase GPX4. RSL3-induced ferroptosis was also potentiated by genetic disruption of ABHD12. Metabolomic experiments revealed that, in addition to elevated lyso-PS, ABHD12-inactivated cells show higher quantities of arachidonate (C20:4)-containing PS and 2-arachidonoyl glycerol, pointing to potential oxidation-sensitive lipid mediators of ferroptosis regulated by ABHD12.
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Affiliation(s)
- Stefan G. Kathman
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Julia Boshart
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Hui Jing
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Benjamin F. Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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83
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Kim JT, Terrell SM, Li VL, Wei W, Fischer CR, Long JZ. Cooperative enzymatic control of N-acyl amino acids by PM20D1 and FAAH. eLife 2020; 9:55211. [PMID: 32271712 PMCID: PMC7145423 DOI: 10.7554/elife.55211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/21/2020] [Indexed: 12/28/2022] Open
Abstract
The N-acyl amino acids are a family of bioactive lipids with pleiotropic physiologic functions, including in energy homeostasis. Their endogenous levels are regulated by an extracellular mammalian N-acyl amino acid synthase/hydrolase called PM20D1 (peptidase M20 domain containing 1). Using an activity-guided biochemical approach, we report the molecular identification of fatty acid amide hydrolase (FAAH) as a second intracellular N-acyl amino acid synthase/hydrolase. In vitro, FAAH exhibits a more restricted substrate scope compared to PM20D1. In mice, genetic ablation or selective pharmacological inhibition of FAAH bidirectionally dysregulates intracellular, but not circulating, N-acyl amino acids. Dual blockade of both PM20D1 and FAAH reveals a dramatic and non-additive biochemical engagement of these two enzymatic pathways. These data establish FAAH as a second intracellular pathway for N-acyl amino acid metabolism and underscore enzymatic division of labor as an enabling strategy for the regulation of a structurally diverse bioactive lipid family.
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Affiliation(s)
- Joon T Kim
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
| | - Stephanie M Terrell
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
| | - Veronica L Li
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
| | - Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States.,Department of Biology, Stanford University, Stanford, United States
| | - Curt R Fischer
- Stanford ChEM-H, Stanford University, Stanford, United States
| | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
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84
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Bun JS, Slack MD, Schemenauer DE, Johnson RJ. Comparative analysis of the human serine hydrolase OVCA2 to the model serine hydrolase homolog FSH1 from S. cerevisiae. PLoS One 2020; 15:e0230166. [PMID: 32182256 PMCID: PMC7077851 DOI: 10.1371/journal.pone.0230166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/20/2020] [Indexed: 11/22/2022] Open
Abstract
Over 100 metabolic serine hydrolases are present in humans with confirmed functions in metabolism, immune response, and neurotransmission. Among potentially clinically-relevant but uncharacterized human serine hydrolases is OVCA2, a serine hydrolase that has been linked with a variety of cancer-related processes. Herein, we developed a heterologous expression system for OVCA2 and determined the comprehensive substrate specificity of OVCA2 against two ester substrate libraries. Based on this analysis, OVCA2 was confirmed as a serine hydrolase with a strong preference for long-chain alkyl ester substrates (>10-carbons) and high selectivity against a variety of short, branched, and substituted esters. Substitutional analysis was used to identify the catalytic residues of OVCA2 with a Ser117-His206-Asp179 classic catalytic triad. Comparison of the substrate specificity of OVCA2 to the model homologue FSH1 from Saccharomyces cerevisiae illustrated the tighter substrate selectivity of OVCA2, but their overlapping substrate preference for extended straight-chain alkyl esters. Conformation of the overlapping biochemical properties of OVCA2 and FSH1 was used to model structural information about OVCA2. Together our analysis provides detailed substrate specificity information about a previously, uncharacterized human serine hydrolase and begins to define the biological properties of OVCA2.
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Affiliation(s)
- Jessica S. Bun
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
| | - Michael D. Slack
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
| | - Daniel E. Schemenauer
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
| | - R. Jeremy Johnson
- Department of Chemistry and Biochemistry, Butler University, Indianapolis, Indiana, United States of America
- * E-mail:
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85
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High-Resolution Confocal Fluorescence Imaging of Serine Hydrolase Activity in Cryosections - Application to Glioma Brain Unveils Activity Hotspots Originating from Tumor-Associated Neutrophils. Biol Proced Online 2020; 22:6. [PMID: 32190011 PMCID: PMC7073015 DOI: 10.1186/s12575-020-00118-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/19/2020] [Indexed: 12/18/2022] Open
Abstract
Background Serine hydrolases (SHs) are a functionally diverse family of enzymes playing pivotal roles in health and disease and have emerged as important therapeutic targets in many clinical conditions. Activity-based protein profiling (ABPP) using fluorophosphonate (FP) probes has been a powerful chemoproteomic approach in studies unveiling roles of SHs in various biological systems. ABPP utilizes cell/tissue proteomes and features the FP-warhead, linked to a fluorescent reporter for in-gel fluorescence imaging or a biotin tag for streptavidin enrichment and LC-MS/MS-based target identification. Existing ABPP approaches characterize global SH activity based on mobility in gel or MS-based target identification and cannot reveal the identity of the cell-type responsible for an individual SH activity originating from complex proteomes. Results Here, by using an activity probe with broad reactivity towards the SH family, we advance the ABPP methodology to glioma brain cryosections, enabling for the first time high-resolution confocal fluorescence imaging of global SH activity in the tumor microenvironment. Tumor-associated cell types were identified by extensive immunohistochemistry on activity probe-labeled sections. Tissue-ABPP indicated heightened SH activity in glioma vs. normal brain and unveiled activity hotspots originating from tumor-associated neutrophils (TANs), rather than tumor-associated macrophages (TAMs). Thorough optimization and validation was provided by parallel gel-based ABPP combined with LC-MS/MS-based target verification. Conclusions Our study advances the ABPP methodology to tissue sections, enabling high-resolution confocal fluorescence imaging of global SH activity in anatomically preserved complex native cellular environment. To achieve global portrait of SH activity throughout the section, a probe with broad reactivity towards the SH family members was employed. As ABPP requires no a priori knowledge of the identity of the target, we envisage no imaginable reason why the presently described approach would not work for sections regardless of species and tissue source.
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86
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Shafi A, Timiri Sathyamurthy RD, Seetharaman J, Sambanthan M, Murugesan R, Sundaram S, Bhanumathy Ramarathinam R. Molecular docking, quantum chemical computational and vibrational studies on bicyclic heterocycle "6-nitro-2,3-dihydro-1,4-benzodioxine": Anti-cancer agent. Comput Biol Chem 2020; 86:107226. [PMID: 32142983 DOI: 10.1016/j.compbiolchem.2020.107226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/15/2020] [Accepted: 01/26/2020] [Indexed: 10/24/2022]
Abstract
The heterocyclic aromatic compounds are primarily used to make pharmaceutical and agrochemicals. In addition, these compounds can be chosen as antioxidants, corrosion inhibitors, electro and opto-electronic devices, polymer material, dye stuff, developers, etc. On the account of this, the heterocyclic aromatic 6-nitro-2,3-dihydro-1,4-benzodioxine (6N3DB) was chosen and the structure is optimized to predict the important properties of it. The structural parameters such as bond length and bond angle have been obtained by DFT/B3LYP/6-311++G(d,p) basis set to know the geometry and orientation of 6N3DB. The molecule has been characterized by FT-IR and FT-Raman spectroscopic techniques to predict the functional groups, vibrational modes and aromatic nature of 6N3DB. The chemical shifts of 1H and 13C have been obtained experimentally and compared with the theoretical data. The parameters such as the band gap between HOMO-LUMO orbitals, λmax, and electron transition probability in frontier orbitals have been estimated to know the NLO and corrosion inhibition activity. HOMO-LUMO orbital diagram has been obtained for different energy levels and their band gap energies have been compared with UV-vis band gap values. The chemical significance of the molecule has been explained using ELF, LOL, and RDG. The binding energy and intermolecular energy values indicate that the title compound possesses anti-cancer property through hydrolase inhibition activity.
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Affiliation(s)
- Aayisha Shafi
- Research and Development Centre, Bharathiar University, Coimbatore, 641046, Tamilnadu, India; Department of Physics, Meenakshi College for Women, Chennai, 600024, Tamilnadu, India
| | | | - Janani Seetharaman
- Department of Physics, Queen Mary's College, Chennai, 600005, Tamilnadu, India
| | - Muthu Sambanthan
- Department of Physics, Arignar Anna Govt.Arts College, Cheyyar, 604407, Tamilnadu, India.
| | - Raja Murugesan
- Department of Physics, Govt. Thirumagal Mill's College, Gudiyattam, 632602, Tamilnadu, India
| | - Sevvanthi Sundaram
- Department of Physics, Arignar Anna Govt.Arts College, Cheyyar, 604407, Tamilnadu, India
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87
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Oral repeated-dose toxicity studies of BIA 10–2474 in cynomolgus monkeys. Regul Toxicol Pharmacol 2020; 111:104547. [DOI: 10.1016/j.yrtph.2019.104547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022]
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88
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Yoo E, Schulze CJ, Stokes BH, Onguka O, Yeo T, Mok S, Gnädig NF, Zhou Y, Kurita K, Foe IT, Terrell SM, Boucher MJ, Cieplak P, Kumpornsin K, Lee MCS, Linington RG, Long JZ, Uhlemann AC, Weerapana E, Fidock DA, Bogyo M. The Antimalarial Natural Product Salinipostin A Identifies Essential α/β Serine Hydrolases Involved in Lipid Metabolism in P. falciparum Parasites. Cell Chem Biol 2020; 27:143-157.e5. [PMID: 31978322 PMCID: PMC8027986 DOI: 10.1016/j.chembiol.2020.01.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/11/2019] [Accepted: 01/03/2020] [Indexed: 12/15/2022]
Abstract
Salinipostin A (Sal A) is a potent antiplasmodial marine natural product with an undefined mechanism of action. Using a Sal A-derived activity-based probe, we identify its targets in the Plasmodium falciparum parasite. All of the identified proteins contain α/β serine hydrolase domains and several are essential for parasite growth. One of the essential targets displays a high degree of homology to human monoacylglycerol lipase (MAGL) and is able to process lipid esters including a MAGL acylglyceride substrate. This Sal A target is inhibited by the anti-obesity drug Orlistat, which disrupts lipid metabolism. Resistance selections yielded parasites that showed only minor reductions in sensitivity and that acquired mutations in a PRELI domain-containing protein linked to drug resistance in Toxoplasma gondii. This inability to evolve efficient resistance mechanisms combined with the non-essentiality of human homologs makes the serine hydrolases identified here promising antimalarial targets.
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Affiliation(s)
- Euna Yoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christopher J Schulze
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Barbara H Stokes
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ouma Onguka
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Nina F Gnädig
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yani Zhou
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Kenji Kurita
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Ian T Foe
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stephanie M Terrell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Michael J Boucher
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Piotr Cieplak
- Infectious & Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | - Marcus C S Lee
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | | | - David A Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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89
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Bonifácio MJ, Sousa F, Aires C, Loureiro AI, Fernandes-Lopes C, Pires NM, Palma PN, Moser P, Soares-da-Silva P. Preclinical pharmacological evaluation of the fatty acid amide hydrolase inhibitor BIA 10-2474. Br J Pharmacol 2020; 177:2123-2142. [PMID: 31901141 PMCID: PMC7161550 DOI: 10.1111/bph.14973] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 11/17/2019] [Accepted: 12/18/2019] [Indexed: 12/18/2022] Open
Abstract
Background and Purpose In 2016, one person died and four others had mild‐to‐severe neurological symptoms during a phase I trial of the fatty acid amide hydrolase (FAAH) inhibitor BIA 10‐2474. Experimental Approach Pharmacodynamic and pharmacokinetic studies were performed with BIA 10‐2474, PF‐04457845 and JNJ‐42165279 using mice, rats and human FAAH expressed in COS cells. Selectivity was evaluated by activity‐based protein profiling (APBB) in rats. BIA 10‐2474 effect in stroke‐prone spontaneously hypertensive rats (SHRSP) was investigated. Key Results BIA 10‐2474 was 10‐fold less potent than PF‐04457845 in inhibiting human FAAH in situ but inhibited mouse brain and liver FAAH with ED50 values of 13.5 and 6.2 μg·kg−1, respectively. Plasma and brain BIA 10‐2474 levels were consistent with in situ potency and neither BIA 10‐2474 nor its metabolites accumulated following repeat administration. FAAH and α/β‐hydrolase domain containing 6 were the primary targets of BIA 10‐2474 and, at higher exposure levels, ABHD11, PNPLA6, PLA2G15, PLA2G6 and androgen‐induced protein 1. At 100 mg·kg−1 for 28 days, the level of several lipid species containing arachidonic acid increased. Daily treatment of SHRSP with BIA 10‐2474 did not affect mortality rate or increased the incidence of haemorrhage or oedema in surviving animals. Conclusions and Implications BIA 10‐2474 potently inhibits FAAH in vivo, similarly to PF‐04457845 and interacts with a number of lipid processing enzymes, some previously identified in human cells as off‐targets particularly at high levels of exposure. These interactions occurred at doses used in toxicology studies, but the implication of these off‐targets in the clinical trial accident remains unclear.
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Affiliation(s)
- Maria-João Bonifácio
- Department of Research, Bial-Portela & Cª., S.A., Coronado (S Mamede & S Romão), Portugal
| | - Filipa Sousa
- Department of Research, Bial-Portela & Cª., S.A., Coronado (S Mamede & S Romão), Portugal
| | - Cátia Aires
- Department of Research, Bial-Portela & Cª., S.A., Coronado (S Mamede & S Romão), Portugal
| | - Ana I Loureiro
- Department of Research, Bial-Portela & Cª., S.A., Coronado (S Mamede & S Romão), Portugal
| | - Carlos Fernandes-Lopes
- Department of Research, Bial-Portela & Cª., S.A., Coronado (S Mamede & S Romão), Portugal
| | - Nuno M Pires
- Department of Research, Bial-Portela & Cª., S.A., Coronado (S Mamede & S Romão), Portugal
| | - Pedro Nuno Palma
- Department of Research, Bial-Portela & Cª., S.A., Coronado (S Mamede & S Romão), Portugal
| | - Paul Moser
- Department of Research, Bial-Portela & Cª., S.A., Coronado (S Mamede & S Romão), Portugal
| | - Patrício Soares-da-Silva
- Department of Research, Bial-Portela & Cª., S.A., Coronado (S Mamede & S Romão), Portugal.,Department of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, Porto, Portugal.,MedInUP-Center for Drug Discovery and Innovative Medicines, University of Porto, Porto, Portugal
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90
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Dubey R, Stivala CE, Nguyen HQ, Goo YH, Paul A, Carette JE, Trost BM, Rohatgi R. Lipid droplets can promote drug accumulation and activation. Nat Chem Biol 2020; 16:206-213. [PMID: 31932720 PMCID: PMC6989039 DOI: 10.1038/s41589-019-0447-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 12/02/2019] [Indexed: 11/28/2022]
Abstract
Genetic screens in cultured human cells represent a powerful unbiased strategy to identify cellular pathways that determine drug efficacy, providing critical information for clinical development. We used insertional mutagenesis-based screens in haploid cells to identify genes required for the sensitivity to lasonolide A (LasA), a macrolide derived from a marine sponge that kills certain types of cancer cells at low nanomolar concentrations. Our screens converged on a single gene, LDAH, encoding a member of the metabolite serine hydrolase family that is localized on the surface of lipid droplets. Mechanistic studies revealed that LasA accumulates in lipid droplets, where it is cleaved into a toxic metabolite by LDAH. We suggest that selective partitioning of hydrophobic drugs into the oil phase of lipid droplets can influence their activation and eventual toxicity to cells.
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Affiliation(s)
- Ramin Dubey
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Craig E Stivala
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Genentech, South San Francisco, CA, USA
| | | | - Young-Hwa Goo
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Antoni Paul
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Barry M Trost
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Rajat Rohatgi
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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91
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Keller LJ, Babin BM, Lakemeyer M, Bogyo M. Activity-based protein profiling in bacteria: Applications for identification of therapeutic targets and characterization of microbial communities. Curr Opin Chem Biol 2019; 54:45-53. [PMID: 31835131 DOI: 10.1016/j.cbpa.2019.10.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/09/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023]
Abstract
Activity-based protein profiling (ABPP) is a robust chemoproteomic technique that uses activity-based probes to globally measure endogenous enzymatic activity in complex proteomes. It has been utilized extensively to characterize human disease states and identify druggable targets in diverse disease conditions. ABPP has also recently found applications in microbiology. This includes using activity-based probes (ABPs) for functional studies of pathogenic bacteria as well as complex communities within a microbiome. This review will focus on recent advances in the use of ABPs to profile enzyme activity in disease models, screen for selective inhibitors of key enzymes, and develop imaging tools to better understand the host-bacterial interface.
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Affiliation(s)
- Laura J Keller
- Department of Chemical & Systems Biology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Brett M Babin
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Markus Lakemeyer
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
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92
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Functional annotation of serine hydrolases in the asexual erythrocytic stage of Plasmodium falciparum. Sci Rep 2019; 9:17532. [PMID: 31772212 PMCID: PMC6879560 DOI: 10.1038/s41598-019-54009-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 11/06/2019] [Indexed: 12/22/2022] Open
Abstract
Enzymes of the serine hydrolase superfamily are ubiquitous, highly versatile catalysts that mediate a wide variety of metabolic reactions in eukaryotic cells, while also being amenable to selective inhibition. We have employed a fluorophosphonate-based affinity capture probe and mass spectrometry to explore the expression profile and metabolic roles of the 56-member P. falciparum serine hydrolase superfamily in the asexual erythrocytic stage of P. falciparum. This approach provided a detailed census of active serine hydrolases in the asexual parasite, with identification of 21 active serine hydrolases from α/β hydrolase, patatin, and rhomboid protease families. To gain insight into their functional roles and substrates, the pan-lipase inhibitor isopropyl dodecylfluorophosphonate was employed for competitive activity-based protein profiling, leading to the identification of seven serine hydrolases with potential lipolytic activity. We demonstrated how a chemoproteomic approach can provide clues to the specificity of serine hydrolases by using a panel of neutral lipase inhibitors to identify an enzyme that reacts potently with a covalent monoacylglycerol lipase inhibitor. In combination with existing phenotypic data, our studies define a set of serine hydrolases that likely mediate critical metabolic reactions in asexual parasites and enable rational prioritization of future functional characterization and inhibitor development efforts.
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93
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Global targeting of functional tyrosines using sulfur-triazole exchange chemistry. Nat Chem Biol 2019; 16:150-159. [PMID: 31768034 PMCID: PMC6982592 DOI: 10.1038/s41589-019-0404-5] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 10/08/2019] [Indexed: 12/22/2022]
Abstract
Covalent probes serve as valuable tools for global investigation of protein function and ligand binding capacity. Despite efforts to expand coverage of residues available for chemical proteomics (e.g. cysteine and lysine), a large fraction of the proteome remains inaccessible with current activity-based probes. Here, we introduce sulfur-triazole exchange (SuTEx) chemistry as a tunable platform for developing covalent probes with broad applications for chemical proteomics. We show modifications to the triazole leaving group can furnish sulfonyl probes with ~5-fold enhanced chemoselectivity for tyrosines over other nucleophilic amino acids to investigate, for the first time, more than 10,000 tyrosine sites in lysates and live cells. We discover that tyrosines with enhanced nucleophilicity are enriched in enzymatic, protein-protein interaction, and nucleotide recognition domains. We apply SuTEx as a chemical phosphoproteomics strategy to monitor activation of phosphotyrosine sites. Collectively, we describe SuTEx as a biocompatible chemistry for chemical biology investigations of the human proteome.
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94
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Dheer D, Nicolas J, Shankar R. Cathepsin-sensitive nanoscale drug delivery systems for cancer therapy and other diseases. Adv Drug Deliv Rev 2019; 151-152:130-151. [PMID: 30690054 DOI: 10.1016/j.addr.2019.01.010] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 01/23/2019] [Indexed: 12/26/2022]
Abstract
Cathepsins are an important category of enzymes that have attracted great attention for the delivery of drugs to improve the therapeutic outcome of a broad range of nanoscale drug delivery systems. These proteases can be utilized for instance through actuation of polymer-drug conjugates (e.g., triggering the drug release) to bypass limitations of many drug candidates. A substantial amount of work has been witnessed in the design and the evaluation of Cathepsin-sensitive drug delivery systems, especially based on the tetra-peptide sequence (Gly-Phe-Leu-Gly, GFLG) which has been extensively used as a spacer that can be cleaved in the presence of Cathepsin B. This Review Article will give an in-depth overview of the design and the biological evaluation of Cathepsin-sensitive drug delivery systems and their application in different pathologies including cancer before discussing Cathepsin B-cleavable prodrugs under clinical trials.
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95
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Recent Advances in Selective and Irreversible Covalent Ligand Development and Validation. Cell Chem Biol 2019; 26:1486-1500. [PMID: 31631011 DOI: 10.1016/j.chembiol.2019.09.012] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/06/2019] [Accepted: 09/26/2019] [Indexed: 12/20/2022]
Abstract
Some of the most widely used drugs, such as aspirin and penicillin, are covalent drugs. Covalent binding can improve potency, selectivity, and duration of the effects, but the intrinsic reactivity represents a potential liability and may result in idiosyncratic toxicity. For decades, the cons were believed to outweigh the pros, and covalent targeting was deprioritized in drug discovery. Recently, several covalent inhibitors have been approved for cancer treatment, thus rebooting the field. In this review, we briefly reflect on the history of selective covalent targeting, and provide a comprehensive overview of emerging developments from a chemical biology stand-point. Our discussion will reflect on efforts to validate irreversible covalent ligands, expand the scope of targets, and discover new ligands and warheads. We conclude with a brief commentary of remaining limitations and emerging opportunities in selective covalent targeting.
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Rajendran A, Vaidya K, Mendoza J, Bridwell-Rabb J, Kamat SS. Functional Annotation of ABHD14B, an Orphan Serine Hydrolase Enzyme. Biochemistry 2019; 59:183-196. [PMID: 31478652 DOI: 10.1021/acs.biochem.9b00703] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The metabolic serine hydrolase family is, arguably, one of the largest functional enzyme classes in mammals, including humans, comprising 1-2% of the total proteome. This enzyme family uses a conserved nucleophilic serine residue in the active site to perform diverse hydrolytic reactions and consists of proteases, lipases, esterases, amidases, and transacylases, which are prototypical members of this family. In humans, this enzyme family consists of >250, of which approximately 40% members remain unannotated, in terms of both their endogenous substrates and the biological pathways that they regulate. The enzyme ABHD14B, an outlying member of this family, is also known as CCG1/TAFII250-interacting factor B, as it was found to be associated with transcription initiation factor TFIID. The crystal structure of human ABHD14B was determined more than a decade ago; however, its endogenous substrates remain elusive. In this paper, we annotate ABHD14B as a lysine deacetylase (KDAC), showing this enzyme's ability to transfer an acetyl group from a post-translationally acetylated lysine to coenzyme A (CoA), to yield acetyl-CoA, while regenerating the free amine of protein lysine residues. We validate these findings by in vitro biochemical assays using recombinantly purified human ABHD14B in conjunction with cellular studies in a mammalian cell line by knocking down ABHD14B and by identification of a putative substrate binding site. Finally, we report the development and characterization of a much-needed, exquisitely selective ABHD14B antibody, and using it, we map the cellular and tissue distribution of ABHD14B and prospective metabolic pathways that this enzyme might biologically regulate.
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Affiliation(s)
- Abinaya Rajendran
- Department of Biology , Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road Pashan , Pune 411008 , Maharashtra , India
| | - Kaveri Vaidya
- Department of Biology , Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road Pashan , Pune 411008 , Maharashtra , India
| | - Johnny Mendoza
- Department of Chemistry, College of Literature, Science and the Arts , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Jennifer Bridwell-Rabb
- Department of Chemistry, College of Literature, Science and the Arts , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Siddhesh S Kamat
- Department of Biology , Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road Pashan , Pune 411008 , Maharashtra , India
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Song PF, Zhu YD, Ma HY, Wang YN, Wang DD, Zou LW, Ge GB, Yang L. Discovery of natural pentacyclic triterpenoids as potent and selective inhibitors against human carboxylesterase 1. Fitoterapia 2019; 137:104199. [DOI: 10.1016/j.fitote.2019.104199] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/30/2019] [Accepted: 06/04/2019] [Indexed: 12/11/2022]
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98
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Wang C, Abegg D, Dwyer BG, Adibekian A. Discovery and Evaluation of New Activity‐Based Probes for Serine Hydrolases. Chembiochem 2019; 20:2212-2216. [DOI: 10.1002/cbic.201900126] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Chao Wang
- Department of ChemistryThe Scripps Research Institute 130 Scripps Way Jupiter FL 33418 USA
| | - Daniel Abegg
- Department of ChemistryThe Scripps Research Institute 130 Scripps Way Jupiter FL 33418 USA
| | - Brendan G. Dwyer
- Department of ChemistryThe Scripps Research Institute 130 Scripps Way Jupiter FL 33418 USA
| | - Alexander Adibekian
- Department of ChemistryThe Scripps Research Institute 130 Scripps Way Jupiter FL 33418 USA
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Abstract
Ongoing advances in chemical proteomic methods have facilitated detection and quantification of enzymatic activity, a highly informative parameter that is not captured in protein abundance measurements. However, some biological questions remain unanswered, since current gel- or LC-MS/MS-based detection methods suffer from limitations stemming from sample homogenization, signal-averaging, and an inherent bias toward abundant proteins. To address these shortcomings, we recently developed an activity-based proximity ligation (ADPL) platform to capture and quantify enzyme activity on the level of single cells, with high intra- and intercellular spatial resolution. In this chapter, we briefly discuss the rationale behind the ADPL platform, the design transition from the initial "sandwich-complex" workflow to the optimized, "direct conjugate" ADPL method, and conclude with detailed protocols for each. We also describe our novel use of the homo-bifunctional linker, disuccinimidyl suberate (DSS), to conjugate proteins and oligonucleotides, thus generating the necessary antibody-oligonucleotide recognition reagents for ADPL. Finally, we demonstrate the utility of ADPL to characterize enzyme activity from cytosol to nucleus, and specifically detect enzyme activity using "direct conjugate" ADPL.
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100
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Fernandes GFS, Denny WA, Dos Santos JL. Boron in drug design: Recent advances in the development of new therapeutic agents. Eur J Med Chem 2019; 179:791-804. [PMID: 31288128 DOI: 10.1016/j.ejmech.2019.06.092] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/25/2019] [Accepted: 06/28/2019] [Indexed: 01/21/2023]
Abstract
Advances in the field of boron chemistry have expanded the application of this element in Medicinal Chemistry. Boron-containing compounds represent a new class for medicinal chemists to use in their drug designs. Bortezomib (Velcade®), a dipeptide boronic acid approved by the FDA in 2003 for treatment of multiple myeloma, paved the way for the discovery of new boron-containing compounds. After its approval, two other boron-containing compounds have been approved, tavaborole (Kerydin®) for the treatment of onychomicosis and crisaborole (Eucrisa®) for the treatment of mild to moderate atopic dermatitis. A number of boron-containing compounds have been described and evaluated for a plethora of therapeutic applications. The present review is intended to highlight the recent advances related to boron-containing compounds and their therapeutic applications. Here, we focused only in those most biologically active compounds with proven in vitro and/or in vivo efficacy in the therapeutic area published in the last years.
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Affiliation(s)
- Guilherme Felipe Santos Fernandes
- School of Pharmaceutical Sciences, São Paulo State University, Araraquara, 14800-903, Brazil; Institute of Chemistry, São Paulo State University, Araraquara, 14800-060, Brazil; Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
| | - William Alexander Denny
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
| | - Jean Leandro Dos Santos
- School of Pharmaceutical Sciences, São Paulo State University, Araraquara, 14800-903, Brazil.
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