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Hobbs KF, Propp J, Vance NR, Kalenkiewicz A, Witkin KR, Spies MA. Allosteric Tuning of Caspase-7: Establishing the Nexus of Structure and Catalytic Power. Chemistry 2023:e202301621. [PMID: 37285583 DOI: 10.1002/chem.202301621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Invited for the cover of this issue is the group of Michael Ashley Spies at the University of Iowa. The image depicts how mapping allosteric structure-activity relationships reveals the nexus between the active site and the remote allosteric pocket. Read the full text of the article at 10.1002/chem.202300872.
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Affiliation(s)
- Kathryn F Hobbs
- Biochemistry and Molecular Biology Department, University of Iowa, 51 Newton Road, 4-403 Bowen Science Building, Iowa City, IA, 52242, USA
| | - Jonah Propp
- Pharmaceutics and Experimental Therapeutics Department, Medicinal and Natural Products Chemistry Division, University of Iowa, 180 South Grand Avenue, Iowa City, IA, 52242, USA
| | - Nicholas R Vance
- Pharmaceutics and Experimental Therapeutics Department, Medicinal and Natural Products Chemistry Division, University of Iowa, 180 South Grand Avenue, Iowa City, IA, 52242, USA
| | - Andrew Kalenkiewicz
- Biochemistry and Molecular Biology Department, University of Iowa, 51 Newton Road, 4-403 Bowen Science Building, Iowa City, IA, 52242, USA
| | - Katie R Witkin
- Pharmaceutics and Experimental Therapeutics Department, Medicinal and Natural Products Chemistry Division, University of Iowa, 180 South Grand Avenue, Iowa City, IA, 52242, USA
| | - M Ashley Spies
- Biochemistry and Molecular Biology Department, University of Iowa, 51 Newton Road, 4-403 Bowen Science Building, Iowa City, IA, 52242, USA
- Pharmaceutics and Experimental Therapeutics Department, Medicinal and Natural Products Chemistry Division, University of Iowa, 180 South Grand Avenue, Iowa City, IA, 52242, USA
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Hobbs KF, Propp J, Vance NR, Kalenkiewicz A, Witkin KR, Spies MA. Allosteric Tuning of Caspase-7: Establishing the Nexus of Structure and Catalytic Power. Chemistry 2023:e202300872. [PMID: 37005499 DOI: 10.1002/chem.202300872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/04/2023]
Abstract
Caspase-7 (C7), a cysteine protease involved in apoptosis, is a valuable drug target for its role in human diseases (e.g. Parkinson's, Alzheimer's, sepsis). The C7 allosteric site has great potential for small molecule targeting, but numerous drug discovery efforts have identified precious few allosteric inhibitors. Here we present the first selective, drug-like inhibitor of C7 along with several other improved inhibitors based on our previous fragment hit. We also provide a rational basis for the impact of allosteric binding on the C7 catalytic cycle using an integrated approach including X-ray crystallography, stopped-flow kinetics, and molecular dynamics simulations. Our findings suggest allosteric binding disrupts C7 pre-acylation via neutralization of the catalytic dyad, displacement of substrate from the oxyanion hole, and altered dynamics of substrate binding loops. This work advances drug targeting efforts and bolsters our understanding of allosteric structure activity relationships (ASARs).
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Affiliation(s)
- Kathryn F Hobbs
- The University of Iowa Roy J and Lucille A Carver College of Medicine, Biochemistry and Molecular Biology, UNITED STATES
| | - Jonah Propp
- The University of Iowa College of Pharmacy, Division of Medicinal and Natural Products Chemistry, UNITED STATES
| | - Nicholas R Vance
- The University of Iowa College of Pharmacy, Division of Medicinal and Natural Products Chemistry, UNITED STATES
| | - Andrew Kalenkiewicz
- The University of Iowa Roy J and Lucille A Carver College of Medicine, Biochemistry and Molecular Biology, UNITED STATES
| | - Katie R Witkin
- The University of Iowa Roy J and Lucille A Carver College of Medicine, Division of Medicinal and Natural Products Chemistry, UNITED STATES
| | - Michael Ashley Spies
- University of Iowa, Division of Medicinal and Natural Products Chemistry, 115 S Grand Ave, 52242, Iowa City, UNITED STATES
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Witkin KR, Vance NR, Caldwell C, Li Q, Yu L, Spies MA. An Atomistic Understanding of Allosteric Inhibition of Glutamate Racemase: a Dampening of Native Activation Dynamics. ChemMedChem 2020; 15:376-384. [PMID: 31876113 PMCID: PMC7337235 DOI: 10.1002/cmdc.201900642] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/11/2019] [Indexed: 11/07/2022]
Abstract
Glutamate racemases (GR) are members of the family of bacterial enzymes known as cofactor-independent racemases and epimerases and catalyze the stereoinversion of glutamate. D-amino acids are universally important for the proper construction of viable bacterial cell walls, and thus have been repeatedly validated as attractive targets for novel antimicrobial drug design. Significant aspects of the mechanism of this challenging stereoinversion remain unknown. The current study employs a combination of MD and QM/MM computational approaches to show that the GR from H. pylori must proceed via a pre-activation step, which is dependent on the enzyme's flexibility. This mechanism is starkly different from previously proposed mechanisms. These findings have immediate pharmaceutical relevance, as the H. pylori GR enzyme is a very attractive allosteric drug target. The results presented in this study offer a distinctly novel understanding of how AstraZeneca's lead series of inhibitors cripple the H. pylori GR's native motions, via prevention of this critical chemical pre-activation step. Our experimental studies, using SPR, fluorescence and NMR WaterLOGSY, show that H. pylori GR is not inhibited by the uncompetitive mechanism originally put forward by Lundqvist et al.. The current study supports a deep connection between native enzyme motions and chemical reactivity, which has strong relevance to the field of allosteric drug discovery.
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Affiliation(s)
- Katie R Witkin
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutics and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, Iowa, 52246, USA
| | - Nicholas R Vance
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutics and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, Iowa, 52246, USA
| | - Colleen Caldwell
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52246, USA
| | - Quinn Li
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52246, USA
| | - Liping Yu
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52246, USA
- NMR Core Facility, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52246, USA
| | - M Ashley Spies
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutics and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, Iowa, 52246, USA
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52246, USA
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Vance NR, Witkin KR, Rooney PW, Li Y, Pope M, Spies MA. Elucidating the Catalytic Power of Glutamate Racemase by Investigating a Series of Covalent Inhibitors. ChemMedChem 2018; 13:2514-2521. [PMID: 30264520 DOI: 10.1002/cmdc.201800592] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Indexed: 12/29/2022]
Abstract
The application of covalent inhibitors has experienced a renaissance within drug discovery programs in the last decade. To leverage the superior potency and drug target residence time of covalent inhibitors, there have been extensive efforts to develop highly specific covalent modifications to decrease off-target liabilities. Herein, we present a series of covalent inhibitors of an antimicrobial drug target, glutamate racemase, discovered through structure-based virtual screening. A combination of enzyme kinetics, mass spectrometry, and surface-plasmon resonance experiments details a highly specific 1,4-conjugate addition of a small-molecule inhibitor with a catalytic cysteine of glutamate racemase. Molecular dynamics simulations and quantum mechanics-molecular mechanics geometry optimizations reveal the chemistry of the conjugate addition. Two compounds from this series of inhibitors display antimicrobial potency similar to β-lactam antibiotics, with significant activity against methicillin-resistant S. aureus strains. This study elucidates a detailed chemical rationale for covalent inhibition and provides a platform for the development of antimicrobials with a novel mechanism of action against a target in the cell wall biosynthesis pathway.
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Affiliation(s)
- Nicholas R Vance
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 115 S. Grand Ave., Iowa City, IA, 52242, USA
| | - Katie R Witkin
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 115 S. Grand Ave., Iowa City, IA, 52242, USA
| | - Patrick W Rooney
- Department of Biochemistry, Carver College of Medicine, University of Iowa, 51 Newton Road, 4-403 Bowen Science Building, Iowa City, IA, 52242, USA
| | - Yalan Li
- Proteomics Facility, Carver College of Medicine, University of Iowa, 355 EMRB, Iowa City, IA, 52242, USA
| | - Marshall Pope
- Proteomics Facility, Carver College of Medicine, University of Iowa, 355 EMRB, Iowa City, IA, 52242, USA
| | - M Ashley Spies
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 115 S. Grand Ave., Iowa City, IA, 52242, USA.,Department of Biochemistry, Carver College of Medicine, University of Iowa, 51 Newton Road, 4-403 Bowen Science Building, Iowa City, IA, 52242, USA
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Vance NR, Gakhar L, Spies MA. Allosteric Tuning of Caspase-7: A Fragment-Based Drug Discovery Approach. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nicholas R. Vance
- Division of Medicinal and Natural Products Chemistry; College of Pharmacy; University of Iowa; 115 S Grand Ave Iowa City IA 52242 USA
| | - Lokesh Gakhar
- Department of Biochemistry; College of Medicine; University of Iowa; 51 Newton Road Iowa City IA 52242 USA
- Protein Crystallography Facility; Roy J. and Lucille A. Carver College of Medicine; University of Iowa; 51 Newton Road Iowa City IA 52242 USA
| | - M. Ashley Spies
- Division of Medicinal and Natural Products Chemistry; College of Pharmacy; University of Iowa; 115 S Grand Ave Iowa City IA 52242 USA
- Department of Biochemistry; College of Medicine; University of Iowa; 51 Newton Road Iowa City IA 52242 USA
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Vance NR, Gakhar L, Spies MA. Allosteric Tuning of Caspase-7: A Fragment-Based Drug Discovery Approach. Angew Chem Int Ed Engl 2017; 56:14443-14447. [PMID: 28940929 PMCID: PMC5698726 DOI: 10.1002/anie.201706959] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/28/2017] [Indexed: 11/12/2022]
Abstract
The caspase family of cysteine proteases are highly sought‐after drug targets owing to their essential roles in apoptosis, proliferation, and inflammation pathways. High‐throughput screening efforts to discover inhibitors have gained little traction. Fragment‐based screening has emerged as a powerful approach for the discovery of innovative drug leads. This method has become a central facet of drug discovery campaigns in the pharmaceutical industry and academia. A fragment‐based drug discovery campaign against human caspase‐7 resulted in the discovery of a novel series of allosteric inhibitors. An X‐ray crystal structure of caspase‐7 bound to a fragment hit and a thorough kinetic characterization of a zymogenic form of the enzyme were used to investigate the allosteric mechanism of inhibition. This work further advances our understanding of the mechanisms of allosteric control of this class of pharmaceutically relevant enzymes, and provides a new path forward for drug discovery efforts.
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Affiliation(s)
- Nicholas R Vance
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 115 S Grand Ave, Iowa City, IA, 52242, USA
| | - Lokesh Gakhar
- Department of Biochemistry, College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA, 52242, USA.,Protein Crystallography Facility, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA, 52242, USA
| | - M Ashley Spies
- Division of Medicinal and Natural Products Chemistry, College of Pharmacy, University of Iowa, 115 S Grand Ave, Iowa City, IA, 52242, USA.,Department of Biochemistry, College of Medicine, University of Iowa, 51 Newton Road, Iowa City, IA, 52242, USA
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