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Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design. Q Rev Biophys 2019; 51:e10. [PMID: 30912486 DOI: 10.1017/s0033583518000082] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.
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Azami-Movahed M, Meratan AA, Ghasemi A, Ebrahim-Habibi A, Nemat-Gorgani M. Acetylation of lysine residues in apomyoglobin: Structural changes, amyloid fibrillation, and role of surface charge. Int J Biol Macromol 2018; 107:626-634. [DOI: 10.1016/j.ijbiomac.2017.09.040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 12/21/2022]
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De Simone G, Langella E, Esposito D, Supuran CT, Monti SM, Winum JY, Alterio V. Insights into the binding mode of sulphamates and sulphamides to hCA II: crystallographic studies and binding free energy calculations. J Enzyme Inhib Med Chem 2017; 32:1002-1011. [PMID: 28738704 PMCID: PMC6445192 DOI: 10.1080/14756366.2017.1349764] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 12/21/2022] Open
Abstract
Sulphamate and sulphamide derivatives have been largely investigated as carbonic anhydrase inhibitors (CAIs) by means of different experimental techniques. However, the structural determinants responsible for their different binding mode to the enzyme active site were not clearly defined so far. In this paper, we report the X-ray crystal structure of hCA II in complex with a sulphamate inhibitor incorporating a nitroimidazole moiety. The comparison with the structure of hCA II in complex with its sulphamide analogue revealed that the two inhibitors adopt a completely different binding mode within the hCA II active site. Starting from these results, we performed a theoretical study on sulphamate and sulphamide derivatives, demonstrating that electrostatic interactions with residues within the enzyme active site play a key role in determining their binding conformation. These findings open new perspectives in the design of effective CAIs using the sulphamate and sulphamide zinc binding groups as lead compounds.
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Affiliation(s)
- Giuseppina De Simone
- Istituto di Biostrutture e Bioimagini, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Emma Langella
- Istituto di Biostrutture e Bioimagini, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Davide Esposito
- Istituto di Biostrutture e Bioimagini, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Claudiu T. Supuran
- Neurofarba Department, Section of Pharmaceutical and Nutriceutical Sciences, Università degli Studi di Firenze, Sesto Fiorentino, Florence, Italy
| | - Simona Maria Monti
- Istituto di Biostrutture e Bioimagini, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Jean-Yves Winum
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, ENSCM, Université de Montpellier, Montpellier, France
| | - Vincenzo Alterio
- Istituto di Biostrutture e Bioimagini, Consiglio Nazionale delle Ricerche, Naples, Italy
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4
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Ren J, Sang Y, Lu J, Yao YF. Protein Acetylation and Its Role in Bacterial Virulence. Trends Microbiol 2017; 25:768-779. [PMID: 28462789 DOI: 10.1016/j.tim.2017.04.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/21/2017] [Accepted: 04/04/2017] [Indexed: 12/13/2022]
Abstract
Protein acetylation is a universal post-translational modification which is found in both eukaryotes and prokaryotes. This process is achieved enzymatically by the protein acetyltransferase Pat, and nonenzymatically by metabolic intermediates (e.g., acetyl phosphate) in bacteria. Protein acetylation plays a role in bacterial chemotaxis, metabolism, DNA replication, and other cellular processes. Recently, accumulating evidence has suggested that protein acetylation might be involved in bacterial virulence because a number of bacterial virulence factors are acetylated. In this review, we summarize the progress in understanding bacterial protein acetylation and discuss how it mediates bacterial virulence.
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Affiliation(s)
- Jie Ren
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Sang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jie Lu
- Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai 200025, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China.
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Bacterial protein acetylation: new discoveries unanswered questions. Curr Genet 2015; 62:335-41. [PMID: 26660885 DOI: 10.1007/s00294-015-0552-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 11/25/2015] [Accepted: 11/26/2015] [Indexed: 10/22/2022]
Abstract
Nε-acetylation is emerging as an abundant post-translational modification of bacterial proteins. Two mechanisms have been identified: one is enzymatic, dependent on an acetyltransferase and acetyl-coenzyme A; the other is non-enzymatic and depends on the reactivity of acetyl phosphate. Some, but not most, of those acetylations are reversed by deacetylases. This review will briefly describe the current status of the field and raise questions that need answering.
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Mahon BP, Lomelino CL, Ladwig J, Rankin GM, Driscoll JM, Salguero AL, Pinard MA, Vullo D, Supuran CT, Poulsen SA, McKenna R. Mapping Selective Inhibition of the Cancer-Related Carbonic Anhydrase IX Using Structure–Activity Relationships of Glucosyl-Based Sulfamates. J Med Chem 2015. [DOI: 10.1021/acs.jmedchem.5b00845] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Brian P. Mahon
- Department
of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, Florida 32610, United States
| | - Carrie L. Lomelino
- Department
of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, Florida 32610, United States
| | - Janina Ladwig
- Eskitis
Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Gregory M. Rankin
- Eskitis
Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Jenna M. Driscoll
- Department
of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, Florida 32610, United States
| | - Antonieta L. Salguero
- Department
of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, Florida 32610, United States
| | - Melissa A. Pinard
- Department
of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, Florida 32610, United States
| | - Daniela Vullo
- Polo
Scientifico, Neurofarba Department and Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudiu T. Supuran
- Polo
Scientifico, Neurofarba Department and Laboratorio di Chimica Bioinorganica, Università degli Studi di Firenze, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Sally-Ann Poulsen
- Eskitis
Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Robert McKenna
- Department
of Biochemistry and Molecular Biology, College of Medicine, University of Florida, 1600 SW Archer Road, PO Box 100245, Gainesville, Florida 32610, United States
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