1
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Sohraby F, Nunes-Alves A. Advances in computational methods for ligand binding kinetics. Trends Biochem Sci 2022; 48:437-449. [PMID: 36566088 DOI: 10.1016/j.tibs.2022.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/16/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
Binding kinetic parameters can be correlated with drug efficacy, which in recent years led to the development of various computational methods for predicting binding kinetic rates and gaining insight into protein-drug binding paths and mechanisms. In this review, we introduce and compare computational methods recently developed and applied to two systems, trypsin-benzamidine and kinase-inhibitor complexes. Methods involving enhanced sampling in molecular dynamics simulations or machine learning can be used not only to predict kinetic rates, but also to reveal factors modulating the duration of residence times, selectivity, and drug resistance to mutations. Methods which require less computational time to make predictions are highlighted, and suggestions to reduce the error of computed kinetic rates are presented.
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Affiliation(s)
- Farzin Sohraby
- Institute of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany
| | - Ariane Nunes-Alves
- Institute of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany.
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2
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Leader DP, Milner-White EJ. The β-link motif in protein architecture. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1040-1049. [PMID: 34342277 DOI: 10.1107/s2059798321006768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/29/2021] [Indexed: 11/10/2022]
Abstract
The β-link is a composite protein motif consisting of a G1β β-bulge and a type II β-turn, and is generally found at the end of two adjacent strands of antiparallel β-sheet. The 1,2-positions of the β-bulge are also the 3,4-positions of the β-turn, with the result that the N-terminal portion of the polypeptide chain is orientated at right angles to the β-sheet. Here, it is reported that the β-link is frequently found in certain protein folds of the SCOPe structural classification at specific locations where it connects a β-sheet to another area of a protein. It is found at locations where it connects one β-sheet to another in the β-sandwich and related structures, and in small (four-, five- or six-stranded) β-barrels, where it connects two β-strands through the polypeptide chain that crosses an open end of the barrel. It is not found in larger (eight-stranded or more) β-barrels that are straightforward β-meanders. In some cases it initiates a connection between a single β-sheet and an α-helix. The β-link also provides a framework for catalysis in serine proteases, where the catalytic serine is part of a conserved β-link, and in cysteine proteases, including Mpro of human SARS-CoV-2, in which two residues of the active site are located in a conserved β-link.
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Affiliation(s)
- David P Leader
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - E James Milner-White
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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3
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Carretas-Valdez MI, Moreno-Cordova EN, Ibarra-Hernandez BG, Cinco-Moroyoqui FJ, Castillo-Yañez FJ, Casas-Flores S, Osuna-Amarillas PS, Islas-Osuna MA, Arvizu-Flores AA. Characterization of the trypsin-III from Monterey sardine (Sardinops caeruleus): Insights on the cold-adaptation from the A236N mutant. Int J Biol Macromol 2020; 164:2701-2710. [PMID: 32827617 DOI: 10.1016/j.ijbiomac.2020.08.136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023]
Abstract
Trypsins (E.C. 3.4.21.4) are digestive enzymes that catalyze the hydrolysis of peptide bonds containing arginine and lysine residues. Some trypsins from fish species are active at temperatures just above freezing, and for that are called cold-adapted enzymes, having many biotechnological applications. In this work, we characterized a recombinant trypsin-III from Monterey sardine (Sardinops caeruleus) and studied the role of a single residue on its cold-adapted features. The A236N mutant from sardine trypsin-III showed higher activation energy for the enzyme-catalyzed reaction, it was more active at higher temperatures, and exhibited a higher thermal stability than the wild-type enzyme, suggesting a key role of this residue. The thermodynamic activation parameters revealed an increase in the activation enthalpy for the A236N mutant, suggesting the existence of more intramolecular contacts during the activation step. Molecular models for both enzymes suggest that a hydrogen-bond involving N236 may contact the C-terminal α-helix to the vicinity of the active site, thus affecting the biochemical and thermodynamic properties of the enzyme.
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Affiliation(s)
- Manuel I Carretas-Valdez
- Universidad de Sonora, Departamento de Investigación y Posgrado en Alimentos, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Elena N Moreno-Cordova
- Universidad de Sonora, Departamento de Ciencias Químico-Biológicas, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Brisa G Ibarra-Hernandez
- Universidad de Sonora, Departamento de Investigación y Posgrado en Alimentos, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Francisco J Cinco-Moroyoqui
- Universidad de Sonora, Departamento de Investigación y Posgrado en Alimentos, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Francisco J Castillo-Yañez
- Universidad de Sonora, Departamento de Ciencias Químico-Biológicas, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico
| | - Sergio Casas-Flores
- IPICYT, División de Biología Molecular, Camino a la Presa San José 2055, Col. Lomas 4a sección, San Luis Potosí, San Luis Potosí 78216, Mexico
| | - Pablo S Osuna-Amarillas
- Universidad Estatal de Sonora, Carretera Navojoa-Huatabampo km 5, Navojoa, Sonora 85874, Mexico
| | - Maria A Islas-Osuna
- Centro de Investigación en Alimentación y Desarrollo, Laboratorio de Genética y Biología Molecular de Plantas, Carr. Gustavo Enrique Astiazarán Rosas, N0. 46. Col. La Victoria, Hermosillo, Sonora 83304, Mexico.
| | - Aldo A Arvizu-Flores
- Universidad de Sonora, Departamento de Ciencias Químico-Biológicas, Blvd. Luis Encinas y Blvd. Rosales s/n, Hermosillo, Sonora 83000, Mexico.
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4
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Liu H, Deng J, Luo Z, Lin Y, Merz KM, Zheng Z. Receptor–Ligand Binding Free Energies from a Consecutive Histograms Monte Carlo Sampling Method. J Chem Theory Comput 2020; 16:6645-6655. [DOI: 10.1021/acs.jctc.0c00457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hao Liu
- School of Mechanical and Electronic Engineering, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, PR China
| | - Jianpeng Deng
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, PR China
| | - Zhou Luo
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, PR China
| | - Yawei Lin
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, PR China
| | - Kenneth M. Merz
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Zheng Zheng
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, PR China
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5
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Troelsen NS, Clausen MH. Library Design Strategies To Accelerate Fragment‐Based Drug Discovery. Chemistry 2020; 26:11391-11403. [DOI: 10.1002/chem.202000584] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/26/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Nikolaj S. Troelsen
- Center for Nanomedicine and Theranostics Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
| | - Mads H. Clausen
- Center for Nanomedicine and Theranostics Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kongens Lyngby Denmark
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6
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Xue G, Xie X, Zhou Y, Yuan C, Huang M, Jiang L. Insight to the residue in P2 position prevents the peptide inhibitor from being hydrolyzed by serine proteases. Biosci Biotechnol Biochem 2020; 84:1153-1159. [PMID: 32019421 DOI: 10.1080/09168451.2020.1723405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Peptidic inhibitors of proteases are attracting increasing interest not only as drug candidates but also for studying the function and regulation mechanisms of these enzymes. Previously, we screened out a cyclic peptide inhibitor of human uPA [Formula: see text] and found that Ala substitution of P2 residue turns upain-1 to a substrate. To further investigate the effect of P2 residue on the peptide behavior transformation, we constructed upain-1-W3F, which has Phe replacement in the P2 position. We determined KD and Ki of upain-1-W3F and found that upain-1-W3F might still exist as an inhibitor. Furthermore, the high-resolution crystal structure of upain-1-W3F·uPA reveals that upain-1-W3F indeed stays as an intact inhibitor bind to uPA. We thus propose that the P2 residue plays a nonnegligible role in the conversion of upain-1 to a substrate. These results also proposed a strategy to optimize the pharmacological properties of peptide-based drug candidates by hydrophobicity and steric hindrance.Abbreviations : uPA: urokinase-type plasminogen activator; SPD: serine protease domain; S1 pocket: specific substrate-binding pocket.
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Affiliation(s)
- Guangpu Xue
- College of Chemistry, Fuzhou University, Fuzhou, China.,National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou, China
| | - Xie Xie
- College of Chemistry, Fuzhou University, Fuzhou, China.,National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou, China
| | - Yang Zhou
- College of Chemistry, Fuzhou University, Fuzhou, China.,National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou, China
| | - Cai Yuan
- National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou, China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Mingdong Huang
- College of Chemistry, Fuzhou University, Fuzhou, China.,National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou, China.,College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Longguang Jiang
- College of Chemistry, Fuzhou University, Fuzhou, China.,National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, College of Chemistry, Fuzhou, China
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7
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Giardina SF, Werner DS, Pingle M, Foreman KW, Bergstrom DE, Arnold LD, Barany F. Target-Directed Self-Assembly of Homodimeric Drugs Against β-Tryptase. ACS Med Chem Lett 2018; 9:827-831. [PMID: 30128075 PMCID: PMC6088348 DOI: 10.1021/acsmedchemlett.8b00204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/05/2018] [Indexed: 02/05/2023] Open
Abstract
![]()
Tryptase,
a serine protease released from mast cells, is implicated
in many allergic and inflammatory disorders. Human tryptase is a donut-shaped
tetramer with the active sites facing inward forming a central pore.
Bivalent ligands spanning two active sites potently inhibit this configuration,
but these large compounds have poor drug-like properties. To overcome
some of these challenges, we developed self-assembling molecules,
called coferons, which deliver a larger compound in two parts. Using
a pharmacophoric core and reversibly binding linkers to span two active
sites, we have successfully produced three novel homodimeric tryptase
inhibitors. Upon binding to tryptase, compounds reassembled into flexible
homodimers, with significant improvements in IC50 (0.19
± 0.08 μM) over controls (5.50 ± 0.09 μM), and
demonstrate good activity in mast cell lines. These studies provide
validation for this innovative technology that is especially well-suited
for the delivery of dimeric drugs to modulate intracellular macromolecular
targets.
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Affiliation(s)
- Sarah F. Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States
| | - Douglas S. Werner
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Maneesh Pingle
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Kenneth W. Foreman
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Donald E. Bergstrom
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall, West Lafayette, Indiana 47907, United States
| | - Lee D. Arnold
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States
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8
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Frei P, Pang L, Silbermann M, Eriş D, Mühlethaler T, Schwardt O, Ernst B. Target-directed Dynamic Combinatorial Chemistry: A Study on Potentials and Pitfalls as Exemplified on a Bacterial Target. Chemistry 2017; 23:11570-11577. [PMID: 28654733 DOI: 10.1002/chem.201701601] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Indexed: 12/28/2022]
Abstract
Target-directed dynamic combinatorial chemistry (DCC) is an emerging technique for the efficient identification of inhibitors of pharmacologically relevant targets. In this contribution, we present an application for a bacterial target, the lectin FimH, a crucial virulence factor of uropathogenic E. coli being the main cause of urinary tract infections. A small dynamic library of acylhydrazones was formed from aldehydes and hydrazides and equilibrated at neutral pH in presence of aniline as nucleophilic catalyst. The major success factors turned out to be an accordingly adjusted ratio of scaffolds and fragments, an adequate sample preparation prior to HPLC analysis, and the data processing. Only then did the ranking of the dynamic library constituents correlate well with affinity data. Furthermore, as a support of DCC applications especially to larger libraries, a new protocol for improved hit identification was established.
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Affiliation(s)
- Priska Frei
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Lijuan Pang
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Marleen Silbermann
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Deniz Eriş
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Tobias Mühlethaler
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Oliver Schwardt
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
| | - Beat Ernst
- Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056, Basel, Switzerland
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9
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The versatility of boron in biological target engagement. Nat Chem 2017; 9:731-742. [DOI: 10.1038/nchem.2814] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/12/2017] [Indexed: 12/20/2022]
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10
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Abstract
This review describes available methods for the preparation of α-aminoboronic acids in their racemic or in their enantiopure form. Both, highly stereoselective syntheses and asymmetric procedures leading to the stereocontrolled generation of α-aminoboronic acid derivatives are included. The preparation of acyclic, carbocyclic and azacyclic α-aminoboronic acid derivatives is covered. Within each section, the different synthetic approaches have been classified according to the key bond which is formed to complete the α-aminoboronic acid skeleton.
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Affiliation(s)
- Patricia Andrés
- Departamento de Química Orgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain.
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11
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Jiang L, Andersen LM, Andreasen PA, Chen L, Huang M. Insights into the serine protease mechanism based on structural observations of the conversion of a peptidyl serine protease inhibitor to a substrate. Biochim Biophys Acta Gen Subj 2015; 1860:599-606. [PMID: 26691138 DOI: 10.1016/j.bbagen.2015.12.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 12/02/2015] [Accepted: 12/11/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND Serine proteases are one of the most studied group of enzymes. Despite the extensive mechanistic studies, some crucial details remain controversial, for example, how the cleaved product is released in the catalysis reaction. A cyclic peptidyl inhibitor (CSWRGLENHRMC, upain-1) of a serine protease, urokinase-type plasminogen activator (uPA), was found to become a slow substrate and cleaved slowly upon the replacement of single residue (W3A). METHODS By taking advantage of the unique property of this peptide, we report the high-resolution structures of uPA in complex with upain-1-W3A peptide at four different pH values by X-ray crystallography. RESULTS In the structures obtained at low pH (pH4.6 and 5.5), the cyclic peptide upain-1-W3A was found to be intact and remained in the active site of uPA. At 7.4, the scissile bond of the peptide was found cleaved, showing that the peptide became a uPA substrate. At pH9.0, the C-terminal part of the substrate was no longer visible, and only the P1 residue occupying the S1 pocket was identified. CONCLUSIONS The analysis of these structures provides explanations why the upain-1-W3A is a slow substrate. In addition, we clearly identified the cleaved fragments of the peptide at both sides of the scissile bond in the active site of the enzyme, showing a slow release of the cleaved peptide. GENERAL SIGNIFICANCE This work indicates that the quick release of the cleaved P' fragment after the first step of hydrolysis may not always be needed for the second hydrolysis.
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Affiliation(s)
- Longguang Jiang
- State Key Lab of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yang Qiao West Road, Fuzhou, Fujian 350002, China; Danish-Chinese Centre for Proteases and Cancer, Denmark. http://www.proteasesandcancer.org
| | - Lisbeth Moreau Andersen
- Danish-Chinese Centre for Proteases and Cancer, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000-DK, Denmark. http://www.proteasesandcancer.org
| | - Peter A Andreasen
- Danish-Chinese Centre for Proteases and Cancer, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Aarhus 8000-DK, Denmark. http://www.proteasesandcancer.org
| | - Liqing Chen
- University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Mingdong Huang
- State Key Lab of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yang Qiao West Road, Fuzhou, Fujian 350002, China; Danish-Chinese Centre for Proteases and Cancer, Denmark.
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12
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Synthesis of Pinacolylboronate-Substituted Stilbenes and their application to the synthesis of boron capped polyenes. J Organomet Chem 2015. [DOI: 10.1016/j.jorganchem.2015.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Burke SJ, Gamrat JM, Santhouse JR, Tomares DT, Tomsho JW. Potassium haloalkyltrifluoroborate salts: synthesis, application, and reversible ligand replacement with MIDA. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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14
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Herrmann A. Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures. Chem Soc Rev 2014; 43:1899-933. [PMID: 24296754 DOI: 10.1039/c3cs60336a] [Citation(s) in RCA: 281] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.
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Affiliation(s)
- Andreas Herrmann
- Firmenich SA, Division Recherche et Développement, Route des Jeunes 1, B. P. 239, CH-1211 Genève 8, Switzerland.
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15
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Ermakova E, Kurbanov R. Effect of ligand binding on the dynamics of trypsin. Comparison of different approaches. J Mol Graph Model 2014; 49:99-109. [PMID: 24642055 DOI: 10.1016/j.jmgm.2014.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 02/07/2014] [Accepted: 02/08/2014] [Indexed: 11/17/2022]
Abstract
The intramolecular signal transduction induced by the binding of ligands to trypsin was investigated by molecular dynamics simulations. Ligand binding changes the residue-residue interaction energies and suppresses the mobility of loops that are in direct contact with the ligand. The reduced mobility of these loops results in the altered flexibility of the nearby loops and thereby transmits the information from ligand binding site to the remote sites. The analysis of the flexibility of all residues confirmed the coupling between loops L1 (185-188) and L2 (221-224) and the residues in the active center. The significance of S1 pocket residues for the signal transduction from the active center to the substrate-binding site was confirmed by the dynamical network and covariance matrix analyses. Gaussian network model and principal component analysis demonstrated that the active center residues had zero amplitude in the slowest fluctuations acting as hinges or anchors. Overall, our results provide a new insight into protein-ligand interactions and show how the allosteric signaling may occur.
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Affiliation(s)
- Elena Ermakova
- Kazan Institute of Biochemistry and Biophysics RAS, P.O. Box 30, Kazan 420111, Russia.
| | - Rauf Kurbanov
- Kazan Institute of Biochemistry and Biophysics RAS, P.O. Box 30, Kazan 420111, Russia
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16
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Clevenger KD, Wu R, Er JAV, Liu D, Fast W. Rational design of a transition state analogue with picomolar affinity for Pseudomonas aeruginosa PvdQ, a siderophore biosynthetic enzyme. ACS Chem Biol 2013; 8:2192-200. [PMID: 23883096 DOI: 10.1021/cb400345h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The Pseudomonas aeruginosa enzyme PvdQ can process different substrates involved in quorum-sensing or in siderophore biosynthesis. Substrate selectivity was evaluated using steady-state kinetic constants for hydrolysis of N-acyl-homoserine lactones (HSLs) and p-nitrophenyl fatty acid esters. PvdQ prefers substrates with alkyl chains between 12 and 14 carbons long that do not bear a 3-oxo substitution and is revealed here to have a relatively high specificity constant for selected N-acyl-HSLs (kcat/KM = 10(5) to 10(6) M(-1) s(-1)). However, endogenous P. aeruginosa N-acyl-HSLs are ≥100-fold disfavored, supporting the conclusion that PvdQ was not primarily evolved to regulate endogenous quorum-sensing. PvdQ plays an essential biosynthetic role for the siderophore pyoverdine, on which P. aeruginosa depends for growth in iron-limited environments. A series of alkylboronate inhibitors was found to be reversible, competitive, and extremely potent (Ki ≥ 190 pM). A 1.8 Å X-ray structure shows that 1-tridecylboronic acid forms a monocovalent bond with the N-terminal β-chain Ser residue in the PvdQ heterodimer, mimicking a reaction transition state. This boronic acid inhibits growth of P. aeruginosa in iron-limited media, reproducing the phenotype of a genetic pvdQ disruption, although co-administration of an efflux pump inhibitor is required to maintain growth inhibition. These findings support the strategy of designing boron-based inhibitors of siderophore biosynthetic enzymes to control P. aeruginosa infections.
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Affiliation(s)
| | - Rui Wu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago Illinois 60660,
United States
| | | | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago Illinois 60660,
United States
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17
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Piergies N, Proniewicz E, Kudelski A, Rydzewska A, Kim Y, Andrzejak M, Proniewicz LM. Fourier Transform Infrared and Raman and Surface-Enhanced Raman Spectroscopy Studies of a Novel Group of Boron Analogues of Aminophosphonic Acids. J Phys Chem A 2012; 116:10004-14. [DOI: 10.1021/jp307064p] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Natalia Piergies
- Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow,
Poland
| | - Edyta Proniewicz
- Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow,
Poland
| | - Andrzej Kudelski
- Faculty of Chemistry, University of Warsaw, ul. L. Pasteura 1, 02-093 Warsaw,
Poland
| | - Agata Rydzewska
- Department of Bioorganic
Chemistry,
Faculty of Chemistry, Wrocław University of Technology, Wybrzeże Wyspianskiego 27, 50-370, Wrocław, Poland
| | - Younkyoo Kim
- Department of Chemistry, Hankuk University of Foreign Studies, Yongin, Kyunggi-Do,
449-791, Korea
| | - Marcin Andrzejak
- Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow,
Poland
| | - Leonard M. Proniewicz
- Faculty of Chemistry, Jagiellonian University, ul. Ingardena 3, 30-060 Krakow,
Poland
- The State Higher Vocational School, ul. Mickiewicza 8, 33-100 Tarnów,
Poland
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18
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Conformational dynamics of threonine 195 and the S1 subsite in functional trypsin variants. J Mol Model 2012; 18:4941-54. [DOI: 10.1007/s00894-012-1541-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 07/16/2012] [Indexed: 12/25/2022]
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19
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Gelin M, Poncet-Montange G, Assairi L, Morellato L, Huteau V, Dugué L, Dussurget O, Pochet S, Labesse G. Screening and in situ synthesis using crystals of a NAD kinase lead to a potent antistaphylococcal compound. Structure 2012; 20:1107-17. [PMID: 22608967 DOI: 10.1016/j.str.2012.03.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 03/09/2012] [Accepted: 03/30/2012] [Indexed: 11/18/2022]
Abstract
Making new ligands for a given protein by in situ ligation of building blocks (or fragments) is an attractive method. However, it suffers from inherent limitations, such as the limited number of available chemical reactions and the low information content of usual chemical library deconvolution. Here, we describe a focused screening of adenosine derivatives using X-ray crystallography. We discovered an unexpected and biocompatible chemical reactivity and have simultaneously identified the mode of binding of the resulting products. We observed that the NAD kinase from Listeria monocytogenes (LmNADK1) can promote amide formation between 5'-amino-5'-deoxyadenosine and carboxylic acid groups. This unexpected reactivity allowed us to bridge in situ two adenosine derivatives to fully occupy the active NAD site. This guided the design of a close analog showing micromolar inhibition of two human pathogenic NAD kinases and potent bactericidal activity against Staphylococcus aureus in vitro.
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Affiliation(s)
- Muriel Gelin
- Atelier de Bio- et Chimie Informatique Structurale, Centre de Biochimie Structurale, CNRS, UMR5048, Universités Montpellier 1 et 2, F-34090 Montpellier, France
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20
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Smoum R, Rubinstein A, Dembitsky VM, Srebnik M. Boron containing compounds as protease inhibitors. Chem Rev 2012; 112:4156-220. [PMID: 22519511 DOI: 10.1021/cr608202m] [Citation(s) in RCA: 303] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Reem Smoum
- The School of Pharmacy, Institute for Drug Research, The Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem, Israel.
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21
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Design, synthesis and biological study of pinacolyl boronate-substituted stilbenes as novel lipogenic inhibitors. Bioorg Med Chem Lett 2011; 21:5638-41. [PMID: 21798740 DOI: 10.1016/j.bmcl.2011.05.124] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 05/29/2011] [Accepted: 05/31/2011] [Indexed: 11/20/2022]
Abstract
A pilot library of novel 4,4,5,5-tetramethyl-2-(4-substitutedstyrylphenyl)-1,3,2 dioxaborolane derivatives has been synthesized. 4-(4,4,5,5-Tetramethyl-1,3,2-dioxaboratophenyl)-methyl triphenylphosphonium bromide 3 was treated with various aldehydes in the presence of 3 equiv of (t)BuONa in DMF, and stirred at room temperature for 4-6h to yield the corresponding boron-containing stilbene derivatives in 71-94% yields. Several of them, including BF102 and BF175, have the lipogenesis inhibitory effect by suppressing lipogenic gene expression in mammalian hepatocytes. Further, BF102 also inhibits cholesterol biosynthesis by suppressing HMG-CoA reductase gene expression in hepatocytes. Interestingly, our preliminary in vivo data suggests that BF102 has no significant toxicity in mice at the highest possible dose we can administered. Thus, BF102 is a potential lead for the next generation of lipid-lowering drugs.
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22
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Fleishman SJ, Corn JE, Strauch EM, Whitehead TA, Andre I, Thompson J, Havranek JJ, Das R, Bradley P, Baker D. Rosetta in CAPRI rounds 13-19. Proteins 2011; 78:3212-8. [PMID: 20597089 PMCID: PMC2952713 DOI: 10.1002/prot.22784] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Modeling the conformational changes that occur on binding of macromolecules is an unsolved challenge. In previous rounds of the Critical Assessment of PRediction of Interactions (CAPRI), it was demonstrated that the Rosetta approach to macromolecular modeling could capture side chain conformational changes on binding with high accuracy. In rounds 13-19 we tested the ability of various backbone remodeling strategies to capture the main-chain conformational changes observed during binding events. These approaches span a wide range of backbone motions, from limited refinement of loops to relieve clashes in homologous docking, through extensive remodeling of loop segments, to large-scale remodeling of RNA. Although the results are encouraging, major improvements in sampling and energy evaluation are clearly required for consistent high accuracy modeling. Analysis of our failures in the CAPRI challenges suggest that conformational sampling at the termini of exposed beta strands is a particularly pressing area for improvement.
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Affiliation(s)
- Sarel J Fleishman
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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23
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Huang SY, Zou X. MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19. Proteins 2011; 78:3096-103. [PMID: 20635420 DOI: 10.1002/prot.22797] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A hierarchical approach has been developed for protein-protein docking. In the first step, a Fast Fourier Transform (FFT)-based docking algorithm is used to globally sample all putative binding modes, in which the protein is represented by a reduced model, that is, each side chain on the protein surface is represented by its center of mass. Compared to conventional FFT docking with all-atom models, the FFT docking method with a reduced model is expected to generate more hits because it allows larger side-chain flexibility. Next, the filtered binding modes (normally several thousands) are refined by an iteratively derived knowledge-based scoring function ITScorePP and by considering backbone/loop flexibility using an ensemble docking algorithm. The distance-dependent potentials of ITScorePP were extracted by a physics-based iterative method, which circumvents the long-standing reference state problem in the knowledge-based approaches. With this hierarchical protocol, we have participated in the CAPRI experiments for Rounds 15-19 of 11 targets (T32-T42). In the predictor experiments, we achieved correct binding modes for six targets: three are with high accuracy (T40 for both distinct binding modes, T41, and T42), two are with medium accuracy (T34 and T37), and one is acceptable (T32). In the scorer experiments, of the seven target complexes that contain at least one acceptable mode submitted by the CAPRI predictor groups, we obtained correct binding modes for four targets: three are with high accuracy (T37, T40, and T41) and one is with medium accuracy (T34), suggesting good accuracy and robustness of ITScorePP.
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Affiliation(s)
- Sheng-You Huang
- Department of Physics and Astronomy, Department of Biochemistry, Dalton Cardiovascular Research Center, and Informatics Institute, University of Missouri, Columbia, MO 65211, USA
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24
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Eisenstein M, Ben-Shimon A, Frankenstein Z, Kowalsman N. CAPRI targets T29-T42: proving ground for new docking procedures. Proteins 2011; 78:3174-81. [PMID: 20607697 DOI: 10.1002/prot.22793] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The critical assessment of protein interactions (CAPRI) experiment provides a unique opportunity for unbiased assessment of docking procedures. The recent CAPRI targets T29-T42 entailed docking of bound, unbound, and modeled structures, presenting a wide range of prediction difficulty. We submitted accurate predictions for targets T40, T41, and T42, a good prediction for T32 and acceptable predictions for T29 and T34. The accuracy of our docking results generally matched the prediction difficulty; hence, docking of modeled proteins produced less accurate results. However, there were interesting exceptions: an accurate prediction was submitted for the dimer of modeled tetratricopeptide repeat (T42) and only an acceptable prediction for the bound/unbound case T29. The ensembles of docking models produced in the scans included an acceptable or better prediction for every target. We show here that our recently developed postscan reevaluation procedure, which tests propensity and solvation measures of the whole interface and the interface core, successfully distinguished these predictions from false docking models. For enzyme-inhibitor targets, we show that the distance of the interface from the enzyme's centroid ranked high native like docking models. Also, for one case we demonstrate that docking of an ensemble of conformers produced by normal modes analysis can improve the accuracy of the prediction.
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Affiliation(s)
- Miriam Eisenstein
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel.
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25
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de Vries SJ, Melquiond ASJ, Kastritis PL, Karaca E, Bordogna A, van Dijk M, Rodrigues JPGLM, Bonvin AMJJ. Strengths and weaknesses of data-driven docking in critical assessment of prediction of interactions. Proteins 2011; 78:3242-9. [PMID: 20718048 DOI: 10.1002/prot.22814] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The recent CAPRI rounds have introduced new docking challenges in the form of protein-RNA complexes, multiple alternative interfaces, and an unprecedented number of targets for which homology modeling was required. We present here the performance of HADDOCK and its web server in the CAPRI experiment and discuss the strengths and weaknesses of data-driven docking. HADDOCK was successful for 6 out of 9 complexes (6 out of 11 targets) and accurately predicted the individual interfaces for two more complexes. The HADDOCK server, which is the first allowing the simultaneous docking of generic multi-body complexes, was successful in 4 out of 7 complexes for which it participated. In the scoring experiment, we predicted the highest number of targets of any group. The main weakness of data-driven docking revealed from these last CAPRI results is its vulnerability for incorrect experimental data related to the interface or the stoichiometry of the complex. At the same time, the use of experimental and/or predicted information is also the strength of our approach as evidenced for those targets for which accurate experimental information was available (e.g., the 10 three-stars predictions for T40!). Even when the models show a wrong orientation, the individual interfaces are generally well predicted with an average coverage of 60% ± 26% over all targets. This makes data-driven docking particularly valuable in a biological context to guide experimental studies like, for example, targeted mutagenesis.
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Affiliation(s)
- Sjoerd J de Vries
- NMR Research Group, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
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26
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Sircar A, Chaudhury S, Kilambi KP, Berrondo M, Gray JJ. A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19. Proteins 2011; 78:3115-23. [PMID: 20535822 DOI: 10.1002/prot.22765] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In CAPRI rounds 13-19, the most native-like structure predicted by RosettaDock resulted in two high, one medium, and one acceptable accuracy model out of 13 targets. The current rounds of CAPRI were especially challenging with many unbound and homology modeled starting structures. Novel docking methods, including EnsembleDock and SnugDock, allowed backbone conformational sampling during docking and enabled the creation of more accurate models. For Target 32, α-amylase/subtilisin inhibitor-subtilisin savinase, we sampled different backbone conformations at an interfacial loop to produce five high-quality models including the most accurate structure submitted in the challenge (2.1 Å ligand rmsd, 0.52 Å interface rmsd). For Target 41, colicin-immunity protein, we used EnsembleDock to sample the ensemble of nuclear magnetic resonance (NMR) models of the immunity protein to generate a medium accuracy structure. Experimental data identifying the catalytic residues at the binding interface for Target 40 (trypsin-inhibitor) were used to filter RosettaDock global rigid body docking decoys to determine high accuracy predictions for the two distinct binding sites in which the inhibitor interacts with trypsin. We discuss our generalized approach to selecting appropriate methods for different types of docking problems. The current toolset provides some robustness to errors in homology models, but significant challenges remain in accommodating larger backbone uncertainties and in sampling adequately for global searches.
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Affiliation(s)
- Aroop Sircar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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27
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Moal IH, Bates PA. SwarmDock and the use of normal modes in protein-protein docking. Int J Mol Sci 2010; 11:3623-48. [PMID: 21152290 PMCID: PMC2996808 DOI: 10.3390/ijms11103623] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 07/29/2010] [Accepted: 09/16/2010] [Indexed: 11/17/2022] Open
Abstract
Here is presented an investigation of the use of normal modes in protein-protein docking, both in theory and in practice. Upper limits of the ability of normal modes to capture the unbound to bound conformational change are calculated on a large test set, with particular focus on the binding interface, the subset of residues from which the binding energy is calculated. Further, the SwarmDock algorithm is presented, to demonstrate that the modelling of conformational change as a linear combination of normal modes is an effective method of modelling flexibility in protein-protein docking.
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Affiliation(s)
- Iain H. Moal
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, 44 Lincoln’s Inn Fields, London, WC2A 3LY, UK
| | - Paul A. Bates
- Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, Lincoln’s Inn Fields Laboratories, 44 Lincoln’s Inn Fields, London, WC2A 3LY, UK
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28
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Shi Y, Jiao D, Schnieders MJ, Ren P. Trypsin-ligand binding free energy calculation with AMOEBA. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2010; 2009:2328-31. [PMID: 19965178 DOI: 10.1109/iembs.2009.5335108] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The binding free energies of several benzamidine -like inhibitors to trypsin were examined using a polarizable molecular mechanics potential. All the computed binding free energies are in good agreement with the experimental data. From free energy decomposition, electrostatic interaction was indicated to be the driving force for the binding. MD simulations show that the ligands form hydrogen bonds with trypsin and water molecules nearby in a competitive fashion. While the binding free energy is independent of the ligand dipole moment, it shows a strong correlation with the ligand molecular polarizability.
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Affiliation(s)
- Yue Shi
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
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29
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Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GNI, Johnson ME, Head-Gordon T. Current status of the AMOEBA polarizable force field. J Phys Chem B 2010; 114:2549-64. [PMID: 20136072 PMCID: PMC2918242 DOI: 10.1021/jp910674d] [Citation(s) in RCA: 945] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models toward more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date, it has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.
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Affiliation(s)
- Jay W Ponder
- Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110, USA
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30
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Jiao D, Zhang J, Duke RE, Li G, Ren P. Trypsin-ligand binding free energies from explicit and implicit solvent simulations with polarizable potential. J Comput Chem 2009; 30:1701-11. [PMID: 19399779 PMCID: PMC2752704 DOI: 10.1002/jcc.21268] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We have calculated the binding free energies of a series of benzamidine-like inhibitors to trypsin with a polarizable force field using both explicit and implicit solvent approaches. Free energy perturbation has been performed for the ligands in bulk water and in protein complex with molecular dynamics simulations. The binding free energies calculated from explicit solvent simulations are well within the accuracy of experimental measurement and the direction of change is predicted correctly in all cases. We analyzed the molecular dipole moments of the ligands in gas, water and protein environments. Neither binding affinity nor ligand solvation free energy in bulk water shows much dependence on the molecular dipole moments of the ligands. Substitution of the aromatic or the charged group in the ligand results in considerable change in the solvation energy in bulk water and protein whereas the binding affinity varies insignificantly due to cancellation. The effect of chemical modification on ligand charge distribution is mostly local. Replacing benzene with diazine has minimal impact on the atomic multipoles at the amidinium group. We have also utilized an implicit solvent based end-state approach to evaluate the binding free energies of these inhibitors. In this approach, the polarizable multipole model combined with Poisson-Boltzmann/surface area (PMPB/SA) provides the electrostatic interaction energy and the polar solvation free energy. Overall the relative binding free energies obtained from the MM-PMPB/SA model are in good agreement with the experimental data.
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Affiliation(s)
- Dian Jiao
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712 USA
| | - Jiajing Zhang
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712 USA
| | - Robert E. Duke
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA and Laboratory of Structural Biology, National Institute of Environmental Health Sciences-National Institutes of Health, Research Triangle Park, NC 27709 USA
| | - Guohui Li
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712 USA
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31
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Structure of a serine protease poised to resynthesize a peptide bond. Proc Natl Acad Sci U S A 2009; 106:11034-9. [PMID: 19549826 DOI: 10.1073/pnas.0902463106] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The serine proteases are among the most thoroughly studied enzymes, and numerous crystal structures representing the enzyme-substrate complex and intermediates in the hydrolysis reactions have been reported. Some aspects of the catalytic mechanism remain controversial, however, especially the role of conformational changes in the reaction. We describe here a high-resolution (1.46 A) crystal structure of a complex formed between a cleaved form of bovine pancreatic trypsin inhibitor (BPTI) and a catalytically inactive trypsin variant with the BPTI cleavage site ideally positioned in the active site for resynthesis of the peptide bond. This structure defines the positions of the newly generated amino and carboxyl groups following the 2 steps in the hydrolytic reaction. Comparison of this structure with those representing other intermediates in the reaction demonstrates that the residues of the catalytic triad are positioned to promote each step of both the forward and reverse reaction with remarkably little motion and with conservation of hydrogen-bonding interactions. The results also provide insights into the mechanism by which inhibitors like BPTI normally resist hydrolysis when bound to their target proteases.
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32
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Wu E, Han K, Zhang J. Selectivity of Neutral/Weakly Basic P1 Group Inhibitors of Thrombin and Trypsin by a Molecular Dynamics Study. Chemistry 2008; 14:8704-14. [DOI: 10.1002/chem.200800277] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Kek Heng C, . SMN, . TSY, . RYO. Biopanning for Banana streak virus Binding Peptide by Phage Display Peptide Library. ACTA ACUST UNITED AC 2007. [DOI: 10.3923/jbs.2007.1382.1387] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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34
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Gräter F, Schwarzl SM, Dejaegere A, Fischer S, Smith JC. Protein/ligand binding free energies calculated with quantum mechanics/molecular mechanics. J Phys Chem B 2007; 109:10474-83. [PMID: 16852269 DOI: 10.1021/jp044185y] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The calculation of binding affinities for flexible ligands has hitherto required the availability of reliable molecular mechanics parameters for the ligands, a restriction that can in principle be lifted by using a mixed quantum mechanics/molecular mechanics (QM/MM) representation in which the ligand is treated quantum mechanically. The feasibility of this approach is evaluated here, combining QM/MM with the Poisson-Boltzmann/surface area model of continuum solvation and testing the method on a set of 47 benzamidine derivatives binding to trypsin. The experimental range of the absolute binding energy (DeltaG = -3.9 to -7.6 kcal/mol) is reproduced well, with a root-mean-square (RMS) error of 1.2 kcal/mol. When QM/MM is applied without reoptimization to the very different ligands of FK506 binding protein the RMS error is only 0.7 kcal/mol. The results show that QM/MM is a promising new avenue for automated docking and scoring of flexible ligands. Suggestions are made for further improvements in accuracy.
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Affiliation(s)
- Frauke Gräter
- IWR--Computational Biochemistry, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
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35
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Moulin A, Bell JH, Pratt R, Ringe D. Inhibition of chymotrypsin by a complex of ortho-vanadate and benzohydroxamic acid: structure of the inert complex and its mechanistic interpretation. Biochemistry 2007; 46:5982-90. [PMID: 17469803 PMCID: PMC2512255 DOI: 10.1021/bi6025209] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Serine proteases, like serine beta-lactamases, are rapidly and covalently inhibited by suitably designed phosph(on)ates. The active sites of these enzymes must, therefore, be able to stabilize the pentacoordinated transition states of phosphyl transfer reactions as well as the tetrahedral transition states of acyl transfers. It follows that these enzymes should also be inhibited by molecules capable of generating inert pentacoordinated species. We (J.H.B. and R.F.P.) have previously shown that these enzymes are, in fact, rapidly and reversibly inhibited by 1:1 complexes of vanadate and hydroxamic acids. In this paper, we present the first crystal structure of an acyl transferase inhibited by vanadate. The complex of vanadate and benzohydroxamic acid is a competitive inhibitor of alpha-chymotrypsin with a KI value of 16 muM. In the structure, obtained at a resolution of 1.5 A, the protein is conformationally little different from the apoenzyme. The vanadium, in a distorted octahedral ligand field, is covalently bound to the active site serine oxygen group. One oxgen ligand, presumably anionic, is located in the oxyanion hole. Another is directed roughly in the direction of the acyl transfer leaving group, and a third in the direction of the S2 site. The hydroxamate is bound to vanadium through the hydroxyl oxygen and also, more weakly, through the carbonyl group, to form a five-membered chelate ring. The effect of this chelation is to place the phenyl group of the inhibitor into the important S1 specificity site. The hydroxamate oxygen is directed in line away from the Ser195 Ogamma, approximating the direction of departure of a leaving group in phosphyl transfer. The entire complex can be seen as a reasonable mimic of a phosphyl transfer transition state where the leaving group is extended into the S1 site.
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Affiliation(s)
- Aaron Moulin
- Rosenstiel Basic Medical Sciences Research Center, Program in Biochemistry, and Program in Biophysics, Brandeis University, Waltham, Massachusetts 02454
| | - Jason H. Bell
- Department of Chemistry, Wesleyan University, Middletown, CT 06459
| | - R.F. Pratt
- Department of Chemistry, Wesleyan University, Middletown, CT 06459
- Corresponding Author: Dr. R.F. Pratt, address above, telephone 860-685-2629; ; Fax: 860-685-2211
| | - Dagmar Ringe
- Rosenstiel Basic Medical Sciences Research Center, Program in Biochemistry, and Program in Biophysics, Brandeis University, Waltham, Massachusetts 02454
- Corresponding Author: Dr. R.F. Pratt, address above, telephone 860-685-2629; ; Fax: 860-685-2211
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36
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Nakamura H, Kuroda H, Saito H, Suzuki R, Yamori T, Maruyama K, Haga T. Synthesis and biological evaluation of boronic acid containing cis-stilbenes as apoptotic tubulin polymerization inhibitors. ChemMedChem 2006; 1:729-40. [PMID: 16902927 DOI: 10.1002/cmdc.200600068] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A series of boronic acid containing cis-stilbenes as potent inhibitors of tubulin polymerization was synthesized by the introduction of boronic acid as an acceptor-type functional group into the aromatic ring B of the combretastatin framework. High cell-growth inhibition was observed with boron compounds 13 c and 13 d, in which a hydroxy group on the aromatic ring B of combretastatin A-4 was replaced with boronic acid; IC50 values toward B-16 and 1-87 cell lines are 0.48-2.1 microM. Compounds 13 c and 13 d exhibited significant inhibitory activity toward tubulin polymerization (IC50=21-22 microM). The carboxylic acid derivative 17, which can be considered as a mimic of boronic acid 13 c, did not show significant inhibition of cell growth or tubulin polymerization. According to the FACScan analysis using Jurkat cells, apoptosis was induced after incubation for 8 h with 13 c at a concentration of >10(-8) M. Growth inhibitory experiments against a panel of 39 human cancer cell lines revealed 13 c to inhibit growth differently than combretastatin A-4; the correlation coefficient (r) between the two compounds was 0.553 in the COMPARE analysis.
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Affiliation(s)
- Hiroyuki Nakamura
- Department of Chemistry, Faculty of Science, Gakushuin University, Mejiro, Toshima-ku, Tokyo 171-8588, Japan.
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37
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de Bruin B, Hauwert P, Reek JNH. Dynamic Combinatorial Chemistry: The Unexpected Choice of Receptors by Guest Molecules. Angew Chem Int Ed Engl 2006; 45:2660-3. [PMID: 16586522 DOI: 10.1002/anie.200504480] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Bas de Bruin
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 129, 1018 WS Amsterdam, The Netherlands
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de Bruin B, Hauwert P, Reek JNH. Dynamische kombinatorische Chemie: die überraschende Rezeptorwahl durch Gastmoleküle. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504480] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Saur I, Scopelliti R, Severin K. Utilization of Self-Sorting Processes To Generate Dynamic Combinatorial Libraries with New Network Topologies. Chemistry 2006; 12:1058-66. [PMID: 16100736 DOI: 10.1002/chem.200500621] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The synthesis of water-soluble, organometallic macrocycles is described. They were obtained by self-assembly in reactions of the half-sandwich complexes [[Ru(C6H5Me)Cl2]2], [[Ru(p-cymene)Cl2]2], [[Rh(Cp)Cl2]2], and [[Ir(Cp*)Cl2]2] with the ligand 5-dimethylaminomethyl-3-hydroxy-2-methyl-4-(1H)-pyridone in buffered aqueous solution at pH 8. The structure of the Ru-(p-cymene) complex was determined by single-crystal X-ray crystallography. Upon mixing, these complexes undergo scrambling reactions to give dynamic combinatorial libraries. In combination with structurally related complexes based on amino-methylated 3-hydroxy-2-(1H)-pyridone ligands, an exchange of metal fragments but no mixing of ligands was observed. This self-sorting behavior was used to construct dynamic combinatorial libraries of macrocycles, in which two four-component sub-libraries are connected by two common building blocks. This type of network topology influences the adaptive behavior of the library as demonstrated in selection experiments with lithium ions as the target.
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Affiliation(s)
- Isabelle Saur
- Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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Engel M, Hoffmann T, Manhart S, Heiser U, Chambre S, Huber R, Demuth HU, Bode W. Rigidity and Flexibility of Dipeptidyl Peptidase IV: Crystal Structures of and Docking Experiments with DPIV. J Mol Biol 2006; 355:768-83. [PMID: 16330047 DOI: 10.1016/j.jmb.2005.11.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Revised: 11/02/2005] [Accepted: 11/04/2005] [Indexed: 11/18/2022]
Abstract
Dipeptidyl peptidase IV (DPIV) is an alpha,beta-hydrolase-like serine exopeptidase, which removes dipeptides, preferentially with a C-terminal l-Pro residue, from the N terminus of longer peptide substrates. Previously, we determined the tetrameric 1.8A crystal structure of native porcine DPIV. Each monomer is composed of a beta-propeller and a catalytic domain, which together embrace an internal cavity housing the active centre. This cavity is connected to the bulk solvent by a "propeller opening" and a "side opening". Here, we analyse DPIV complexes with a t-butyl-Gly-Pro-Ile tripeptide, Pro-boroPro, a piperazine purine compound, and aminoethyl phenyl sulfonylfluoride. The latter two compounds bind to the active-site groove in a compact and a quite bulky manner, respectively, causing considerable shifts of the catalytic Ser630 side-chain and of the Tyr547 phenolic group, which forms the oxyanion hole. The tripeptide, mimicking a peptide substrate, is clamped to the active site through tight interactions via its N-terminal alpha-ammonium group, the P2 carbonyl group, the P1-l-Pro side-chain, the C-terminal carboxylate group, and the stable orthoacid ester amide formed between the scissile peptide carbonyl group and Ser630 O(gamma). This stable trapping of the tripeptide could be due to stabilization of the protonated His740 imidazolium cation by the adjacent negatively charged C-terminal carboxylate group, preventing proton transfer to the leaving group nitrogen atom. Docking experiments with the compact rigid 58 residue protein aprotinin, which had been shown to be processed by DPIV, indicate that the Arg1-Pro2 N terminus can access the DPIV active site only upon widening of its side openings, probably by separation of the first and the last propeller blades, and/or of the catalytic and the propeller domain.
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Affiliation(s)
- Michael Engel
- Max-Planck-Institut für Biochemie, AG Proteinaseforschung, Am Klopferspitz 18, D-82152 Martinsried, Germany
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41
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Magill C, Katz BA, Mackman RL. Emerging therapeutic targets in oncology: urokinase-type plasminogen activator system. ACTA ACUST UNITED AC 2005. [DOI: 10.1517/14728222.3.1.109] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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42
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Asano T, Nakamura H, Uehara Y, Yamamoto Y. Design, synthesis, and biological evaluation of aminoboronic acids as growth-factor receptor inhibitors of EGFR and VEGFR-1 tyrosine kinases. Chembiochem 2004; 5:483-90. [PMID: 15185372 DOI: 10.1002/cbic.200300748] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A series of aminoboronic acids was synthesized based on the structure of lavendustin pharmacophore 1. Their inhibitory activities against the epidermal growth-factor receptor (EGFR) and vascular endothelial growth-factor receptor-1 (VEGFR-1, Flt-1) protein tyrosine kinases, and various protein kinases, PKA, PKC, PTK, and eEF2K were evaluated. Selective inhibition activities were observed in a series of aminoboronic acids. 4-Methoxy-3-((2- methoxyphenylamino)methyl)phenylboronic acid 10 inhibited EGFR tyrosine kinase, whereas 4-(2,5-dihydroxybenzylamino)phenylboronic acid 12 inhibited Flt-1 protein kinase, although lavendustin pharmacophore 1 inhibited both EGFR and Flt-1 kinases at a compound concentration of 1.0 microg mL(-1). The selective inhibition of EGFR by 10 is considered to be due to the substitution of the dihydroxy groups on the benzyl moiety for a boronic acid group at the para position, whereas the selective inhibition of Flt-1 by 12 is due to the substitution of the carboxyl group on the aniline moiety in the lavendustin pharmacophore 1 for a boronic acid group.
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Affiliation(s)
- Toru Asano
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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43
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Hansen KK, Grosch B, Greiveldinger-Poenaru S, Bartlett PA. Synthesis and evaluation of macrocyclic transition state analogue inhibitors for alpha-chymotrypsin. J Org Chem 2004; 68:8465-70. [PMID: 14575472 DOI: 10.1021/jo034837z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lactams 1 and 2 are readily formed from acyclic precursors in the presence of trypsin and chymotrypsin, respectively, identifying the macrocyclic ring system as a potential motif for constrained transition state analogue inhibitors of the serine peptidases. Ketone 3 was synthesized and shown to be a modest inhibitor of chymotrypsin (Ki = 220 microM), albeit 4-fold more potent than the acyclic hydroxy acid 25 (Ki = 1.5 mM as a mixture of epimers). A precursor (31) to the amino boronic acid 4 was also prepared; although this derivative was a potent inhibitor of chymotrypsin (Ki = 130 nM) by virtue of the boronic acid moiety, it showed no advantage over the des-amino analogue 32 (Ki = 120 nM), which is not capable of cyclizing.
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Affiliation(s)
- Kristina K Hansen
- Center for New Directions in Organic Synthesis, Department of Chemistry, University of California, Berkeley, California 94720-1460, USA
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44
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Abstract
A Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo move, which allows transitions between the unbound and bound states. Provided that an accurate protein structure is given, that the protein-ligand binding site is known, and that an accurate chemical force field together with a continuum solvation model is used, this method provides a quantitative estimate of the free energy of binding.
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Rankin KN, Sulea T, Purisima EO. On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations. J Comput Chem 2003; 24:954-62. [PMID: 12720316 DOI: 10.1002/jcc.10261] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Using molecular mechanics force field partial atomic charges, we show the nonuniqueness of the parametrization of continuum electrostatics models with respect to solute atomic radii and interior dielectric constant based on hydration (vacuum-to-water transfer) free energy data available for small molecules. Moreover, parameter sets that are optimal and equivalent for hydration free energy calculations lead to large variations of calculated absolute and relative electrostatic binding free energies. Hence, parametrization of solvation effects based on hydration data, although a necessary condition, is not sufficient to guarantee its transferability to the calculation of binding free energies in solution.
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Affiliation(s)
- Kathryn N Rankin
- Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
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Sulea T, Purisima EO. Profiling charge complementarity and selectivity for binding at the protein surface. Biophys J 2003; 84:2883-96. [PMID: 12719221 PMCID: PMC1302852 DOI: 10.1016/s0006-3495(03)70016-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel analysis and representation of the protein surface in terms of electrostatic binding complementarity and selectivity is presented. The charge optimization methodology is applied in a probe-based approach that simulates the binding process to the target protein. The molecular surface is color coded according to calculated optimal charge or according to charge selectivity, i.e., the binding cost of deviating from the optimal charge. The optimal charge profile depends on both the protein shape and charge distribution whereas the charge selectivity profile depends only on protein shape. High selectivity is concentrated in well-shaped concave pockets, whereas solvent-exposed convex regions are not charge selective. This suggests the synergy of charge and shape selectivity hot spots toward molecular selection and recognition, as well as the asymmetry of charge selectivity at the binding interface of biomolecular systems. The charge complementarity and selectivity profiles map relevant electrostatic properties in a readily interpretable way and encode information that is quite different from that visualized in the standard electrostatic potential map of unbound proteins.
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Affiliation(s)
- Traian Sulea
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec H4P 2R2, Canada
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47
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Nguyen R, Huc I. Optimizing the reversibility of hydrazone formation for dynamic combinatorial chemistry. Chem Commun (Camb) 2003:942-3. [PMID: 12744310 DOI: 10.1039/b211645f] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrazones from hydrazines bearing electron withdrawing groups, and aromatic or aliphatic aldehydes form and hydrolyse rapidly in water at neutral pH.
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Affiliation(s)
- Régis Nguyen
- Institut Européen de Chimie et Biologie, 16 Av. Pey Berland, 33607 Pessac Cedex, France
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48
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Gray CW, Walker BT, Foley RA, Houston TA. Boronate derivatives of bioactive amines: potential neutral receptors for anionic oligosaccharides. Tetrahedron Lett 2003. [DOI: 10.1016/s0040-4039(03)00616-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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49
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Toyota E, Ng KKS, Kuninaga S, Sekizaki H, Itoh K, Tanizawa K, James MNG. Crystal structure and nucleotide sequence of an anionic trypsin from chum salmon (Oncorhynchus keta) in comparison with Atlantic salmon (Salmo salar) and bovine trypsin. J Mol Biol 2002; 324:391-7. [PMID: 12445776 DOI: 10.1016/s0022-2836(02)01097-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The nucleotide sequence and crystal structure of chum salmon trypsin (CST) are now reported. The cDNA isolated from the pyloric caeca of chum salmon encodes 222 amino acid residues, the same number of residues as the anionic Atlantic salmon trypsin (AST), but one residue less than bovine beta-trypsin (BT). The net charge on CST determined from the sum of all charged amino acid side-chains is -3. There are 79 sequence differences between CST and BT, but only seven sequence differences between CST and AST. Anionic CST isolated from pyloric caeca has also been purified and crystallized; the structure of the CST-benzamidine complex has been determined to 1.8A resolution. The overall tertiary structure of CST is similar to that of AST and BT, but some differences are observed among the three trypsins. The most striking difference is at the C terminus of CST, where the expected last two residues are absent. The absence of these residues likely increases the flexibility of CST by the loss of important interactions between the N and C-terminal domains. Similarly, the lack of Tyr151 in CST (when compared with BT) allows more space for Gln192 in the active site thereby increasing substrate accessibility to the binding pocket. Lys152 in CST also adopts the important role of stabilizing the loop from residue 142 to 153. These observations on CST provide a complementary view of a second cold-adapted trypsin, which in comparison with the structures of AST and BT, suggest a structural basis for differences in enzymatic activity between enzymes from cold-adapted species and mammals.
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Affiliation(s)
- Eiko Toyota
- Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Ishikari-Tobestu, 061-0293, Hokkaido, Japan
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50
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Schwarzl SM, Tschopp TB, Smith JC, Fischer S. Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction? J Comput Chem 2002; 23:1143-9. [PMID: 12116383 DOI: 10.1002/jcc.10112] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The prediction of a ligand binding constant requires generating three-dimensional structures of the complex concerned and reliably scoring these structures. Here, the scoring problem is investigated by examining benzamidine-like inhibitors of trypsin, a system for which errors in the structures are small. Precise and consistent binding free energies for the inhibitors are determined experimentally for this test system. To examine possible improvement of scoring methods, we test the suitability of continuum electrostatics to account for solvation effects and use an ideal-gas entropy correction to account for the changes in the degrees of freedom of the ligand. The small observed root-mean-square deviation of 0.55 kcal/mol of the calculated relative to the experimental values indicates that the essentials of the binding process have been captured. Even though all six ligands make the same salt bridge and H-bonds to the protein, the electrostatic contribution varies among the ligands by as much as 2 kcal/mol. Moreover, although the ligands are rigid and similar in size, the entropic terms also significantly affect the relative binding affinities (by up to 2.7 kcal/mol). The present approach to solvation and entropy may allow the ranking of the ligands to be considerably improved at a cost that makes the method applicable to the optimization of lead compounds or to the screening of small collections of ligands.
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Affiliation(s)
- Sonja M Schwarzl
- IWR-Biocomputing, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany
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