1
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Walther R, Park M, Ashman N, Welch M, Carroll JS, Spring DR. Tuneable thiol exchange linkers for traceless drug release applications in prodrugs and ADCs. Chem Commun (Camb) 2024; 60:7025-7028. [PMID: 38888299 PMCID: PMC11223184 DOI: 10.1039/d4cc01558d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
We describe a versatile and tuneable thiol responsive linker system using thiovinylketones, which relies on the conjugate addition-elimination mechanism of Michael acceptors for the traceless release of therapeutics. In a proof-of-principle study, we translate our findings to exhibit potent thiol-cleavable antibiotic prodrugs and antibody-drug conjugates.
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Affiliation(s)
- Raoul Walther
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
| | - Mahri Park
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
| | - Nicola Ashman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, CB2 1QW Cambridge, UK
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, Robinson Way, CB2 0RE Cambridge, UK
| | - David R Spring
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, UK
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2
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Jo J, Upadhyay T, Woods EC, Park KW, Pedowitz NJ, Jaworek-Korjakowska J, Wang S, Valdez TA, Fellner M, Bogyo M. Development of Oxadiazolone Activity-Based Probes Targeting FphE for Specific Detection of Staphylococcus aureus Infections. J Am Chem Soc 2024; 146:6880-6892. [PMID: 38411555 DOI: 10.1021/jacs.3c13974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Staphylococcus aureus (S. aureus) is a major human pathogen that is responsible for a wide range of systemic infections. Since its propensity to form biofilms in vivo poses formidable challenges for both detection and treatment, tools that can be used to specifically image S. aureus biofilms are highly valuable for clinical management. Here, we describe the development of oxadiazolone-based activity-based probes to target the S. aureus-specific serine hydrolase FphE. Because this enzyme lacks homologues in other bacteria, it is an ideal target for selective imaging of S. aureus infections. Using X-ray crystallography, direct cell labeling, and mouse models of infection, we demonstrate that oxadiazolone-based probes enable specific labeling of S. aureus bacteria through the direct covalent modification of the FphE active site serine. These results demonstrate the utility of the oxadizolone electrophile for activity-based probes and validate FphE as a target for the development of imaging contrast agents for the rapid detection of S. aureus infections.
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Affiliation(s)
- Jeyun Jo
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Tulsi Upadhyay
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Emily C Woods
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Ki Wan Park
- Department of Otolaryngology-Head & Neck Surgery Divisions, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Nichole J Pedowitz
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | | | - Sijie Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Tulio A Valdez
- Department of Otolaryngology-Head & Neck Surgery Divisions, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Matthias Fellner
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, United States
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, United States
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3
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Jo J, Upadhyay T, Woods EC, Park KW, Pedowitz NJ, Jaworek-Korjakowska J, Wang S, Valdez TA, Fellner M, Bogyo M. Development of Oxadiazolone Activity-Based Probes Targeting FphE for Specific Detection of S. aureus Infections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571116. [PMID: 38168396 PMCID: PMC10760020 DOI: 10.1101/2023.12.11.571116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Staphylococcus aureus is a major human pathogen responsible for a wide range of systemic infections. Since its propensity to form biofilms in vivo poses formidable challenges for both detection and treatment, tools that can be used to specifically image S. aureus biofilms are highly valuable for clinical management. Here we describe the development of oxadiazolonebased activity-based probes to target the S. aureus-specific serine hydrolase FphE. Because this enzyme lacks homologs in other bacteria, it is an ideal target for selective imaging of S. aureus infections. Using X-ray crystallography, direct cell labeling and mouse models of infection we demonstrate that oxadiazolone-based probes enable specific labeling of S. aureus bacteria through the direct covalent modification of the FphE active site serine. These results demonstrate the utility of the oxadizolone electrophile for activity-based probes (ABPs) and validate FphE as a target for development of imaging contrast agents for the rapid detection of S. aureus infections.
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Affiliation(s)
- Jeyun Jo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tulsi Upadhyay
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Emily C. Woods
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ki Wan Park
- Department of Otolaryngology–Head & Neck Surgery Divisions, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nichole J. Pedowitz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Sijie Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tulio A. Valdez
- Department of Otolaryngology–Head & Neck Surgery Divisions, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthias Fellner
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - 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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4
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Malarney KP, Chang PV. Chemoproteomic Approaches for Unraveling Prokaryotic Biology. Isr J Chem 2023; 63:e202200076. [PMID: 37842282 PMCID: PMC10575470 DOI: 10.1002/ijch.202200076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Indexed: 03/07/2023]
Abstract
Bacteria are ubiquitous lifeforms with important roles in the environment, biotechnology, and human health. Many of the functions that bacteria perform are mediated by proteins and enzymes, which catalyze metabolic transformations of small molecules and modifications of proteins. To better understand these biological processes, chemical proteomic approaches, including activity-based protein profiling, have been developed to interrogate protein function and enzymatic activity in physiologically relevant contexts. Here, chemoproteomic strategies and technological advances for studying bacterial physiology, pathogenesis, and metabolism are discussed. The development of chemoproteomic approaches for characterizing protein function and enzymatic activity within bacteria remains an active area of research, and continued innovations are expected to provide breakthroughs in understanding bacterial biology.
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Affiliation(s)
- Kien P Malarney
- Department of Microbiology, Cornell University, Ithaca, NY 14853 (USA)
| | - Pamela V Chang
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Center for Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853 (USA)
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5
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Racioppo B, Qiu N, Adibekian A. Serine Hydrolase Activity‐Based Probes for use in Chemical Proteomics. Isr J Chem 2023. [DOI: 10.1002/ijch.202300016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Brittney Racioppo
- Department of Chemistry University of Illinois Chicago Chicago Illinois 60607 United States
- Skaggs Doctoral Program in the Chemical and Biological Sciences, Scripps Research La Jolla California 92037 United States
| | - Nan Qiu
- Department of Chemistry University of Illinois Chicago Chicago Illinois 60607 United States
- Skaggs Doctoral Program in the Chemical and Biological Sciences, Scripps Research La Jolla California 92037 United States
| | - Alexander Adibekian
- Department of Chemistry University of Illinois Chicago Chicago Illinois 60607 United States
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6
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Shirley JD, Nauta KM, Carlson EE. Live-Cell Profiling of Penicillin-Binding Protein Inhibitors in Escherichia coli MG1655. ACS Infect Dis 2022; 8:1241-1252. [PMID: 35763562 PMCID: PMC10040144 DOI: 10.1021/acsinfecdis.2c00004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Penicillin-binding proteins (PBPs) make up an essential class of bacterial enzymes that carry out the final steps of peptidoglycan synthesis and regulate the recycling of this polymeric structure. PBPs are an excellent drug target and have been the most clinically relevant antibacterial target since the 1940s with the introduction of β-lactams. Despite this, a large gap in knowledge remains regarding the individual function and regulation of each PBP homologue in most bacteria. This can be attributed to a lack of chemical tools and methods that enable the study of individual PBPs in an activity-dependent manner and in their native environment. The development of such methods in Gram-negative bacteria has been particularly challenging due to the presence of an outer membrane and numerous resistance mechanisms. To address this, we have developed an optimized live-cell assay for screening inhibitors of the PBPs in Escherichia coli MG1655. We utilized EDTA to permeabilize Gram-negative cells, enabling increased penetration of our readout probe, Bocillin-FL, and subsequent analysis of PBP-inhibition profiles. To identify scaffolds for future development of PBP-selective activity-based probes, we screened ten β-lactams, one diazabicyclooctane, and one monobactam for their PBP-selectivity profiles in E. coli MG1655. These results demonstrate the utility of our assay for the screening of inhibitors in live, non-hypersusceptible Gram-negative organisms.
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Affiliation(s)
- Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States
| | - Kelsie M Nauta
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Erin E Carlson
- Department of Medicinal Chemistry, University of Minnesota, 208 Harvard Street SE, Minneapolis, Minnesota 55454, United States.,Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55454, United States.,Department of Pharmacology, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55454, United States
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7
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Fellner M. Newly discovered Staphylococcus aureus serine hydrolase probe and drug targets. ADMET AND DMPK 2022; 10:107-114. [PMID: 35350120 PMCID: PMC8957240 DOI: 10.5599/admet.1137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/25/2021] [Indexed: 11/18/2022] Open
Abstract
There is an urgent need for new diagnosis and treatment options for the bacterial pathogen Staphylococcus aureus. This review will summarize data on ten recently discovered biofilm-associated serine hydrolases called fluorophosphonate-binding hydrolases (FphA-J). Based on the summarized findings, many of these proteins represent intriguing new targets for probe and drug development.
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Affiliation(s)
- Matthias Fellner
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand. ; Tel.: +64 34797897
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Saidjalolov S, Braud E, Edoo Z, Iannazzo L, Rusconi F, Riomet M, Sallustrau A, Taran F, Arthur M, Fonvielle M, Etheve-Quelquejeu M. Click and Release Chemistry for Activity-Based Purification of β-Lactam Targets. Chemistry 2021; 27:7687-7695. [PMID: 33792096 DOI: 10.1002/chem.202100653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Indexed: 12/30/2022]
Abstract
β-Lactams, the cornerstone of antibiotherapy, inhibit multiple and partially redundant targets referred to as transpeptidases or penicillin-binding proteins. These enzymes catalyze the essential cross-linking step of the polymerization of cell wall peptidoglycan. The understanding of the mechanisms of action of β-lactams and of resistance to these drugs requires the development of reliable methods to characterize their targets. Here, we describe an activity-based purification method of β-lactam targets based on click and release chemistry. We synthesized alkyne-carbapenems with suitable properties with respect to the kinetics of acylation of a model target, the Ldtfm L,D-transpeptidase, the stability of the resulting acylenzyme, and the reactivity of the alkyne for the cycloaddition of an azido probe containing a biotin moiety for affinity purification and a bioorthogonal cleavable linker. The probe provided access to the fluorescent target in a single click and release step.
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Affiliation(s)
- Saidbakhrom Saidjalolov
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université de Paris, 45, rue des saints-pères, Paris, 75006, France
| | - Emmanuelle Braud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université de Paris, 45, rue des saints-pères, Paris, 75006, France
| | - Zainab Edoo
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06, Sorbonne Paris Cité, Université de Paris, Centre de recherche des Cordeliers, Paris, 75006, France
| | - Laura Iannazzo
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université de Paris, 45, rue des saints-pères, Paris, 75006, France
| | - Filippo Rusconi
- PAPPSO, Université Paris-Saclay, INRAE, CNRS, AgroParisTech GQE - Le Moulon, Gif-sur-Yvette, 91190, France
| | - Margaux Riomet
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Gif-sur-Yvette, 91191, France
| | - Antoine Sallustrau
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Gif-sur-Yvette, 91191, France
| | - Frédéric Taran
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Gif-sur-Yvette, 91191, France
| | - Michel Arthur
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06, Sorbonne Paris Cité, Université de Paris, Centre de recherche des Cordeliers, Paris, 75006, France
| | - Matthieu Fonvielle
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06, Sorbonne Paris Cité, Université de Paris, Centre de recherche des Cordeliers, Paris, 75006, France
| | - Mélanie Etheve-Quelquejeu
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université de Paris, 45, rue des saints-pères, Paris, 75006, France
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9
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Lu Y, Wang Y, Wang J, Zhao Y, Zhong Q, Li G, Fu Z, Lu S. Phage Endolysin LysP108 Showed Promising Antibacterial Potential Against Methicillin-resistant Staphylococcus aureus. Front Cell Infect Microbiol 2021; 11:668430. [PMID: 33937105 PMCID: PMC8082462 DOI: 10.3389/fcimb.2021.668430] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/26/2021] [Indexed: 12/16/2022] Open
Abstract
As a potential antibacterial agent, endolysin can directly lyse Gram-positive bacteria from the outside and does not lead to drug resistance. Considering that XN108 is the first reported methicillin-resistant Staphylococcus aureus (MRSA) strain in mainland China with a vancomycin MIC that exceeds 8 µg mL-1, we conducted a systematic study on its phage-encoded endolysin LysP108. Standard plate counting method revealed that LysP108 could lyse S. aureus and Pseudomonas aeruginosa with damaged outer membrane, resulting in a significant reduction in the number of live bacteria. Scanning electron microscopy results showed that S. aureus cells could be lysed directly from the outside by LysP108. Live/dead bacteria staining results indicated that LysP108 possessed strong bactericidal ability, with an anti-bacterial rate of approximately 90%. Crystal violet staining results implied that LysP108 could also inhibit and destroy bacterial biofilms. In vivo animal experiments suggested that the area of subcutaneous abscess of mice infected with MRSA was significantly reduced after the combined injection of LysP108 and vancomycin in comparison with monotherapy. The synergistic antibacterial effects of LysP108 and vancomycin were confirmed. Therefore, the present data strongly support the idea that endolysin LysP108 exhibits promising antibacterial potential to be used as a candidate for the treatment of infections caused by MRSA.
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Affiliation(s)
- Yifei Lu
- Institute of Burn Research, Southwest Hospital, State Key Lab of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, China
| | - Yingran Wang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, Chongqing, China
| | - Jing Wang
- Department of Microbiology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Yan Zhao
- Department of Microbiology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Qiu Zhong
- Department of Clinical Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Gang Li
- Department of Microbiology, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Zhifeng Fu
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Shuguang Lu
- Department of Microbiology, College of Basic Medical Science, Army Medical University, Chongqing, China
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10
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Levine SR, Beatty KE. Investigating β-Lactam Drug Targets in Mycobacterium tuberculosis Using Chemical Probes. ACS Infect Dis 2021; 7:461-470. [PMID: 33470787 DOI: 10.1021/acsinfecdis.0c00809] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB), caused by the bacterial pathogen Mycobacterium tuberculosis (Mtb), infects 10 million people a year. An estimated 25% of humans harbor latent TB infections, an asymptomatic form of the disease. In both active and latent infections, Mtb relies on cell wall peptidoglycan for viability. In the current work, we synthesized fluorescent analogues of β-lactam antibiotics to study two classes of enzymes that maintain Mtb's peptidoglycan: penicillin-binding proteins (PBPs) and l,d-transpeptidases (LDTs). This set of activity-based probes included analogues of three classes of β-lactams: a monobactam (aztreonam-Cy5), a cephalosporin (cephalexin-Cy5), and a carbapenem (meropenem-Cy5). We used these probes to profile enzyme activity in protein gel-resolved lysates of Mtb. All three out-performed the commercial reagent Bocillin-FL, a penam. Meropenem-Cy5 was used to identify β-lactam targets by mass spectrometry, including PBPs, LDTs, and the β-lactamase BlaC. New probes were also used to compare PBP and LDT activity in two metabolic states: dormancy and active replication. We provide the first direct evidence that Mtb dynamically regulates the enzymes responsible for maintaining peptidoglycan in dormancy. Lastly, we profiled drug susceptibility in lysates and found that meropenem inhibits PBPs, LDTs, and BlaC.
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Affiliation(s)
- Samantha R. Levine
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92617, United States
| | - Kimberly E. Beatty
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92617, United States
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11
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Fluorescent probes for investigating peptidoglycan biosynthesis in mycobacteria. Curr Opin Chem Biol 2020; 57:50-57. [DOI: 10.1016/j.cbpa.2020.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/31/2020] [Accepted: 04/08/2020] [Indexed: 02/02/2023]
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12
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Wang Y, He Y, Bhattacharyya S, Lu S, Fu Z. Recombinant Bacteriophage Cell-Binding Domain Proteins for Broad-Spectrum Recognition of Methicillin-Resistant Staphylococcus aureus Strains. Anal Chem 2020; 92:3340-3345. [DOI: 10.1021/acs.analchem.9b05295] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yingran Wang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Yong He
- Department of Pharmacy, Affiliated Hospital of Zunyi Medical College, Zunyi 563000, China
| | - Sanjib Bhattacharyya
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Shuguang Lu
- Department of Microbiology, College of Basic Medical Science, Army Medical University, Chongqing 400038, China
| | - Zhifeng Fu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
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13
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Zhang ZJ, Wang YC, Yang X, Hang HC. Chemical Reporters for Exploring Microbiology and Microbiota Mechanisms. Chembiochem 2019; 21:19-32. [PMID: 31730246 DOI: 10.1002/cbic.201900535] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/14/2019] [Indexed: 12/11/2022]
Abstract
The advances made in bioorthogonal chemistry and the development of chemical reporters have afforded new strategies to explore the targets and functions of specific metabolites in biology. These metabolite chemical reporters have been applied to diverse classes of bacteria including Gram-negative, Gram-positive, mycobacteria, and more complex microbiota communities. Herein we summarize the development and application of metabolite chemical reporters to study fundamental pathways in bacteria as well as microbiota mechanisms in health and disease.
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Affiliation(s)
- Zhenrun J Zhang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Yen-Chih Wang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Xinglin Yang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
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14
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Kuskovsky R, Lloyd D, Arora K, Plotkin BJ, Green JM, Boshoff HI, Barry C, Deschamps J, Konaklieva MI. C4-Phenylthio β-lactams: Effect of the chirality of the β-lactam ring on antimicrobial activity. Bioorg Med Chem 2019; 27:115050. [PMID: 31474471 DOI: 10.1016/j.bmc.2019.115050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/16/2019] [Accepted: 08/15/2019] [Indexed: 01/02/2023]
Abstract
C4-phenylthio β-lactams are a new family of antibacterial agents that have activity against two phylogenetically distant bacteria - Mycobacterium tuberculosis (Mtb) and Moraxella catarrhalis (M. cat). These compounds are effective against β-lactamase producing Mtb and M. cat unlike the clinically relevant β-lactam antibiotics. The structure-activity relationship for the C4 phenylthio β-lactams has not yet been completely defined. Earlier efforts in our laboratories established that the C4-phenylthio substituent is essential for antimicrobial activity, while the N1 carbamyl substituent plays a more subtle role. In this present study, we investigated the role that the stereochemistry at C4 plays in these compounds' antibacterial activity. This was achieved by synthesizing and testing the antimicrobial activity of diastereomers with a chiral carbamyl group at N1. Our findings indicate that a strict stereochemistry for the C4-phenylthio β-lactams is not required to obtain optimal anti-Mtb and anti-M. cat activity. Furthermore, the structure-bioactivity profiles more closely relate to the electronic requirement of the phenylthiogroup. In addition, the MICs of Mtb are sensitive to growth medium composition. Select compounds showed activity against non-replicating and multi-drug resistant Mtb.
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Affiliation(s)
| | - Dina Lloyd
- Department of Chemistry, American University, Washington, DC 20016, USA
| | - Kriti Arora
- Tuberculosis Research Section, LCIM, NIAID, NIH, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Balbina J Plotkin
- Department of Microbiology and Immunology, Midwestern University, Chicago, IL 60515, USA
| | - Jacalyn M Green
- Department of Biochemistry, Midwestern University, Chicago, IL 60515, USA
| | - Helena I Boshoff
- Tuberculosis Research Section, LCIM, NIAID, NIH, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Clifton Barry
- Tuberculosis Research Section, LCIM, NIAID, NIH, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Jeffrey Deschamps
- Naval Research Laboratory, Code 6930 4555 Overlook Ave., Washington, DC 20375, USA
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15
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Peng H, Hulleman JD. Prospective Application of Activity-Based Proteomic Profiling in Vision Research-Potential Unique Insights into Ocular Protease Biology and Pathology. Int J Mol Sci 2019; 20:ijms20163855. [PMID: 31398819 PMCID: PMC6720450 DOI: 10.3390/ijms20163855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 07/30/2019] [Indexed: 12/12/2022] Open
Abstract
Activity-based proteomic profiling (ABPP) is a powerful tool to specifically target and measure the activity of a family of enzymes with the same function and reactivity, which provides a significant advantage over conventional proteomic strategies that simply provide abundance information. A number of inherited and age-related eye diseases are caused by polymorphisms/mutations or abnormal expression of proteases including serine proteases, cysteine proteases, and matrix metalloproteinases, amongst others. However, neither conventional genomic, transcriptomic, nor traditional proteomic profiling directly interrogate protease activities. Thus, leveraging ABPP to probe the activity of these enzyme classes as they relate to normal function and pathophysiology of the eye represents a unique potential opportunity for disease interrogation and possibly intervention.
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Affiliation(s)
- Hui Peng
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9057, USA
| | - John D Hulleman
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9057, USA.
- Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.
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16
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Kulkarni A, Soni I, Kelkar DS, Dharmaraja AT, Sankar RK, Beniwal G, Rajendran A, Tamhankar S, Chopra S, Kamat SS, Chakrapani H. Chemoproteomics of an Indole-Based Quinone Epoxide Identifies Druggable Vulnerabilities in Vancomycin-Resistant Staphylococcus aureus. J Med Chem 2019; 62:6785-6795. [PMID: 31241934 PMCID: PMC6660313 DOI: 10.1021/acs.jmedchem.9b00774] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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The alarming global
rise in fatalities from multidrug-resistant Staphylococcus
aureus (S. aureus)
infections has underscored a need to develop new therapies to address
this epidemic. Chemoproteomics is valuable in identifying targets
for new drugs in different human diseases including bacterial infections.
Targeting functional cysteines is particularly attractive, as they
serve critical catalytic functions that enable bacterial survival.
Here, we report an indole-based quinone epoxide scaffold with a unique
boat-like conformation that allows steric control in modulating thiol
reactivity. We extensively characterize a lead compound (4a), which potently inhibits clinically derived vancomycin-resistant S. aureus. Leveraging diverse chemoproteomic platforms,
we identify and biochemically validate important transcriptional factors
as potent targets of 4a. Interestingly, each identified
transcriptional factor has a conserved catalytic cysteine residue
that confers antibiotic tolerance to these bacteria. Thus, the chemical
tools and biological targets that we describe here prospect new therapeutic
paradigms in combatting S. aureus infections.
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Affiliation(s)
| | - Isha Soni
- Division of Microbiology , CSIR-Central Drug Research Institute , Sector 10, Janakipuram Extension, Sitapur Road , Lucknow 226021 , Uttar Pradesh , India
| | | | | | | | | | | | | | - Sidharth Chopra
- Division of Microbiology , CSIR-Central Drug Research Institute , Sector 10, Janakipuram Extension, Sitapur Road , Lucknow 226021 , Uttar Pradesh , India
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17
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Natural product derivatization with β-lactones, β-lactams and epoxides toward ‘infinite’ binders. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.04.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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18
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Konaklieva MI. Addressing Antimicrobial Resistance through New Medicinal and Synthetic Chemistry Strategies. SLAS DISCOVERY 2018; 24:419-439. [PMID: 30523713 DOI: 10.1177/2472555218812657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past century, a multitude of derivatives of structural scaffolds with established antimicrobial potential have been prepared and tested, and a variety of new scaffolds have emerged. The effectiveness of antibiotics, however, is in sharp decline because of the emergence of drug-resistant microorganisms. The prevalence of drug resistance, both in clinical and community settings, is a consequence of bacterial ingenuity in altering pathways and/or cell morphology, making it a persistent threat to human health. The fundamental ability of pathogens to survive in a multitude of habitats can be triggered by recognition of chemical signals that warn organisms of exposure to a potentially harmful environment. Host immune defenses, including reactive oxygen intermediates and antibacterial substances, are among the multitude of chemical signals that can subsequently trigger expression of phenotypes better adapted for survival in that hostile environment. Thus, resistance development appears to be unavoidable, which leads to the conclusion that developing an alternative perspective for treatment options is vital. This review will discuss emerging medicinal chemistry approaches for addressing the global multidrug resistance in the 21st century.
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19
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Lentz CS, Sheldon JR, Crawford LA, Cooper R, Garland M, Amieva MR, Weerapana E, Skaar EP, Bogyo M. Identification of a S. aureus virulence factor by activity-based protein profiling (ABPP). Nat Chem Biol 2018; 14:609-617. [PMID: 29769740 PMCID: PMC6202179 DOI: 10.1038/s41589-018-0060-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/27/2018] [Indexed: 12/22/2022]
Abstract
Serine hydrolases play diverse roles in regulating host-pathogen interactions in a number of organisms, yet few have been characterized in the human pathogen Staphylococcus aureus. Here we describe a chemical proteomic screen that identified ten previously uncharacterized S. aureus serine hydrolases that mostly lack human homologs. We termed these enzymes fluorophosphonate-binding hydrolases (FphA-J). One hydrolase, FphB, can process short fatty acid esters, exhibits increased activity in response to host cell factors, is located predominantly on the bacterial cell surface in a subset of cells, and is concentrated in the division septum. Genetic disruption of fphB confirmed that the enzyme is dispensable for bacterial growth in culture but crucial for establishing infection in distinct sites in vivo. A selective small molecule inhibitor of FphB effectively reduced infectivity in vivo, suggesting that it may be a viable therapeutic target for the treatment or management of Staphylococcus infections.
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Affiliation(s)
- Christian S Lentz
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jessica R Sheldon
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lisa A Crawford
- Department of Chemistry, Boston College, Chestnut Hill, MA, USA
| | - Rachel Cooper
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Megan Garland
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Manuel R Amieva
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Eric P Skaar
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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20
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Target Identification of Bioactive Covalently Acting Natural Products. Curr Top Microbiol Immunol 2018; 420:351-374. [PMID: 30105423 DOI: 10.1007/82_2018_121] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There are countless natural products that have been isolated from microbes, plants, and other living organisms that have been shown to possess therapeutic activities such as antimicrobial, anticancer, or anti-inflammatory effects. However, developing these bioactive natural products into drugs has remained challenging in part because of their difficulty in isolation, synthesis, mechanistic understanding, and off-target effects. Among the large pool of bioactive natural products lies classes of compounds that contain potential reactive electrophilic centers that can covalently react with nucleophilic amino acid hotspots on proteins and other biological molecules to modulate their biological action. Covalently acting natural products are more amenable to rapid target identification and mapping of specific druggable hotspots within proteins using activity-based protein profiling (ABPP)-based chemoproteomic strategies. In addition, the granular biochemical insights afforded by knowing specific sites of protein modifications of covalently acting natural products enable the pharmacological interrogation of these sites with more synthetically tractable covalently acting small molecules whose structures are more easily tuned. Both discovering binding pockets and targets hit by natural products and exploiting druggable modalities targeted by natural products with simpler molecules may overcome some of the challenges faced with translating natural products into drugs.
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21
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Wright MH, Sieber SA. Chemical proteomics approaches for identifying the cellular targets of natural products. Nat Prod Rep 2017; 33:681-708. [PMID: 27098809 PMCID: PMC5063044 DOI: 10.1039/c6np00001k] [Citation(s) in RCA: 258] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This review focuses on chemical probes to identify the protein binding partners of natural products in living systems.
Covering: 2010 up to 2016 Deconvoluting the mode of action of natural products and drugs remains one of the biggest challenges in chemistry and biology today. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to understand protein function. In the context of natural products, chemical proteomics can be used to identify the protein binding partners or targets of small molecules in live cells. Here, we highlight recent examples of chemical probes based on natural products and their application for target identification. The review focuses on probes that can be covalently linked to their target proteins (either via intrinsic chemical reactivity or via the introduction of photocrosslinkers), and can be applied “in situ” – in living systems rather than cell lysates. We also focus here on strategies that employ a click reaction, the copper-catalysed azide–alkyne cycloaddition reaction (CuAAC), to allow minimal functionalisation of natural product scaffolds with an alkyne or azide tag. We also discuss ‘competitive mode’ approaches that screen for natural products that compete with a well-characterised chemical probe for binding to a particular set of protein targets. Fuelled by advances in mass spectrometry instrumentation and bioinformatics, many modern strategies are now embracing quantitative proteomics to help define the true interacting partners of probes, and we highlight the opportunities this rapidly evolving technology provides in chemical proteomics. Finally, some of the limitations and challenges of chemical proteomics approaches are discussed.
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Affiliation(s)
- M H Wright
- Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany.
| | - S A Sieber
- Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany.
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22
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Abstract
Understanding the molecular mechanisms of bacterial pathogenesis and virulence is of great importance from both an academic and clinical perspective, especially in view of an alarming increase in bacterial resistance to existing antibiotics and antibacterial agents. Use of small molecules to dissect the basis of these dynamic processes is a very attractive approach due to their ability for rapid spatiotemporal control of specific biochemical functions. Activity-based protein profiling (ABPP), employing small molecule probes to interrogate enzyme activities in complex proteomes, has emerged as a powerful tool to study bacterial pathogenesis. In this chapter, we present a set of ABPP methods to identify and analyze enzymes essential for growth, metabolism and virulence of different pathogens including S. aureus and L. monocytogenes using natural product-inspired activity-based probes.
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23
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Strmiskova M, Desrochers GF, Shaw TA, Powdrill MH, Lafreniere MA, Pezacki JP. Chemical Methods for Probing Virus-Host Proteomic Interactions. ACS Infect Dis 2016; 2:773-786. [PMID: 27933785 DOI: 10.1021/acsinfecdis.6b00084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Interactions between host and pathogen proteins constitute an important aspect of both infectivity and the host immune response. Different viruses have evolved complex mechanisms to hijack host-cell machinery and metabolic pathways to redirect resources and energy flow toward viral propagation. These interactions are often critical to the virus, and thus understanding these interactions at a molecular level gives rise to opportunities to develop novel antiviral strategies for therapeutic intervention. This review summarizes current advances in chemoproteomic methods for studying these molecular altercations between different viruses and their hosts.
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Affiliation(s)
- Miroslava Strmiskova
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Geneviève F. Desrochers
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Tyler A. Shaw
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Megan H. Powdrill
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - Matthew A. Lafreniere
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, Centre
for Chemical and Synthetic Biology, University of Ottawa, 10 Marie-Curie Private, Ottawa, Ontario, Canada K1N 6N5
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24
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Zhu X, Zhang W. Tagging polyketides/non-ribosomal peptides with a clickable functionality and applications. Front Chem 2015; 3:11. [PMID: 25815285 PMCID: PMC4356899 DOI: 10.3389/fchem.2015.00011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 02/05/2015] [Indexed: 01/08/2023] Open
Abstract
Bioorthogonal chemistry has recently emerged to be one of the most powerful tools in drug discovery and chemical biology. The exploration of it has successfully advanced the field of natural product research. In this Perspective, we survey current strategies for the installation of chemical handles into the molecular scaffolds of several major classes of natural products, including polyketides (PKs), non-ribosomal peptides (NRPs), and their hybrids. By tagging these natural products with chemical handles and coupling them with subsequent bioorthogonal reactions, researchers have visualized and studied the mode of action of natural products, as well as synthesized derivatives with better pharmaceutical properties. We conclude this Perspective by considering two questions: is there a general way to synthesize tagged PKs/NRPs? Does natural product labeling have a broader impact in the field of natural product research beyond current known applications?
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Affiliation(s)
- Xuejun Zhu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley Berkeley, CA, USA ; Energy Biosciences Institute, University of California, Berkeley Berkeley, CA, USA
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley Berkeley, CA, USA ; Energy Biosciences Institute, University of California, Berkeley Berkeley, CA, USA ; Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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25
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Yang P, Liu K. Activity-based protein profiling: recent advances in probe development and applications. Chembiochem 2015; 16:712-24. [PMID: 25652106 DOI: 10.1002/cbic.201402582] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Indexed: 11/08/2022]
Abstract
The completion of the human genome sequencing project has provided a wealth of new information regarding the genomic blueprint of the cell. Although, to date, there are roughly 20,000 genes in the human genome, the functions of only a handful of proteins are clear. The major challenge lies in translating genomic information into an understanding of their cellular functions. The recently developed activity-based protein profiling (ABPP) is an unconventional approach that is complementary for gene expression analysis and an ideal utensil in decoding this overflow of genomic information. This approach makes use of synthetic small molecules that covalently modify a set of related proteins and subsequently facilitates identification of the target protein, enabling rapid biochemical analysis and inhibitor discovery. This tutorial review introduces recent advances in the field of ABPP and its applications.
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Affiliation(s)
- Pengyu Yang
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037 (USA)
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26
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Beck TN, Lloyd D, Kuskovsky R, Minah J, Arora K, Plotkin BJ, Green JM, Boshoff HI, Barry C, Deschamps J, Konaklieva MI. Non-transpeptidase binding arylthioether β-lactams active against Mycobacterium tuberculosis and Moraxella catarrhalis. Bioorg Med Chem 2015; 23:632-47. [PMID: 25549898 PMCID: PMC6415315 DOI: 10.1016/j.bmc.2014.11.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/08/2014] [Accepted: 11/18/2014] [Indexed: 10/24/2022]
Abstract
The prevalence of drug resistance in both clinical and community settings as a consequence of alterations of biosynthetic pathways, enzymes or cell wall architecture is a persistent threat to human health. We have designed, synthesized, and tested a novel class of non-transpeptidase, β-lactamase resistant monocyclic β-lactams that carry an arylthio group at C4. These thioethers exhibit inhibitory and cidal activity against serine β-lactamase producing Mycobacterium tuberculosis wild type strain (Mtb) and multiple (n=8) β-lactamase producing Moraxella catarrhalis clinical isolates.
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Affiliation(s)
- Tim N Beck
- Department of Chemistry, American University, Washington, DC 20016, USA
| | - Dina Lloyd
- Department of Chemistry, American University, Washington, DC 20016, USA
| | | | - Jeanette Minah
- Department of Chemistry, American University, Washington, DC 20016, USA
| | - Kriti Arora
- Tuberculosis Research Section, LCID, NIAID, NIH 33 North Drive, Bldg 33, Rm 2W20C, Bethesda, MD 20892, USA
| | - Balbina J Plotkin
- Department of Microbiology and Immunology, Midwestern University, Chicago, IL 60515, USA
| | - Jacalyn M Green
- Department of Microbiology and Immunology, Midwestern University, Chicago, IL 60515, USA
| | - Helena I Boshoff
- Tuberculosis Research Section, LCID, NIAID, NIH 33 North Drive, Bldg 33, Rm 2W20C, Bethesda, MD 20892, USA
| | - Clifton Barry
- Tuberculosis Research Section, LCID, NIAID, NIH 33 North Drive, Bldg 33, Rm 2W20C, Bethesda, MD 20892, USA
| | - Jeffrey Deschamps
- Naval Research Laboratory, Code 6930 4555 Overlook Ave., Washington, DC 20375, USA
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27
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Kucharova V, Wiker HG. Proteogenomics in microbiology: taking the right turn at the junction of genomics and proteomics. Proteomics 2014; 14:2360-675. [PMID: 25263021 DOI: 10.1002/pmic.201400168] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/18/2014] [Accepted: 09/23/2014] [Indexed: 12/14/2022]
Abstract
High-accuracy and high-throughput proteomic methods have completely changed the way we can identify and characterize proteins. MS-based proteomics can now provide a unique supplement to genomic data and add a new level of information to the interpretation of genomic sequences. Proteomics-driven genome annotation has become especially relevant in microbiology where genomes are sequenced on a daily basis and limitations of an in silico driven annotation process are well recognized. In this review paper, we outline different strategies on how one can design a proteogenomic experiment, for example on genome-sequenced (synonymous proteogenomics) versus unsequenced organisms (ortho-proteogenomics) or with the aid of other "omic" data such as RNA-seq. We touch upon many challenges that are encountered during a typical proteogenomic study, mostly concerning bioinformatics methods and downstream data analysis, but also related to creation and use of sequence databases. A large list of proteogenomic case studies of different microorganisms is provided to illustrate the mapping of MS/MS-derived peptide spectra to genomic DNA sequences. These investigations have led to accurate determination of translational initiation sites, pointed out eventual read-throughs or programmed frameshifts, detected signal peptide processing or other protein maturation events, removed questionable annotation assignments, and provided evidence for predicted hypothetical proteins.
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Affiliation(s)
- Veronika Kucharova
- Department of Clinical Science, The Gade Research Group for Infection and Immunity, University of Bergen, Norway
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28
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Nasheri N, McKay CS, Fulton K, Twine S, Powdrill MH, Sherratt AR, Pezacki JP. Hydrophobic triaryl-substituted β-lactams as activity-based probes for profiling eukaryotic enzymes and host-pathogen interactions. Chembiochem 2014; 15:2195-200. [PMID: 25179744 DOI: 10.1002/cbic.201402097] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Indexed: 02/06/2023]
Affiliation(s)
- Neda Nasheri
- Life Sciences Division, National Research Council of Canada, 100 Sussex Drive, Ottawa, ON, K1A 0R6 (Canada); Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5 (Canada)
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29
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Strategies in the Design of Small-Molecule Fluorescent Probes for Peptidases. Med Res Rev 2014; 34:1217-41. [DOI: 10.1002/med.21316] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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30
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Molecular Targets of β-Lactam-Based Antimicrobials: Beyond the Usual Suspects. Antibiotics (Basel) 2014; 3:128-42. [PMID: 27025739 PMCID: PMC4790389 DOI: 10.3390/antibiotics3020128] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/24/2014] [Accepted: 02/25/2014] [Indexed: 12/20/2022] Open
Abstract
The common practice in antibacterial drug development has been to rapidly make an attempt to find ever-more stable and broad-spectrum variants for a particular antibiotic, once a drug resistance for that antibiotic is detected. We are now facing bacterial resistance toward our clinically relevant antibiotics of such a magnitude that the conversation for antimicrobial drug development ought to include effective new antibiotics with alternative mechanisms of action. The electrophilic β-lactam ring is amenable for the inhibition of different enzyme classes by a suitable decoration of the core scaffold. Monocyclic β-lactams lacking an ionizable group at the lactam nitrogen exhibit target preferences toward bacterial enzymes important for resistance and virulence. The present review intends to draw attention to the versatility of the β-lactams as antimicrobials with "unusual" molecular targets.
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31
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François P, Scherl A, Hochstrasser D, Schrenzel J. Proteomic approach to investigate pathogenicity and metabolism of methicillin-resistant Staphylococcus aureus. Methods Mol Biol 2014; 1085:231-50. [PMID: 24085700 DOI: 10.1007/978-1-62703-664-1_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the last two decades, numerous genomes of pathogenic bacteria have been fully sequenced and annotated, while others are continuously being sequenced. To date, the sequences of more than 8,500 whole bacterial genomes are publicly available for research purposes. These efforts in high-throughput sequencing simultaneously to progresses in methods allowing to study whole transcriptome and proteome of bacteria provide the basis of comprehensive understanding of metabolism, adaptability to environment, regulation, resistance pathways, or pathogenicity mechanisms of bacterial pathogens. Staphylococcus aureus is a Gram-positive human pathogen causing a wide variety of infections ranging from benign skin infection to life-threatening diseases. Furthermore, the spreading of multidrug-resistant isolates requiring the use of last barrier drugs has resulted in a particular attention of the medical and scientific community to this pathogen. We describe here proteomic methods to prepare, identify, and analyze protein fractions, which allow studying Staphylococcus aureus on the organism level. Besides evaluation of the whole bacterial transcriptome, this approach might contribute to the development of rapid diagnostic tests and to the identification of new drug targets to improve public health.
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Affiliation(s)
- Patrice François
- Service of Infectious Diseases, Genomic Research Laboratory, Geneva, Switzerland
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32
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Kolb R, Bach NC, Sieber SA. β-Sultams exhibit discrete binding preferences for diverse bacterial enzymes with nucleophilic residues. Chem Commun (Camb) 2014; 50:427-9. [DOI: 10.1039/c3cc46002a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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33
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Puri AW, Bogyo M. Applications of small molecule probes in dissecting mechanisms of bacterial virulence and host responses. Biochemistry 2013; 52:5985-96. [PMID: 23937332 DOI: 10.1021/bi400854d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Elucidating the molecular and biochemical details of bacterial infections can be challenging because of the many complex interactions that exist between a pathogen and its host. Consequently, many tools have been developed to aid the study of bacterial pathogenesis. Small molecules are a valuable complement to traditional genetic techniques because they can be used to rapidly perturb genetically intractable systems and to monitor post-translationally regulated processes. Activity-based probes are a subset of small molecules that covalently label an enzyme of interest based on its catalytic mechanism. These tools allow monitoring of enzyme activation within the context of a native biological system and can be used to dissect the biochemical details of enzyme function. This review describes the development and application of activity-based probes for examining aspects of bacterial infection on both sides of the host-pathogen interface.
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Affiliation(s)
- Aaron W Puri
- Department of Chemical and Systems Biology, ‡Department of Microbiology and Immunology, and §Department of Pathology, Stanford University School of Medicine , 300 Pasteur Drive, Stanford, California 94305, United States
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34
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2-Nitrobenzyl Esters of Penam and Cephem Derivatives as Inhibitors of Penicillin-Binding Proteins. ASIAN J ORG CHEM 2013. [DOI: 10.1002/ajoc.201300108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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35
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Park KD, Yang XF, Lee H, Dustrude ET, Wang Y, Khanna R, Kohn H. Discovery of lacosamide affinity bait agents that exhibit potent voltage-gated sodium channel blocking properties. ACS Chem Neurosci 2013; 4:463-74. [PMID: 23509982 DOI: 10.1021/cn300188h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Lacosamide ((R)-1) is a recently marketed, first-in-class, antiepileptic drug. Patch-clamp electrophysiology studies are consistent with the notion that (R)-1 modulates voltage-gated Na(+) channel function by increasing and stabilizing the slow inactivation state without affecting fast inactivation. The molecular pathway(s) that regulate slow inactivation are poorly understood. Affinity baits are chemical reactive units, which when appended to a ligand (drug) can lead to irreversible, covalent modification of the receptor thus permitting drug binding site identification including, possibly, the site of ligand function. We describe, herein, the synthesis of four (R)-1 affinity baits, (R)-N-(4″-isothiocyanatobiphenyl-4'-yl)methyl 2-acetamido-3-methoxypropionamide ((R)-8), (S)-N-(4″-isothiocyanatobiphenyl-4'-yl)methyl 2-acetamido-3-methoxypropionamide ((S)-8), (R)-N-(3″-isothiocyanatobiphenyl-4'-yl)methyl 2-acetamido-3-methoxypropionamide ((R)-9), and (R)-N-(3″-acrylamidobiphenyl-4'-yl)methyl 2-acetamido-3-methoxypropionamide ((R)-10). The affinity bait compounds were designed to interact with the receptor(s) responsible for (R)-1-mediated slow inactivation. We show that (R)-8 and (R)-9 are potent inhibitors of Na(+) channel function and function by a pathway similar to that observed for (R)-1. We further demonstrate that (R)-8 function is stereospecific. The calculated IC50 values determined for Na(+) channel slow inactivation for (R)-1, (R)-8, and (R)-9 were 85.1, 0.1, and 0.2 μM, respectively. Incubating (R)-9 with the neuronal-like CAD cells led to appreciable levels of Na(+) channel slow inactivation after cellular wash, and the level of slow inactivation only modestly decreased with further incubation and washing. Collectively, these findings have identified a promising structural template to investigate the voltage-gated Na(+) channel slow inactivation process.
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Affiliation(s)
- Ki Duk Park
- Departments of Pharmacology and
Toxicology, ‡Biochemistry and Molecular Biology, and §Program in Medical Neuroscience, Paul and Carole Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis,
Indiana 46202, United States
- Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, and ⊥Department of Chemistry, University of North Carolina, Chapel
Hill, North Carolina 27599, United States
| | - Xiao-Fang Yang
- Departments of Pharmacology and
Toxicology, ‡Biochemistry and Molecular Biology, and §Program in Medical Neuroscience, Paul and Carole Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis,
Indiana 46202, United States
- Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, and ⊥Department of Chemistry, University of North Carolina, Chapel
Hill, North Carolina 27599, United States
| | - Hyosung Lee
- Departments of Pharmacology and
Toxicology, ‡Biochemistry and Molecular Biology, and §Program in Medical Neuroscience, Paul and Carole Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis,
Indiana 46202, United States
- Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, and ⊥Department of Chemistry, University of North Carolina, Chapel
Hill, North Carolina 27599, United States
| | - Erik T. Dustrude
- Departments of Pharmacology and
Toxicology, ‡Biochemistry and Molecular Biology, and §Program in Medical Neuroscience, Paul and Carole Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis,
Indiana 46202, United States
- Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, and ⊥Department of Chemistry, University of North Carolina, Chapel
Hill, North Carolina 27599, United States
| | - Yuying Wang
- Departments of Pharmacology and
Toxicology, ‡Biochemistry and Molecular Biology, and §Program in Medical Neuroscience, Paul and Carole Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis,
Indiana 46202, United States
- Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, and ⊥Department of Chemistry, University of North Carolina, Chapel
Hill, North Carolina 27599, United States
| | - Rajesh Khanna
- Departments of Pharmacology and
Toxicology, ‡Biochemistry and Molecular Biology, and §Program in Medical Neuroscience, Paul and Carole Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis,
Indiana 46202, United States
- Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, and ⊥Department of Chemistry, University of North Carolina, Chapel
Hill, North Carolina 27599, United States
| | - Harold Kohn
- Departments of Pharmacology and
Toxicology, ‡Biochemistry and Molecular Biology, and §Program in Medical Neuroscience, Paul and Carole Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis,
Indiana 46202, United States
- Division of Chemical Biology and Medicinal
Chemistry, UNC Eshelman School of Pharmacy, and ⊥Department of Chemistry, University of North Carolina, Chapel
Hill, North Carolina 27599, United States
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36
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Wang K, Yang T, Wu Q, Zhao X, Nice EC, Huang C. Chemistry-based functional proteomics for drug target deconvolution. Expert Rev Proteomics 2013; 9:293-310. [PMID: 22809208 DOI: 10.1586/epr.12.19] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Drug target deconvolution, a process that identifies targets to small molecules in complex biological samples, which underlie the biological responses that are observed when a drug is administered, plays an important role in current drug discovery. Despite the fact that genomics and proteomics have provided a flood of information that contributes to the progress of drug target identification and validation, the current approach to drug target deconvolution still poses dilemmas. Chemistry-based functional proteomics, a multidisciplinary strategy, has become the preferred method of choice to deconvolute drug target pools, based on direct interactions between small molecules and their protein targets. This approach has already identified a broad panel of previously undefined enzymes with potential as drug targets and defined targets that can rationalize side effects and toxicity for new drug candidates and existing therapeutics. Herein, the authors discuss both activity-based protein profiling and compound-centric chemical proteomics approaches used in chemistry-based functional proteomics and their applications for the identification and characterization of small molecular targets.
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Affiliation(s)
- Kui Wang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, PR China
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37
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Kaschani F, Clerc J, Krahn D, Bier D, Hong TN, Ottmann C, Niessen S, Colby T, van der Hoorn RAL, Kaiser M. Identification of a selective, activity-based probe for glyceraldehyde 3-phosphate dehydrogenases. Angew Chem Int Ed Engl 2012; 51:5230-3. [PMID: 22489074 DOI: 10.1002/anie.201107276] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Farnusch Kaschani
- Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstrasse 2, 45117 Essen, Germany
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Kaschani F, Clerc J, Krahn D, Bier D, Hong TN, Ottmann C, Niessen S, Colby T, van der Hoorn RAL, Kaiser M. Identifizierung einer selektiven aktivitätsbasierten Sonde für Glycerinaldehyd-3-phosphat-Dehydrogenasen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201107276] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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39
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Li N, Overkleeft HS, Florea BI. Activity-based protein profiling: an enabling technology in chemical biology research. Curr Opin Chem Biol 2012; 16:227-33. [DOI: 10.1016/j.cbpa.2012.01.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 01/11/2012] [Accepted: 01/18/2012] [Indexed: 12/25/2022]
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40
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Serim S, Haedke U, Verhelst SHL. Activity-based probes for the study of proteases: recent advances and developments. ChemMedChem 2012; 7:1146-59. [PMID: 22431376 DOI: 10.1002/cmdc.201200057] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 02/28/2012] [Indexed: 11/11/2022]
Abstract
Proteases are important targets for the treatment of human disease. Several protease inhibitors have failed in clinical trials due to a lack of in vivo specificity, indicating the need for studies of protease function and inhibition in complex, disease-related models. The tight post-translational regulation of protease activity complicates protease analysis by traditional proteomics methods. Activity-based protein profiling is a powerful technique that can resolve this issue. It uses small-molecule tools-activity-based probes-to label and analyze active enzymes in lysates, cells, and whole animals. Over the last twelve years, a wide variety of protease activity-based probes have been developed. These synthetic efforts have enabled techniques ranging from real-time in vivo imaging of protease activity to high-throughput screening of uncharacterized proteases. This Review introduces the general principles of activity-based protein profiling and describes the recent advancements in probe design and analysis techniques, which have increased the knowledge of protease biology and will aid future protease drug discovery.
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Affiliation(s)
- Sevnur Serim
- Center for Integrated Protein Science Munich (CIPS(M)), Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
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41
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Prasad G, Amoroso JW, Borketey LS, Schnarr NA. N-activated β-lactams as versatile reagents for acyl carrier protein labeling. Org Biomol Chem 2012; 10:1992-2002. [PMID: 22293823 DOI: 10.1039/c2ob06846j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Acyl carrier proteins are critical components of fatty acid and polyketide biosynthesis. Their primary function is to shuttle intermediates between active sites via a covalently bound phosphopantetheine arm. Small molecules capable of acylating this prosthetic group will provide a simple and reversible means of introducing novel functionality onto carrier protein domains. A series of N-activated β-lactams are prepared to examine site-specific acylation of the phosphopantetheine-thiol. In general, β-lactams are found to be significantly more reactive than our previously studied β-lactones. Selectivity for the holo over apo-form of acyl carrier proteins is demonstrated indicating that only the phosphopantetheine-thiol is modified. Incorporation of an N-propargyloxycarbonyl group provides an alkyne handle for conjugation to fluorophores and affinity labels. The utility of these groups for mechanistic interrogation of a critical step in polyketide biosynthesis is examined through comparison to traditional probes. In all, we expect the probes described in this study to serve as valuable and versatile tools for mechanistic interrogation.
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Affiliation(s)
- Gitanjeli Prasad
- Department of Chemistry, University of Massachusetts, 710 N. Pleasant Street, Amherst, Massachusetts 01003, USA
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42
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Deu E, Verdoes M, Bogyo M. New approaches for dissecting protease functions to improve probe development and drug discovery. Nat Struct Mol Biol 2012; 19:9-16. [PMID: 22218294 DOI: 10.1038/nsmb.2203] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Proteases are well-established targets for pharmaceutical development because of their known enzymatic mechanism and their regulatory roles in many pathologies. However, many potent clinical lead compounds have been unsuccessful either because of a lack of specificity or because of our limited understanding of the biological roles of the targeted protease. In order to successfully develop protease inhibitors as drugs, it is necessary to understand protease functions and to expand the platform of inhibitor development beyond active site-directed design and in vitro optimization. Several newly developed technologies will enhance assessment of drug selectivity in living cells and animal models, allowing researchers to focus on compounds with high specificity and minimal side effects in vivo. In this review, we highlight advances in the development of chemical probes, proteomic methods and screening tools that we feel will help facilitate this paradigm shift in drug discovery.
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Affiliation(s)
- Edgar Deu
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
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Böttcher T, Sieber SA. β-Lactams and β-lactones as activity-based probes in chemical biology. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md00275b] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Pitscheider M, Mäusbacher N, Sieber SA. Antibiotic activity and target discovery of three-membered natural product-derived heterocycles in pathogenic bacteria. Chem Sci 2012. [DOI: 10.1039/c2sc20290e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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45
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Probing small molecule–protein interactions: A new perspective for functional proteomics. J Proteomics 2011; 75:100-15. [DOI: 10.1016/j.jprot.2011.07.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 07/01/2011] [Accepted: 07/13/2011] [Indexed: 11/22/2022]
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Chang JW, Nomura DK, Cravatt BF. A potent and selective inhibitor of KIAA1363/AADACL1 that impairs prostate cancer pathogenesis. ACTA ACUST UNITED AC 2011; 18:476-84. [PMID: 21513884 DOI: 10.1016/j.chembiol.2011.02.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 02/07/2011] [Accepted: 02/08/2011] [Indexed: 01/17/2023]
Abstract
Cancer cells show alterations in metabolism that support malignancy and disease progression. Prominent among these metabolic changes is elevations in neutral ether lipids (NELs). We have previously shown that the hydrolytic enzyme KIAA1363 (or AADACL1) is highly elevated in aggressive cancer cells, where it plays a key role in generating the monoalkylglycerol ether (MAGE) class of NELs. Here, we use activity-based protein profiling-guided medicinal chemistry to discover a highly potent and selective inhibitor of KIAA1363, the carbamate JW480. We show that JW480, and an shRNA probe that targets KIAA1363, reduce MAGEs and impair the migration, invasion, survival, and in vivo tumor growth of human prostate cancer cell lines. These findings indicate that the KIAA1363-MAGE pathway is important for prostate cancer pathogenesis and designate JW480 as a versatile pharmacological probe for disrupting this pro-tumorigenic metabolic pathway.
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Affiliation(s)
- Jae Won Chang
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Park KD, Kim D, Reamtong O, Eyers C, Gaskell SJ, Liu R, Kohn H. Identification of a lacosamide binding protein using an affinity bait and chemical reporter strategy: 14-3-3 ζ. J Am Chem Soc 2011; 133:11320-30. [PMID: 21692503 DOI: 10.1021/ja2034156] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have advanced a useful strategy to elucidate binding partners of ligands (drugs) with modest binding affinity. Key to this strategy is attaching to the ligand an affinity bait (AB) and a chemical reporter (CR) group, where the AB irreversibly attaches the ligand to the receptor upon binding and the CR group is employed for receptor detection and isolation. We have tested this AB&CR strategy using lacosamide ((R)-1), a low-molecular-weight antiepileptic drug. We demonstrate that using a (R)-lacosamide AB&CR agent ((R)-2) 14-3-3 ζ in rodent brain soluble lysates is preferentially adducted, adduction is stereospecific with respect to the AB&CR agent, and adduction depends upon the presence of endogenous levels of the small molecule metabolite xanthine. Substitution of lacosamide AB agent ((R)-5) for (R)-2 led to the identification of the 14-3-3 ζ adduction site (K120) by mass spectrometry. Competition experiments using increasing amounts of (R)-1 in the presence of (R)-2 demonstrated that (R)-1 binds at or near the (R)-2 modification site on 14-3-3 ζ. Structure-activity studies of xanthine derivatives provided information concerning the likely binding interaction between this metabolite and recombinant 14-3-3 ζ. Documentation of the 14-3-3 ζ-xanthine interaction was obtained with isothermal calorimetry using xanthine and the xanthine analogue 1,7-dimethylxanthine.
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Affiliation(s)
- Ki Duk Park
- Division of Medicinal Chemistry and Natural Products, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599-7568, USA
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Blaby-Haas CE, de Crécy-Lagard V. Mining high-throughput experimental data to link gene and function. Trends Biotechnol 2011; 29:174-82. [PMID: 21310501 DOI: 10.1016/j.tibtech.2011.01.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 12/21/2010] [Accepted: 01/04/2011] [Indexed: 12/25/2022]
Abstract
Nearly 2200 genomes that encode around 6 million proteins have now been sequenced. Around 40% of these proteins are of unknown function, even when function is loosely and minimally defined as 'belonging to a superfamily'. In addition to in silico methods, the swelling stream of high-throughput experimental data can give valuable clues for linking these unknowns with precise biological roles. The goal is to develop integrative data-mining platforms that allow the scientific community at large to access and utilize this rich source of experimental knowledge. To this end, we review recent advances in generating whole-genome experimental datasets, where this data can be accessed, and how it can be used to drive prediction of gene function.
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Affiliation(s)
- Crysten E Blaby-Haas
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
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Riofski MV, John JP, Zheng MM, Kirshner J, Colby DA. Exploiting the facile release of trifluoroacetate for the α-methylenation of the sterically hindered carbonyl groups on (+)-sclareolide and (-)-eburnamonine. J Org Chem 2011; 76:3676-83. [PMID: 21491928 DOI: 10.1021/jo102114f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An efficient method for the α-methylenation of carbonyl groups is reported, and this transformation is accomplished by a facile elimination of trifluoroacetate during the formation of the olefin. This method represents an improvement beyond existing protocol in cases of steric hindrance, and we have demonstrated the utility of the process across a series of ketones, lactams, and lactones. Additionally, we have applied this method to produce semisynthetic derivatives of the natural products (+)-sclareolide and (-)-eburnamonine, in which the carbonyl group is proximal to bulky functional groups. Mechanistic insight is also provided from a time course of (19)F NMR. Biological evaluation of the natural-product-derived enones led to the identification of a derivative of (-)-eburnamonine with significant cytotoxicity (LC(50) = 14.12 μM) in drug-resistant MDA-MB-231 breast cancer cells.
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Affiliation(s)
- Mark V Riofski
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
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50
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Application of Activity-Based Protein Profiling to the Study of Microbial Pathogenesis. Top Curr Chem (Cham) 2011; 324:115-35. [DOI: 10.1007/128_2011_299] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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