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Georgiadis D, Skoulikas N, Papakyriakou A, Stratikos E. Phosphinic Peptides as Tool Compounds for the Study of Pharmacologically Relevant Zn-Metalloproteases. ACS Pharmacol Transl Sci 2022; 5:1228-1253. [PMID: 36524013 PMCID: PMC9745897 DOI: 10.1021/acsptsci.2c00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Indexed: 11/29/2022]
Abstract
Phosphinic peptides constitute an important class of bioactive compounds that have found a wide range of applications in the field of biology and pharmacology of Zn-metalloproteases, the largest family of proteases in humans. They are designed to mimic the structure of natural substrates during their proteolysis, thus acting as mechanism-based, transition state analogue inhibitors. A combination of electrostatic interactions between the phosphinic acid group and the Zn cation as well as optimal noncovalent enzyme-ligand interactions can result in both high binding affinity for the desired target and selectivity against other proteases. Due to these unique properties, phosphinic peptides have been mainly employed as tool compounds for (a) the purposes of rational drug design by serving as ligands in X-ray crystal structures of target enzymes and allowing the identification of crucial interactions that govern optimal molecular recognition, and (b) the delineation of biological pathways where Zn-metalloproteases are key regulators. For the latter objective, inhibitors of the phosphinopeptidic type have been used either unmodified or after being transformed to probes of various types, thus expanding the arsenal of functional tools available to researchers. The aim of this review is to summarize all recent research achievements in which phosphinic peptides have played a central role as tool compounds in the understanding of the mechanism and biological functions of Zn-metalloproteases in both health and disease.
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Affiliation(s)
- Dimitris Georgiadis
- Department
of Chemistry, National and Kapodistrian
University of Athens, GR-15784 Athens, Greece
| | - Nikolaos Skoulikas
- Department
of Chemistry, National and Kapodistrian
University of Athens, GR-15784 Athens, Greece
| | - Athanasios Papakyriakou
- National
Centre for Scientific Research “Demokritos”, Agia Paraskevi GR-15341 Athens, Greece
| | - Efstratios Stratikos
- Department
of Chemistry, National and Kapodistrian
University of Athens, GR-15784 Athens, Greece
- National
Centre for Scientific Research “Demokritos”, Agia Paraskevi GR-15341 Athens, Greece
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2
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Kemp MT, Lewandowski EM, Chen Y. Low barrier hydrogen bonds in protein structure and function. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2021; 1869:140557. [PMID: 33148530 PMCID: PMC7736181 DOI: 10.1016/j.bbapap.2020.140557] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 01/05/2023]
Abstract
Low-barrier hydrogen bonds (LBHBs) are a special type of short hydrogen bond (HB) that is characterized by the equal sharing of a hydrogen atom. The existence and catalytic role of LBHBs in proteins has been intensely contested. Advancements in X-ray and neutron diffraction methods has revealed delocalized hydrogen atoms involved in potential LBHBs in a number of proteins, while also demonstrating that short HBs are not necessarily LBHBs. More importantly, a series of experiments on ketosteroid isomerase (KSI) have suggested that LBHBs are significantly stronger than standard HBs in the protein microenvironment in terms of enthalpy, but not free energy. The discrepancy between the enthalpy and free energy of LBHBs offers clues to the challenges, and potential solutions, of the LBHB debate, where the unique strength of LBHBs plays a special role in the kinetic processes of enzyme function and structure, together with other molecular forces in a pre-organized environment.
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Affiliation(s)
- M Trent Kemp
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Eric M Lewandowski
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States.
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3
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Stuckey JI, Cantone NR, Côté A, Arora S, Vivat V, Ramakrishnan A, Mertz JA, Khanna A, Brenneman J, Gehling VS, Moine L, Sims RJ, Audia JE, Trojer P, Levell JR, Cummings RT. Identification and characterization of second-generation EZH2 inhibitors with extended residence times and improved biological activity. J Biol Chem 2021; 296:100349. [PMID: 33524394 PMCID: PMC7949150 DOI: 10.1016/j.jbc.2021.100349] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 12/28/2022] Open
Abstract
The histone methyltransferase EZH2 has been the target of numerous small-molecule inhibitor discovery efforts over the last 10+ years. Emerging clinical data have provided early evidence for single agent activity with acceptable safety profiles for first-generation inhibitors. We have developed kinetic methodologies for studying EZH2-inhibitor-binding kinetics that have allowed us to identify a unique structural modification that results in significant increases in the drug-target residence times of all EZH2 inhibitor scaffolds we have studied. The unexpected residence time enhancement bestowed by this modification has enabled us to create a series of second-generation EZH2 inhibitors with sub-pM binding affinities. We provide both biophysical evidence validating this sub-pM potency and biological evidence demonstrating the utility and relevance of such high-affinity interactions with EZH2.
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Affiliation(s)
- Jacob I Stuckey
- Constellation Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Nico R Cantone
- Constellation Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Alexandre Côté
- Constellation Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Shilpi Arora
- Constellation Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Valerie Vivat
- Constellation Pharmaceuticals, Cambridge, Massachusetts, USA
| | | | | | - Avinash Khanna
- Constellation Pharmaceuticals, Cambridge, Massachusetts, USA
| | | | | | - Ludivine Moine
- Constellation Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Robert J Sims
- Constellation Pharmaceuticals, Cambridge, Massachusetts, USA
| | - James E Audia
- Constellation Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Patrick Trojer
- Constellation Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Julian R Levell
- Constellation Pharmaceuticals, Cambridge, Massachusetts, USA
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4
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Covaleda-Cortés G, Hernández M, Trejo SA, Mansur M, Rodríguez-Calado S, García-Pardo J, Lorenzo J, Vendrell J, Chávez MÁ, Alonso-Del-Rivero M, Avilés FX. Characterization, Recombinant Production and Structure-Function Analysis of NvCI, A Picomolar Metallocarboxypeptidase Inhibitor from the Marine Snail Nerita versicolor. Mar Drugs 2019; 17:md17090511. [PMID: 31470614 PMCID: PMC6780499 DOI: 10.3390/md17090511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 02/05/2023] Open
Abstract
A very powerful proteinaceous inhibitor of metallocarboxypeptidases has been isolated from the marine snail Nerita versicolor and characterized in depth. The most abundant of four, very similar isoforms, NvCla, was taken as reference and N-terminally sequenced to obtain a 372-nucleotide band coding for the protein cDNA. The mature protein contains 53 residues and three disulphide bonds. NvCIa and the other isoforms show an exceptionally high inhibitory capacity of around 1.8 pM for human Carboxypeptidase A1 (hCPA1) and for other A-like members of the M14 CPA subfamily, whereas a twofold decrease in inhibitory potency is observed for carboxypeptidase B-like members as hCPB and hTAFIa. A recombinant form, rNvCI, was produced in high yield and HPLC, mass spectrometry and spectroscopic analyses by CD and NMR indicated its homogeneous, compact and thermally resistant nature. Using antibodies raised with rNvCI and histochemical analyses, a preferential distribution of the inhibitor in the surface regions of the animal body was observed, particularly nearby the open entrance of the shell and gut, suggesting its involvement in biological defense mechanisms. The properties of this strong, small and stable inhibitor of metallocarboxypeptidases envisage potentialities for its direct applicability, as well as leading or minimized forms, in biotechnological/biomedical uses.
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Affiliation(s)
- Giovanni Covaleda-Cortés
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Martha Hernández
- Faculty of Forestry Science, Biotechnology Center, Universidad de Concepción, Victoria 631, Barrio Universitario, 2407 Concepción, Chile
| | - Sebastián Alejandro Trejo
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Manuel Mansur
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Sergi Rodríguez-Calado
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Javier García-Pardo
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Julia Lorenzo
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
| | - Josep Vendrell
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - María Ángeles Chávez
- Center for Protein Research, Faculty of Biology, Universidad de la Habana, 10400 La Habana, Cuba
| | - Maday Alonso-Del-Rivero
- Center for Protein Research, Faculty of Biology, Universidad de la Habana, 10400 La Habana, Cuba.
| | - Francesc Xavier Avilés
- Institute of Biotechnology and Biomedicine and Departament of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.
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Covaleda G, Gallego P, Vendrell J, Georgiadis D, Lorenzo J, Dive V, Aviles FX, Reverter D, Devel L. Synthesis and Structural/Functional Characterization of Selective M14 Metallocarboxypeptidase Inhibitors Based on Phosphinic Pseudopeptide Scaffold: Implications on the Design of Specific Optical Probes. J Med Chem 2019; 62:1917-1931. [PMID: 30688452 DOI: 10.1021/acs.jmedchem.8b01465] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Metallocarboxypeptidases (MCPs) of the M14 family are Zn2+-dependent exoproteases present in almost every tissue or fluid in mammals. These enzymes perform a large variety of physiological functions and are involved in several pathologies, such as pancreatic diseases, inflammation, fibrinolysis, and cancer. Here, we describe the synthesis and functional/structural characterization of a series of reversible tight-binding phosphinic pseudopeptide inhibitors that show high specificity and potency toward these proteases. Characterization of their inhibitory potential against a large variety of MCPs, combined with high-resolution crystal structures of three selected candidates in complex with human carboxypeptidase A (CPA)1, allowed to decipher the structural determinants governing selectivity for type-A of the M14A MCP family. Further, the phosphinic pseudopeptide framework was exploited to generate an optical probe selectively targeting human CPAs. The phosphinic pseudopeptides presented here constitute the first example of chemical probes useful to selectively report on type-A MCPs activity in complex media.
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Affiliation(s)
- Giovanni Covaleda
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular , Universitat Autònoma de Barcelona , Bellaterra, 08193 Barcelona , Spain
| | - Pablo Gallego
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular , Universitat Autònoma de Barcelona , Bellaterra, 08193 Barcelona , Spain
| | - Josep Vendrell
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular , Universitat Autònoma de Barcelona , Bellaterra, 08193 Barcelona , Spain
| | - Dimitris Georgiadis
- Department of Chemistry, Laboratory of Organic Chemistry , University of Athens , Panepistimiopolis Zografou, 15771 Athens , Greece
| | - Julia Lorenzo
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular , Universitat Autònoma de Barcelona , Bellaterra, 08193 Barcelona , Spain
| | - Vincent Dive
- CEA, Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Université Paris-Saclay , Gif-sur-Yvette 91190 , France
| | - Francesc Xavier Aviles
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular , Universitat Autònoma de Barcelona , Bellaterra, 08193 Barcelona , Spain
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i de Biologia Molecular , Universitat Autònoma de Barcelona , Bellaterra, 08193 Barcelona , Spain
| | - Laurent Devel
- CEA, Institut des Sciences du Vivant Frédéric Joliot, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO) , Université Paris-Saclay , Gif-sur-Yvette 91190 , France
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6
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Bogdanović X, Palm GJ, Schwenteit J, Singh RK, Gudmundsdóttir BK, Hinrichs W. Structural evidence of intramolecular propeptide inhibition of the aspzincin metalloendopeptidase AsaP1. FEBS Lett 2016; 590:3280-94. [DOI: 10.1002/1873-3468.12356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 08/03/2016] [Accepted: 08/05/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Xenia Bogdanović
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
- Institute for Biochemistry and Molecular Biology; ZBMZ; Medical Faculty; University of Freiburg; Freiburg im Breisgau Germany
| | - Gottfried J. Palm
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
| | - Johanna Schwenteit
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
- Institute for Experimental Pathology; University of Iceland, Keldur; Reykjavík Iceland
| | - Rajesh K. Singh
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
| | | | - Winfried Hinrichs
- Department of Molecular Structural Biology; Institute for Biochemistry; University of Greifswald; Germany
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7
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Palermo G, Campomanes P, Cavalli A, Rothlisberger U, De Vivo M. Anandamide Hydrolysis in FAAH Reveals a Dual Strategy for Efficient Enzyme-Assisted Amide Bond Cleavage via Nitrogen Inversion. J Phys Chem B 2014; 119:789-801. [DOI: 10.1021/jp5052276] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Giulia Palermo
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Pablo Campomanes
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne
(EPFL), CH-1015 Lausanne, Switzerland
| | - Andrea Cavalli
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Institute of Chemical
Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne
(EPFL), CH-1015 Lausanne, Switzerland
| | - Marco De Vivo
- Department
of Drug Discovery and Development, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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8
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Bolia A, Gerek ZN, Ozkan SB. BP-Dock: a flexible docking scheme for exploring protein-ligand interactions based on unbound structures. J Chem Inf Model 2014; 54:913-25. [PMID: 24380381 DOI: 10.1021/ci4004927] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular docking serves as an important tool in modeling protein-ligand interactions. However, it is still challenging to incorporate overall receptor flexibility, especially backbone flexibility, in docking due to the large conformational space that needs to be sampled. To overcome this problem, we developed a novel flexible docking approach, BP-Dock (Backbone Perturbation-Dock) that can integrate both backbone and side chain conformational changes induced by ligand binding through a multi-scale approach. In the BP-Dock method, we mimic the nature of binding-induced events as a first-order approximation by perturbing the residues along the protein chain with a small Brownian kick one at a time. The response fluctuation profile of the chain upon these perturbations is computed using the perturbation response scanning method. These response fluctuation profiles are then used to generate binding-induced multiple receptor conformations for ensemble docking. To evaluate the performance of BP-Dock, we applied our approach on a large and diverse data set using unbound structures as receptors. We also compared the BP-Dock results with bound and unbound docking, where overall receptor flexibility was not taken into account. Our results highlight the importance of modeling backbone flexibility in docking for recapitulating the experimental binding affinities, especially when an unbound structure is used. With BP-Dock, we can generate a wide range of binding site conformations realized in nature even in the absence of a ligand that can help us to improve the accuracy of unbound docking. We expect that our fast and efficient flexible docking approach may further aid in our understanding of protein-ligand interactions as well as virtual screening of novel targets for rational drug design.
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Affiliation(s)
- Ashini Bolia
- Center for Biological Physics, Department of Physics, Arizona State University , Tempe, Arizona 85287, United States
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9
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Fujimoto Z, Kimura K. Crystal structure of bacteriophage ϕNIT1 zinc peptidase PghP that hydrolyzes γ-glutamyl linkage of bacterial poly-γ-glutamate. Proteins 2011; 80:722-32. [PMID: 22105902 DOI: 10.1002/prot.23229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 10/07/2011] [Accepted: 10/17/2011] [Indexed: 11/12/2022]
Abstract
Poly-γ-glutamate hydrolase P (PghP) of Bacillus subtilis bacteriophage ΦNIT1 hydrolyzes the γ-glutamyl peptide linkage of extracellular poly-γ-glutamate produced by bacilli, which facilitates infection and propagation of phage progenies. Crystal structure of PghP was determined at a resolution of 1.9 Å. Structure of PghP was elucidated as a globular protein with an open α/β mixed core structure and a seven-stranded parallel/anti-parallel β-sheet. The β-sheet contained a core four-stranded parallel β-sheet. A zinc-binding motif, His-Glu-His, was identified at the C-terminal end of the β-sheet. Structure analysis demonstrated that PghP, which had not been previously classified into any peptidase/protease family due to lack of amino acid sequence similarity with known enzymes, had a catalytic center containing a zinc ion and an overall topology resembling mammalian carboxypeptidase A and related enzymes. Structural comparisons indicated important amino acid residues of PghP for catalysis and recognition of the γ-peptide bond of poly-γ-glutamate, which was confirmed by site-directed mutagenesis of PghP.
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Affiliation(s)
- Zui Fujimoto
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
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10
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Shushanyan M, Khoshtariya DE, Tretyakova T, Makharadze M, van Eldik R. Diverse role of conformational dynamics in carboxypeptidase A-driven peptide and ester hydrolyses: Disclosing the “Perfect Induced Fit” and “Protein Local Unfolding” pathways by altering protein stability. Biopolymers 2011; 95:852-70. [DOI: 10.1002/bip.21688] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 06/05/2011] [Indexed: 11/11/2022]
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12
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Fernández D, Pallarès I, Vendrell J, Avilés FX. Progress in metallocarboxypeptidases and their small molecular weight inhibitors. Biochimie 2010; 92:1484-500. [PMID: 20466032 DOI: 10.1016/j.biochi.2010.05.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 05/04/2010] [Indexed: 01/11/2023]
Abstract
In what corresponds to a life span, metallocarboxypeptidases (MCPs) have jumped from being mere contaminants in animal pancreas powders (in depression year 1929) to be key players in cellular and molecular processes (in yet-another-depression years 2009-2010). MCPs are unique zinc-dependent enzymes that catalyze the breakdown of the amide bond at the C-terminus of peptide and protein substrates and participate in the recovery of dietary amino acids, tissue organogenesis, neurohormone and cytokine maturation and other important physiological processes. More than 26 genes code for MCPs in the human genome, many of them still waiting to be fully understood in terms of physiological function. A variety of MCPs have been linked to diseases in man: acute pancreatitis and pancreas cancer, type 2 diabetes, Alzheimer's Disease, various types of cancer, and fibrinolysis and inflammation. Many of these discoveries have been made possible thanks to recent advances, as exemplified by plasma carboxypeptidases N and B, known for fifty and twenty years, respectively, which have had their structures released only very recently. Plasma carboxypeptidase B is a biological target for therapy because of its involvement in the coagulation/fibrinolysis processes. Besides, the widespread use of carboxypeptidase A as a benchmark metalloprotease since the early days of Biochemistry has allowed the identification and design of an increasingly vast repertory of small molecular weight inhibitors. With these two examples we wish to emphasize that MCPs have become part of the drug discovery portfolio of pharmaceutical companies and academic research laboratories. This paper will review key developments in the discovery and design of MCP small molecular weight inhibitors, with an emphasis on the discovery of chemically diverse entities. Although encouraging advances have been achieved in the last few years, the specificity and oral bioavailability of the new chemotherapeutic agents seem to pose a challenge to medicinal chemists.
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Affiliation(s)
- Daniel Fernández
- Departament de Bioquímica i Biologia Molecular, Facultat de Biociències and Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
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13
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Li X, Liu Z, Li Y, Li J, Li J, Wang R. A Statistical Survey on the Binding Constants of Covalently Bound Protein-Ligand Complexes. Mol Inform 2010; 29:87-96. [DOI: 10.1002/minf.200900003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2009] [Accepted: 12/15/2009] [Indexed: 11/07/2022]
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14
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Cleland W. The low-barrier hydrogen bond in enzymic catalysis. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2010. [DOI: 10.1016/s0065-3160(08)44001-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Pícha J, Buděšínský M, Hančlová I, Šanda M, Fiedler P, Vaněk V, Jiráček J. Efficient synthesis of phosphonodepsipeptides derived from norleucine. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.05.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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Shin W, Hyun SA, Chae CH, Chon JK. Flexible Alignment of Small Molecules Using the Penalty Method. J Chem Inf Model 2009; 49:1879-88. [DOI: 10.1021/ci8004463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Whanchul Shin
- Department of Chemistry and Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea, and Korea Research Institute of Chemical Technology, Yuseong-Gu, Daejeon 305-600, Korea
| | - Seung Ah Hyun
- Department of Chemistry and Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea, and Korea Research Institute of Chemical Technology, Yuseong-Gu, Daejeon 305-600, Korea
| | - Chong Hak Chae
- Department of Chemistry and Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea, and Korea Research Institute of Chemical Technology, Yuseong-Gu, Daejeon 305-600, Korea
| | - Jae Kyung Chon
- Department of Chemistry and Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea, and Korea Research Institute of Chemical Technology, Yuseong-Gu, Daejeon 305-600, Korea
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17
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Deng X, Gujjar R, El Mazouni F, Kaminsky W, Malmquist NA, Goldsmith EJ, Rathod PK, Phillips MA. Structural plasticity of malaria dihydroorotate dehydrogenase allows selective binding of diverse chemical scaffolds. J Biol Chem 2009; 284:26999-7009. [PMID: 19640844 DOI: 10.1074/jbc.m109.028589] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Malaria remains a major global health burden and current drug therapies are compromised by resistance. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) was validated as a new drug target through the identification of potent and selective triazolopyrimidine-based DHODH inhibitors with anti-malarial activity in vivo. Here we report x-ray structure determination of PfDHODH bound to three inhibitors from this series, representing the first of the enzyme bound to malaria specific inhibitors. We demonstrate that conformational flexibility results in an unexpected binding mode identifying a new hydrophobic pocket on the enzyme. Importantly this plasticity allows PfDHODH to bind inhibitors from different chemical classes and to accommodate inhibitor modifications during lead optimization, increasing the value of PfDHODH as a drug target. A second discovery, based on small molecule crystallography, is that the triazolopyrimidines populate a resonance form that promotes charge separation. These intrinsic dipoles allow formation of energetically favorable H-bond interactions with the enzyme. The importance of delocalization to binding affinity was supported by site-directed mutagenesis and the demonstration that triazolopyrimidine analogs that lack this intrinsic dipole are inactive. Finally, the PfDHODH-triazolopyrimidine bound structures provide considerable new insight into species-selective inhibitor binding in this enzyme family. Together, these studies will directly impact efforts to exploit PfDHODH for the development of anti-malarial chemotherapy.
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Affiliation(s)
- Xiaoyi Deng
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9041, USA
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Walther T, Renner S, Waldmann H, Arndt HD. Synthesis and structure-activity correlation of a brunsvicamide-inspired cyclopeptide collection. Chembiochem 2009; 10:1153-62. [PMID: 19360807 DOI: 10.1002/cbic.200900035] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cyanobacterial cyclopeptides: A series of analogues of the cyanobacterial cyclopeptide brunsvicamide A was prepared by effective solid-support-based total synthesis. Variations in stereochemistry revealed the importance of the D-lysine and the L-isoleucine residues for the substrate-competitive inhibitory activity of brunsvicamide A against carboxypeptidase A. The brunsvicamides are modified cyclopeptides from cyanobacteria, cyclised through the epsilon-amino group of a D-lysine unit. They are functionalised with urea groups and show potent carboxypeptidase inhibitory activities. In order to unravel the structural parameters that determine their activities, a collection of brunsvicamide analogues with varied amino acid structures and stereochemistries was synthesised by a combined solution- and solid-phase approach. Biochemical investigation of the compound collection for carboxypeptidase A inhibition revealed that the presence of D-lysine and L-isoleucine in the urea section is important for inhibition. It was found that brunsvicamide A is a substrate-competitive inhibitor of carboxypeptidase A. These findings are in agreement with the substrate specificity of the enzyme and were rationalised by computational studies, which showed the high relevance of the lysine stereochemistry for inhibitory activity.
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Affiliation(s)
- Thilo Walther
- Technische Universität Dortmund, Fakultät Chemie, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
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19
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Szeto MW, Mujika JI, Zurek J, Mulholland AJ, Harvey JN. QM/MM study on the mechanism of peptide hydrolysis by carboxypeptidase A. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.06.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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21
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Grishin AM, Akparov VK, Chestukhina GG. Leu254 residue and calcium ions as new structural determinants of carboxypeptidase T substrate specificity. BIOCHEMISTRY (MOSCOW) 2008; 73:1140-5. [DOI: 10.1134/s0006297908100118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Niemirowicz G, Fernández D, Solà M, Cazzulo JJ, Avilés FX, Gomis-Rüth FX. The molecular analysis of Trypanosoma cruzi metallocarboxypeptidase 1 provides insight into fold and substrate specificity. Mol Microbiol 2008; 70:853-66. [PMID: 18793339 DOI: 10.1111/j.1365-2958.2008.06444.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Trypanosoma cruzi is the aetiological agent of Chagas' disease, a chronic infection that affects millions in Central and South America. Proteolytic enzymes are involved in the development and progression of this disease and two metallocarboxypeptidases, isolated from T. cruzi CL Brener clone, have recently been characterized: TcMCP-1 and TcMCP-2. Although both are cytosolic and closely related in sequence, they display different temporary expression patterns and substrate preferences. TcMCP-1 removes basic C-terminal residues, whereas TcMCP-2 prefers hydrophobic/aromatic residues. Here we report the three-dimensional structure of TcMCP-1. It resembles an elongated cowry, with a long, deep, narrow active-site cleft mimicking the aperture. It has an N-terminal dimerization subdomain, involved in a homodimeric catalytically active quaternary structure arrangement, and a proteolytic subdomain partitioned by the cleft into an upper and a lower moiety. The cleft accommodates a catalytic metal ion, most likely a cobalt, which is co-ordinated by residues included in a characteristic zinc-binding sequence, HEXXH and a downstream glutamate. The structure of TcMCP-1 shows strong topological similarity with archaeal, bacterial and mammalian metallopeptidases including angiotensin-converting enzyme, neurolysin and thimet oligopeptidase. A crucial residue for shaping the S(1') pocket in TcMCP-1, Met-304, was mutated to the respective residue in TcMCP-2, an arginine, leading to a TcMCP-1 variant with TcMCP-2 specificity. The present studies pave the way for a better understanding of a potential target in Chagas' disease at the molecular level and provide a template for the design of novel therapeutic approaches.
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Affiliation(s)
- Gabriela Niemirowicz
- Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de General San Martín-CONICET, Avenida General Paz 5445, AR-1650 San Martín, Buenos Aires, Argentina
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Ilter EE, Kiliç Z. C-bis-pivot lariat ethers: synthesis and spectral investigations on new 15- and 17-membered coronands containing dimethoxyphosphoryl groups. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2008; 70:542-9. [PMID: 17851122 DOI: 10.1016/j.saa.2007.07.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Revised: 07/26/2007] [Accepted: 07/31/2007] [Indexed: 05/17/2023]
Abstract
The reactions of dibenzo-diaza crown ethers (coronands) (1 and 2) with dimethylphosphite led to the formation of the mixture of meso and racemic C-bis-pivot lariat ethers (3 and 4) containing dimethoxyphosphoryl groups. We have failed to make the resolution of the mixture, nevertheless, the detailed characterization and spectral investigations of compounds 3 and 4 have been made by elemental analyses, FTIR, (1)H NMR, (13)C NMR, (31)P NMR, COSY, DEPT, HETCOR and HMBC spectral data. The salient features of the spectral data of these compounds have been presented.
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Affiliation(s)
- Elif Ece Ilter
- Department of Chemistry, Faculty of Science, Ankara University, 06100 Tandoğan, Ankara, Turkey
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24
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Grishin A, Akparov V, Chestukhina G. Structural principles of the broad substrate specificity of Thermoactinomyces vulgaris carboxypeptidase T--role of amino acid residues at positions 260 and 262. Protein Eng Des Sel 2008; 21:545-51. [DOI: 10.1093/protein/gzn031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Fernández D, Illa O, Avilés FX, Branchadell V, Vendrell J, Ortuño RM. Thioxophosphoranyl aryl- and heteroaryloxiranes as the representants of a new class of metallocarboxypeptidase inhibitors. Bioorg Med Chem 2008; 16:4823-8. [DOI: 10.1016/j.bmc.2008.03.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 03/12/2008] [Accepted: 03/20/2008] [Indexed: 11/30/2022]
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26
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27
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28
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Seebeck B, Reulecke I, Kämper A, Rarey M. Modeling of metal interaction geometries for protein-ligand docking. Proteins 2007; 71:1237-54. [DOI: 10.1002/prot.21818] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Miao Z, Zhang J, Cui Z, Wang B, Chen R. Synthesis and Structure ofO,O-DiethylN-[(trans-4-Aryl-5,5-dimethyl-2-oxido-2λ5-1,3,2-dioxaphosphorinan-2-yl)methyl]phosphoramidothioates. Helv Chim Acta 2007. [DOI: 10.1002/hlca.200790201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Hershfield JR, Pattabiraman N, Madhavarao CN, Namboodiri MA. Mutational analysis of aspartoacylase: implications for Canavan disease. Brain Res 2007; 1148:1-14. [PMID: 17391648 PMCID: PMC1933483 DOI: 10.1016/j.brainres.2007.02.069] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Revised: 02/07/2007] [Accepted: 02/11/2007] [Indexed: 11/18/2022]
Abstract
Mutations that result in near undetectable activity of aspartoacylase, which catalyzes the deacetylation of N-acetyl-l-aspartate, correlate with Canavan Disease, a neurodegenerative disorder usually fatal during childhood. The underlying biochemical mechanisms of how these mutations ablate activity are poorly understood. Therefore, we developed and tested a three-dimensional homology model of aspartoacylase based on zinc dependent carboxypeptidase A. Mutations of the putative zinc-binding residues (H21G, E24D/G, and H116G), the general proton donor (E178A), and mutants designed to switch the order of the zinc-binding residues (H21E/E24H and E24H/H116E) yielded wild-type aspartoacylase protein levels and undetectable ASPA activity. Mutations that affect substrate carboxyl binding (R71N) and transition state stabilization (R63N) also yielded wild-type aspartoacylase protein levels and undetectable aspartoacylase activity. Alanine substitutions of Cys124 and Cys152, residues indicated by homology modeling to be in close proximity and in the proper orientation for disulfide bonding, yielded reduced ASPA protein and activity levels. Finally, expression of several previously tested (E24G, D68A, C152W, E214X, D249V, E285A, and A305E) and untested (H21P, A57T, I143T, P183H, M195R, K213E/G274R, G274R, and F295S) Canavan Disease mutations resulted in undetectable enzyme activity, and only E285A and P183H showed wild-type aspartoacylase protein levels. These results show that aspartoacylase is a member of the caboxypeptidase A family and offer novel explanations for most loss-of-function aspartoacylase mutations associated with Canavan Disease.
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Affiliation(s)
- Jeremy R. Hershfield
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20814
| | - Nagarajan Pattabiraman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057
| | - Chikkathur N. Madhavarao
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20814
| | - M.A. Aryan Namboodiri
- Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20814
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31
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Kim H, Lipscomb WN. Structure and mechanism of bovine lens leucine aminopeptidase. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 68:153-213. [PMID: 8154324 DOI: 10.1002/9780470123140.ch4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- H Kim
- Gibbs Chemical Laboratory, Harvard University, Cambridge, MA
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32
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Berreau LM. Bioinorganic Chemistry of Group 12 Complexes Supported by Tetradentate Tripodal Ligands Having Internal Hydrogen‐Bond Donors. Eur J Inorg Chem 2006. [DOI: 10.1002/ejic.200500886] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lisa M. Berreau
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT, 84322‐0300, USA, Fax: + 1‐435‐797‐3390
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Cyclen-Containing Inhibitors of Carboxypeptidase A Synthesized in Search of Target-Selective Artificial Proteases. B KOREAN CHEM SOC 2004. [DOI: 10.5012/bkcs.2004.25.11.1703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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34
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Swaminathan S, Eswaramoorthy S, Kumaran D. Structure and enzymatic activity of botulinum neurotoxins. Mov Disord 2004; 19 Suppl 8:S17-22. [PMID: 15027050 DOI: 10.1002/mds.20005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The structure of botulinum neurotoxin type B (BoNT/B) is analyzed, and it is demonstrated that the carbonyl oxygen of the scissile bond comes close to the zinc ion to form a Michaelis complex. The hydrated carbonyl is activated by the nucleophilic water, which moves closer to Glu 230 to form hydrogen bonds to side-chain carboxylate. This process frees up the lone pair, which forms a bond with carbonyl carbon, corresponding to the tetrahedral transition state. The hydrated peptide oxygen is stabilized by a zinc ion and a water molecule close by. The proton from the nucleophile moves to NH of the scissile bond. The other proton is shuttled by Glu 230 to the NH2 group to make it NH3+ and allows it to leave. This mechanism is consistent with that proposed for thermolysin and BoNT/A. On the basis of these studies, we have shown that Tyr372 or Arg369 may not have any significant role in catalytic activity except for a secondary role such as stabilizing the transition state. Thus, the sulfate ion mimics the transition state of the scissile carbonyl carbon atom. However, the sulfate ion by itself does not inhibit the toxicity.
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35
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Hu X, Balaz S, Shelver WH. A practical approach to docking of zinc metalloproteinase inhibitors. J Mol Graph Model 2004; 22:293-307. [PMID: 15177081 DOI: 10.1016/j.jmgm.2003.11.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2003] [Indexed: 10/26/2022]
Abstract
Forty zinc-dependent metalloproteinase/ligand complexes with known crystal structures were re-docked using five docking/scoring approaches (DOCK, FlexX, DrugScore, GOLD, and AutoDock). Correct geometry of the coordination bonds between the ligand's zinc binding group (ZBG) and the catalytic zinc is important for docking accuracy and scoring reliability. More than 75% of docked poses with RMSD less than 2A were found to have appropriate ZBG binding, but for poor ZBG binding, about 95% of poses failed to dock correctly. Elimination of poses with inappropriate zinc binding resulted in better binding energy predictions that were further improved by dividing the ligands into subsets according to the ZBG (carboxylates, hydroxamates, and phosphorus containing groups). After a subset re-scoring using the regression functions obtained for individual subsets, DrugScore was able to explain 77% and the consensus scoring scheme X-CSCORE even 88% of variance in binding energies. The approach combining ZBG-based pose selection and subset re-scoring improved the hit rate in virtual screening for metalloproteinase inhibitors for all tested methods by 4-16%.
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Affiliation(s)
- Xin Hu
- Department of Pharmaceutical Science and the Center for Protease Research, North Dakota State University, Fargo, ND 58105, USA
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36
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Farkas E, Katz Y, Bhusare S, Reich R, Röschenthaler GV, Königsmann M, Breuer E. Carbamoylphosphonate-based matrix metalloproteinase inhibitor metal complexes: solution studies and stability constants. Towards a zinc-selective binding group. J Biol Inorg Chem 2004; 9:307-15. [PMID: 14762707 DOI: 10.1007/s00775-004-0524-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2003] [Accepted: 12/15/2003] [Indexed: 11/25/2022]
Abstract
Overactive matrix metalloproteinases (MMPs) are associated with a variety of disease states. Therefore, their inhibition is a highly desirable goal. Yet, more than a decade of worldwide activity has not produced even one clinically useful inhibitor. Because of the crucial role of zinc in the activity of the enzyme, the design of inhibitors is usually based upon a so-called zinc binding group (ZBG). Yet, many of the hitherto synthesized potent inhibitors failed clinically, presumably because they bind stronger to metals other than zinc. We have developed in vivo potent inhibitors based on the carbamoylphosphonic group as a putative ZBG. In this paper we report stability constants for Ca(II), Mg(II), Zn(II) and Cu(II) complexes of two potent, in vivo active, MMP inhibitors, cyclopentylcarbamoylphosphonic acid (1) and 2-( N, N-dimethylamino)ethylcarbamoylphosphonic acid (2). Precipitation prevented the determination of stability constants for iron(III) complexes of1 and2. For comparison with carbamoylphosphonates1 and2, we synthesized 2-cyclohexyl-1,1-difluoroethylphosphonic acid (3), which does not inhibit MMP, and determined the stability constants of its complexes with Mg(II), Ca(II) and Zn(II). Comparison with the values obtained from the complexes of1 and2 with those from3 indicates participation of the C=O group in the metal binding of the former compounds. The complex stability orders for both1 and2 are Ca(II)<Mg(II)<Zn(II)<Cu(II). In addition, the results indicate that at pH>8 the dimethylamino group of compound2 can also participate in the binding of the transition metals Cu and Zn. On the other hand, the amino group in carbamoylphosphonic acid2 lowers the stability of the complexes with metals favoring oxygen ligands (Ca, Mg and Fe) and increases the selectivity towards Zn. These results are helpful for rationalizing the results observed on our MMP inhibitors hitherto examined, and are expected to be useful for the design of new selective inhibitors.
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Affiliation(s)
- Etelka Farkas
- Department of Inorganic and Analytical Chemistry, University of Debrecen, 4010, Debrecen, Hungary.
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37
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Matczak-Jon E, Kurzak B, Sawka-Dobrowolska W. Crystal structures, solution conformations and zinc(II) complex-forming abilities of two uncommon phosphonic derivatives of glutamic acid. J Mol Struct 2004. [DOI: 10.1016/j.molstruc.2003.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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38
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Carauta ANM, de Souza V, Hollauer E, Téllez S CA. Vibrational study of dialkylphosphonates: di-n-propyl- and di-i-propylphosphonates by semiempirical and ab initio methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2004; 60:41-51. [PMID: 14670460 DOI: 10.1016/s1386-1425(03)00215-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Fourier transform infrared and Fourier transform Raman spectra of n-C(3)H(7) and i-C(3)H(7) dialkylphosphonates have been obtained. Semiempirical AM1 and the ab initio orbital molecular RHF/6-31G* theories have been used to study the molecular geometry, and the harmonic vibrational spectra with the purpose to assist the experimental assignments of these compounds. An extensive discussion on the assignment of the C-C, C-O, P-O and P=O stretching is carried out based on experimental data of compounds which have the propyl and isopropyl groups, as well as comparing the vibrational spectra of propane. Most of the RHF/6-31G* and AM1 results, once applied the appropriate scaling factor, showed an excellent agreement with the experimental wavenumbers. A few calculated frequencies related to CC and CO stretching do not agree well with the experimental trends.
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Affiliation(s)
- Alexandre N M Carauta
- Instituto de Química, Departamento de Química Geral e Inorgânica, Universidade Federal Fluminense (UFF), Morro do Valonguinho s/n, Niterói-Centro, Cep: 24210-150, RJ, Rio de Janeiro, Brazil
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Rivas JCM, Salvagni E, de Rosales RTM, Parsons S. Internal hydrogen bonding in tetrahedral and trigonal bipyramidal zinc(ii) complexes of pyridine-based ligands. Dalton Trans 2003. [DOI: 10.1039/b305476b] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Mareque Rivas JC, Torres Martín de Rosales R, Parsons S. Internal hydrogen bonding and amide co-ordination in zinc(ii) complexes of a tripodal N4 ligand: structural, spectroscopic and reactivity studies. Dalton Trans 2003. [DOI: 10.1039/b301651j] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Lowther WT, Matthews BW. Metalloaminopeptidases: common functional themes in disparate structural surroundings. Chem Rev 2002; 102:4581-608. [PMID: 12475202 DOI: 10.1021/cr0101757] [Citation(s) in RCA: 260] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- W Todd Lowther
- Institute of Molecular Biology, Howard Hughes Medical Institute and Department of Physics, 1229 University of Oregon, Eugene, Oregon 97403-1229, USA
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42
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Wouters MA, Husain A. Changes in zinc ligation promote remodeling of the active site in the zinc hydrolase superfamily. J Mol Biol 2001; 314:1191-207. [PMID: 11743734 DOI: 10.1006/jmbi.2000.5161] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The zinc hydrolase superfamily is a group of divergently related proteins that are predominantly enzymes with a zinc-based catalytic mechanism. The common structural scaffold of the superfamily consists of an eight-stranded beta-sheet flanked by six alpha-helices. Previous analyses, while acknowledging the likely divergent origins of leucine aminopeptidase, carboxypeptidase A and the co-catalytic enzymes of the metallopeptidase H clan based on their structural scaffolds, have failed to find any homology between the active sites in leucine aminopeptidase and the metallopeptidase H clan enzymes. Here we show that these two groups of co-catalytic enzymes have overlapping dizinc centers where one of the two zinc atoms is conserved in each group. Carboxypeptidase A and leucine aminopeptidase, on the other hand, no longer share any homologous zinc-binding sites. At least three catalytic zinc-binding sites have existed in the structural scaffold over the period of history defined by available structures. Comparison of enzyme-inhibitor complexes show that major remodeling of the substrate-binding site has occurred in association with each change in zinc ligation in the binding site. These changes involve re-registration and re-orientation of the substrate. Some residues important to the catalytic mechanism are not conserved amongst members. We discuss how molecules acting in trans may have facilitated the mutation of catalytically important residues in the active site in this group.
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Affiliation(s)
- M A Wouters
- Enzyme Research Unit, Victor Chang Cardiac Research Institute, Sydney, NSW 2010, Australia.
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43
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Katz BA, Elrod K, Luong C, Rice MJ, Mackman RL, Sprengeler PA, Spencer J, Hataye J, Janc J, Link J, Litvak J, Rai R, Rice K, Sideris S, Verner E, Young W. A novel serine protease inhibition motif involving a multi-centered short hydrogen bonding network at the active site. J Mol Biol 2001; 307:1451-86. [PMID: 11292354 DOI: 10.1006/jmbi.2001.4516] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe a new serine protease inhibition motif in which binding is mediated by a cluster of very short hydrogen bonds (<2.3 A) at the active site. This protease-inhibitor binding paradigm is observed at high resolution in a large set of crystal structures of trypsin, thrombin, and urokinase-type plasminogen activator (uPA) bound with a series of small molecule inhibitors (2-(2-phenol)indoles and 2-(2-phenol)benzimidazoles). In each complex there are eight enzyme-inhibitor or enzyme-water-inhibitor hydrogen bonds at the active site, three of which are very short. These short hydrogen bonds connect a triangle of oxygen atoms comprising O(gamma)(Ser195), a water molecule co-bound in the oxyanion hole (H(2)O(oxy)), and the phenolate oxygen atom of the inhibitor (O6'). Two of the other hydrogen bonds between the inhibitor and active site of the trypsin and uPA complexes become short in the thrombin counterparts, extending the three-centered short hydrogen-bonding array into a tetrahedral array of atoms (three oxygen and one nitrogen) involved in short hydrogen bonds. In the uPA complexes, the extensive hydrogen-bonding interactions at the active site prevent the inhibitor S1 amidine from forming direct hydrogen bonds with Asp189 because the S1 site is deeper in uPA than in trypsin or thrombin. Ionization equilibria at the active site associated with inhibitor binding are probed through determination and comparison of structures over a wide range of pH (3.5 to 11.4) of thrombin complexes and of trypsin complexes in three different crystal forms. The high-pH trypsin-inhibitor structures suggest that His57 is protonated at pH values as high as 9.5. The pH-dependent inhibition of trypsin, thrombin, uPA and factor Xa by 2-(2-phenol)benzimidazole analogs in which the pK(a) of the phenol group is modulated is shown to be consistent with a binding process involving ionization of both the inhibitor and the enzyme. These data further suggest that the pK(a) of His57 of each protease in the unbound state in solution is about the same, approximately 6.8. By comparing inhibition constants (K(i) values), inhibitor solubilities, inhibitor conformational energies and corresponding structures of short and normal hydrogen bond-mediated complexes, we have estimated the contribution of the short hydrogen bond networks to inhibitor affinity ( approximately 1.7 kcal/mol). The structures and K(i) values associated with the short hydrogen-bonding motif are compared with those corresponding to an alternate, Zn(2+)-mediated inhibition motif at the active site. Structural differences among apo-enzymes, enzyme-inhibitor and enzyme-inhibitor-Zn(2+) complexes are discussed in the context of affinity determinants, selectivity development, and structure-based inhibitor design.
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Affiliation(s)
- B A Katz
- Axys Pharmaceuticals Corporation, 385 Oyster Point Boulevard, Suite 3, South San Francisco, CA, 94080, USA.
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Grembecka J, Sokalski WA, Kafarski P. Computer-aided design and activity prediction of leucine aminopeptidase inhibitors. J Comput Aided Mol Des 2000; 14:531-44. [PMID: 10921770 DOI: 10.1023/a:1008189716955] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The Ligand Design (LUDI) approach has been used in order to design leucine aminopeptidase inhibitors, predict their activity and analyze their interactions with the enzyme. The investigation was based on the crystal structure of bovine lens leucine aminopeptidase (LAP) complexed with its inhibitor--the phosphonic acid analogue of leucine (LeuP). More than 50 potential leucine aminopeptidase inhibitors have been obtained, including the most potent aminophosphonic LAP inhibitors with experimentally known activity, which have been the subject of more detailed studies. A reasonable agreement between theoretical and experimental activities has been obtained for most of the studied inhibitors. Our results confirm that LUDI is a powerful tool for the design of enzyme inhibitors as well as in the prediction of their activity. In addition, for inhibitor-active site interactions dominated by the electrostatic effects it is possible to improve binding energy estimates by using a more accurate description of inhibitor charge distribution.
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Affiliation(s)
- J Grembecka
- Institute of Organic Chemistry, Biochemistry and Biotechnology, Wrocław University of Technology, Poland
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45
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Rahmo A, Fife TH. Inhibition Effects in the Hydrolysis Reactions of Esters and Peptides Catalyzed by Carboxypeptidase A: An Example of Cooperative Binding Effects with a Monomeric Enzyme. Bioorg Chem 2000; 28:226-241. [PMID: 11034784 DOI: 10.1006/bioo.2000.1161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
N-benzoyl-L-phenylalanyl-L-phenylalanine is an excellent peptide substrate for carboxy-peptidase A; at 30 degrees C and pH 7.5, K(m) is 2.6 x 10(-5) M while k(cat) is 177 s(-1) (k(cat)/K(m) = 6.8 x 10(6) M(-1) s(-1)). Indole-3-acetic acid is a noncompetitive or mixed inhibitor towards the peptide and toward hippuryl-L-phenylalanine; plots of E/V vs [Inhibitor] are linear. N-Benzoyl-L-phenylalanine is a competitive inhibitor of peptide hydrolysis, and plots of E/V vs [Inhibitor] are again linear. One molecule of inhibitor binds per active site, and these inhibitors bind in different sites. At constant peptide substrate concentration and a series of constant concentrations of indole-3-acetic acid, plots of E/V vs the concentration of N-benzoyl-L-phenylalanine are linear and intersect behind the E/V axis and above the [Inhibitor] axis. This shows that both inhibitors can bind simultaneously and that binding of one facilitates the binding of the other (beta = 0.18). Employing the ester substrate hippuryl-DL,beta-phenyllactate, the same type of behavior is observed in the reverse sense; N-benzoyl-L-phenylalanine is a linear noncompetitive inhibitor and indole-3-acetic acid is a linear competitive inhibitor. Again the two inhibitor plot is linear and intersects above the [Inhibitor] axis (beta = 0.12). Previous X-ray crystallographic studies have indicated that indole-3-acetic acid binds in the hydrophobic pocket of the S'(1) site, while N-benzoyl-L-phenylalanine binds in the S(1)-S(2) site. The product complex for hydrolysis of N-benzoyl-L-phenylalanyl-L-phenylalanine (phenylalanine + N-benzoyl-L-phenylalanine) occupies both of these sites. However, the present work shows that the peptide substrate does not bind to the enzyme at pH 7.5 so as to be competitive with indole-3-acetic acid. The binding sites may be formed via conformational changes induced or stabilized by substrate and product binding. Copyright 2000 Academic Press.
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Affiliation(s)
- A Rahmo
- Department of Biochemistry, University of Southern California, Los Angeles, California
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46
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Vendrell J, Querol E, Avilés FX. Metallocarboxypeptidases and their protein inhibitors. Structure, function and biomedical properties. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1477:284-98. [PMID: 10708864 DOI: 10.1016/s0167-4838(99)00280-0] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Among the different aspects of recent progress in the field of metallocarboxypeptidases has been the elucidation of the three dimensional structures of the pro-segments (in monomeric or oligomeric species) and their role in the expression, folding and inhibition/activation of the pancreatic and pancreatic-like forms. Also of great significance has been the cloning and characterization of several new regulatory carboxypeptidases, enzymes that are related with important functions in protein and peptide processing and that show significant structural differences among them and also with the digestive ones. Many regulatory carboxypeptidases lack a pro-region, unlike the digestive forms or others in between from the evolutionary point of view. Finally, important advances have been made on the finding and characterization of new protein inhibitors of metallocarboxypeptidases, some of them with interesting potential applications in the biotechnological/biomedical fields. These advances are analyzed here and compared with the earlier observations in this field, which was first explored by Hans Neurath and collaborators.
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Affiliation(s)
- J Vendrell
- Departament de Bioquímica i Biologia Molecular, Facultat de Ciències, and Institut de Biologia Fonamental. Universitat Autònoma de Barcelona, E-08193, Bellaterra, Spain
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47
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Searching for the Lowest Energy Conformation of Substrates in the Carboxypeptidase A Active Site Using Monte Carlo/Energy Minimization Techniques. Bioorg Chem 1998. [DOI: 10.1006/bioo.1998.1118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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48
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Böhm HJ. Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs. J Comput Aided Mol Des 1998; 12:309-23. [PMID: 9777490 DOI: 10.1023/a:1007999920146] [Citation(s) in RCA: 352] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A dataset of 82 protein-ligand complexes of known 3D structure and binding constant Ki was analysed to elucidate the important factors that determine the strength of protein-ligand interactions. The following parameters were investigated: the number and geometry of hydrogen bonds and ionic interactions between the protein and the ligand, the size of the lipophilic contact surface, the flexibility of the ligand, the electrostatic potential in the binding site, water molecules in the binding site, cavities along the protein-ligand interface and specific interactions between aromatic rings. Based on these parameters, a new empirical scoring function is presented that estimates the free energy of binding for a protein-ligand complex of known 3D structure. The function distinguishes between buried and solvent accessible hydrogen bonds. It tolerates deviations in the hydrogen bond geometry of up to 0.25 A in the length and up to 30 degrees in the hydrogen bond angle without penalizing the score. The new energy function reproduces the binding constants (ranging from 3.7 x 10(-2) M to 1 x 10(-14) M, corresponding to binding energies between -8 and -80 kJ/mol) of the dataset with a standard deviation of 7.3 kJ/mol corresponding to 1.3 orders of magnitude in binding affinity. The function can be evaluated very fast and is therefore also suitable for the application in a 3D database search or de novo ligand design program such as LUDI. The physical significance of the individual contributions is discussed.
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Affiliation(s)
- H J Böhm
- BASF AG, Central Research, Ludwigshafen, Germany
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49
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Toward the development of metal-based synthetic nucleases and peptidases: a rationale and progress report in applying the principles of coordination chemistry. Coord Chem Rev 1998. [DOI: 10.1016/s0010-8545(98)00157-x] [Citation(s) in RCA: 487] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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50
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Khan AR, James MN. Molecular mechanisms for the conversion of zymogens to active proteolytic enzymes. Protein Sci 1998; 7:815-36. [PMID: 9568890 PMCID: PMC2143990 DOI: 10.1002/pro.5560070401] [Citation(s) in RCA: 342] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Proteolytic enzymes are synthesized as inactive precursors, or "zymogens," to prevent unwanted protein degradation, and to enable spatial and temporal regulation of proteolytic activity. Upon sorting or appropriate compartmentalization, zymogen conversion to the active enzyme typically involves limited proteolysis and removal of an "activation segment." The sizes of activation segments range from dipeptide units to independently folding domains comprising more than 100 residues. A common form of the activation segment is an N-terminal extension of the mature enzyme, or "prosegment," that sterically blocks the active site, and thereby prevents binding of substrates. In addition to their inhibitory role, prosegments are frequently important for the folding, stability, and/or intracellular sorting of the zymogen. The mechanisms of conversion to active enzymes are diverse in nature, ranging from enzymatic or nonenzymatic cofactors that trigger activation, to a simple change in pH that results in conversion by an autocatalytic mechanism. Recent X-ray crystallographic studies of zymogens and comparisons with their active counterparts have identified the structural changes that accompany conversion. This review will focus upon the structural basis for inhibition by activation segments, as well as the molecular events that lead to the conversion of zymogens to active enzymes.
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Affiliation(s)
- A R Khan
- Department of Biochemistry, University of Alberta, Edmonton, Canada
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