1
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Karim MRU, Harunari E, Oku N, Akasaka K, Igarashi Y. Bulbimidazoles A-C, Antimicrobial and Cytotoxic Alkanoyl Imidazoles from a Marine Gammaproteobacterium Microbulbifer Species. JOURNAL OF NATURAL PRODUCTS 2020; 83:1295-1299. [PMID: 32191468 DOI: 10.1021/acs.jnatprod.0c00082] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Three new alkanoyl imidazoles, designated bulbimidazoles A-C (1-3), were found from the culture extract of the gammaproteobacterium Microbulbifer sp. DC3-6 isolated from a stony coral of the genus Tubastraea. The absolute configuration of the anteiso-methyl substitution in 1 was established to be a mixture of (R)- and (S)-configurations in a ratio of 9:91 by applying the Ohrui-Akasaka method. Compounds 1-3 displayed unique broad-spectrum antimicrobial activity against Gram-positive and -negative bacteria and fungi with MICs ranging from 0.78 to 12.5 μg/mL. They also exhibited cytotoxicity toward P388 murine leukemia cells with IC50 in the micromolar range.
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Affiliation(s)
- Md Rokon Ul Karim
- Biotechnology Research Center, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
| | - Enjuro Harunari
- Biotechnology Research Center, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
| | - Naoya Oku
- Biotechnology Research Center, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
| | - Kazuaki Akasaka
- Shokei Gakuin University, 4-10-1 Yurigaoka, Natori, Miyagi 981-1295, Japan
| | - Yasuhiro Igarashi
- Biotechnology Research Center, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
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2
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Jamali H, Khan HA, Tjin CC, Ellman JA. Cellular Activity of New Small Molecule Protein Arginine Deiminase 3 (PAD3) Inhibitors. ACS Med Chem Lett 2016; 7:847-51. [PMID: 27660689 DOI: 10.1021/acsmedchemlett.6b00215] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 07/11/2016] [Indexed: 12/14/2022] Open
Abstract
The protein arginine deiminases (PADs) catalyze the post-translational deimination of arginine side chains. Multiple PAD isozymes have been characterized, and abnormal PAD activity has been associated with several human disease states. PAD3 has been characterized as a modulator of cell growth via apoptosis inducing factor and has been implicated in the neurodegenerative response to spinal cord injury. Here, we describe the design, synthesis, and evaluation of conformationally constrained versions of the potent and selective PAD3 inhibitor 2. The cell activity of representative inhibitors in this series was also demonstrated for the first time by rescue of thapsigargin-induced cell death in PAD3-expressing HEK293T cells.
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Affiliation(s)
- Haya Jamali
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Hasan A. Khan
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Caroline C. Tjin
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Jonathan A. Ellman
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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3
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Clay supported titanium catalyst for the solvent free synthesis of tetrasubstituted imidazoles and benzimidazoles. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcata.2013.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Le G, Vandegraaff N, Rhodes DI, Jones ED, Coates JAV, Thienthong N, Winfield LJ, Lu L, Li X, Yu C, Feng X, Deadman JJ. Design of a series of bicyclic HIV-1 integrase inhibitors. Part 2: azoles: effective metal chelators. Bioorg Med Chem Lett 2010; 20:5909-12. [PMID: 20727753 DOI: 10.1016/j.bmcl.2010.07.081] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 07/18/2010] [Accepted: 07/20/2010] [Indexed: 11/16/2022]
Abstract
Synthesis of a diverse set of azoles and their utilizations as an amide isostere in the design of HIV integrase inhibitors is described. The Letter identified thiazole, oxazole, and imidazole as the most promising heterocycles. Initial SAR studies indicated that these novel series of integrase inhibitors are amenable to lead optimization. Several compounds with low nanomolar inhibitory potency are reported.
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Affiliation(s)
- Giang Le
- Avexa Ltd, 576 Swan Street, Richmond, Victoria 3121, Australia
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5
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Tsou HR, Liu X, Birnberg G, Kaplan J, Otteng M, Tran T, Kutterer K, Tang Z, Suayan R, Zask A, Ravi M, Bretz A, Grillo M, McGinnis JP, Rabindran SK, Ayral-Kaloustian S, Mansour TS. Discovery of 4-(benzylaminomethylene)isoquinoline-1,3-(2H,4H)-diones and 4-[(pyridylmethyl)aminomethylene]isoquinoline-1,3-(2H,4H)-diones as potent and selective inhibitors of the cyclin-dependent kinase 4. J Med Chem 2009; 52:2289-310. [PMID: 19317452 DOI: 10.1021/jm801026e] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The series of 4-(benzylaminomethylene)isoquinoline-1,3-(2H,4H)-dione and 4-[(pyridylmethyl)aminomethylene]isoquinoline-1,3-(2H,4H)-dione derivatives reported here represents a novel class of potential antitumor agents, which potently and selectively inhibit CDK4 over CDK2 and CDK1. In the benzylamino headpiece, a 3-OH substituent is required on the phenyl ring for CDK4 inhibitory activity, which is further enhanced when an iodo, aryl, heteroaryl, t-butyl, or cyclopentyl substituent is introduced at the C-6 position of the isoquinoline-1,3-dione core. To circumvent the metabolic liability associated with the phenolic OH group on the 4-substituted 3-OH phenyl headpiece, we take two approaches: first, introduce a nitrogen o- or p- to the 3-OH group in the phenyl ring; second, replace the phenyl headpiece with N-substituted 2-pyridones. We present here the synthesis, SAR data, metabolic stability data, and a CDK4 mimic model that explains the binding, potency, and selectivity of our CDK4 selective inhibitors.
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Affiliation(s)
- Hwei-Ru Tsou
- Chemical and Screening Sciences, and Oncology Research, Wyeth Research, 401 N. Middletown Road, Pearl River, New York 10965, USA.
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6
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1-Arylaminoimidazole-2-thiones as intermediates in the synthesis of imidazo[2,1-b][1,3,4]thiadiazines. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.01.136] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Paul Beckett R. Patent Update Oncologic, Endocrine & Metabolic: Oncologic, Endocrine & Metabolic: Recent advances in the field of matrix metalloproteinase inhibitors. Expert Opin Ther Pat 2008. [DOI: 10.1517/13543776.6.12.1305] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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8
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Kawakami JI, Kimura K, Yamaoka M. A Concise Synthesis of Racemic 1-(6,7-Dimethoxy-2-naphthyl)-1-(1H-imidazol-4-yl)-2-methylpropan-1-ol for a Potent C17,20-Lyase Inhibitor. Org Process Res Dev 2007. [DOI: 10.1021/op060171+] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Michalik L, Zoete V, Krey G, Grosdidier A, Gelman L, Chodanowski P, Feige JN, Desvergne B, Wahli W, Michielin O. Combined simulation and mutagenesis analyses reveal the involvement of key residues for peroxisome proliferator-activated receptor alpha helix 12 dynamic behavior. J Biol Chem 2007; 282:9666-9677. [PMID: 17200111 DOI: 10.1074/jbc.m610523200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The dynamic properties of helix 12 in the ligand binding domain of nuclear receptors are a major determinant of AF-2 domain activity. We investigated the molecular and structural basis of helix 12 mobility, as well as the involvement of individual residues with regard to peroxisome proliferator-activated receptor alpha (PPARalpha) constitutive and ligand-dependent transcriptional activity. Functional assays of the activity of PPARalpha helix 12 mutants were combined with free energy molecular dynamics simulations. The agreement between the results from these approaches allows us to make robust claims concerning the mechanisms that govern helix 12 functions. Our data support a model in which PPARalpha helix 12 transiently adopts a relatively stable active conformation even in the absence of a ligand. This conformation provides the interface for the recruitment of a coactivator and results in constitutive activity. The receptor agonists stabilize this conformation and increase PPARalpha transcription activation potential. Finally, we disclose important functions of residues in PPARalpha AF-2, which determine the positioning of helix 12 in the active conformation in the absence of a ligand. Substitution of these residues suppresses PPARalpha constitutive activity, without changing PPARalpha ligand-dependent activation potential.
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Affiliation(s)
- Liliane Michalik
- Center for Integrative Genomics and National Research Center "Frontiers in Genetics," University of Lausanne, Le Génopode, CH-1015 Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Institute for Bioinformatics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Grigorios Krey
- National Agricultural Research Foundation, Fisheries Research Institute, Nea Peramos, GR-64007 Kavala, Greece
| | - Aurélien Grosdidier
- Swiss Institute for Bioinformatics, University of Lausanne, CH-1015 Lausanne, Switzerland; Ludwig Institute for Cancer Research and National Research Center "Molecular Oncology," CH-1066 Epalinges, Switzerland
| | - Laurent Gelman
- Center for Integrative Genomics and National Research Center "Frontiers in Genetics," University of Lausanne, Le Génopode, CH-1015 Lausanne, Switzerland
| | - Pierre Chodanowski
- Swiss Institute for Bioinformatics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Jérôme N Feige
- Center for Integrative Genomics and National Research Center "Frontiers in Genetics," University of Lausanne, Le Génopode, CH-1015 Lausanne, Switzerland
| | - Béatrice Desvergne
- Center for Integrative Genomics and National Research Center "Frontiers in Genetics," University of Lausanne, Le Génopode, CH-1015 Lausanne, Switzerland
| | - Walter Wahli
- Center for Integrative Genomics and National Research Center "Frontiers in Genetics," University of Lausanne, Le Génopode, CH-1015 Lausanne, Switzerland.
| | - Olivier Michielin
- Swiss Institute for Bioinformatics, University of Lausanne, CH-1015 Lausanne, Switzerland; Ludwig Institute for Cancer Research and National Research Center "Molecular Oncology," CH-1066 Epalinges, Switzerland; Multidisciplinary Oncology Center (CePO), Lausanne University Hospital, CH-1011 Lausanne, Switzerland.
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10
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Gohda K. A quantitative structure-activity relationship study for structurally diverse HIV-1 protease inhibitors: Contribution of conformational flexibility to inhibitory activity. J Enzyme Inhib Med Chem 2006; 21:609-15. [PMID: 17194035 DOI: 10.1080/14756360600810233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
In this study, we investigated by linear regression model the SAR data of the 15 HIV-1 protease inhibitors possessing structurally diverse scaffolds. First, a regression model was developed only using the enzyme-inhibitor interaction energy as a term of the model, but did not provide a good correlation with the inhibitory activity (R2 = 0.580 and Q2 = 0.500). Then, we focused on the conformational flexibility of the inhibitors which may represent the diversity of the inhibitors, and added two conformational parameters into the model, respectively: the number of rotatable bonds of ligands (deltaSrot) and the distortion energy of ligands (deltaElig). The regression model by adding deltaElig successfully improved the quality of the model (R2 = 0.771 and Q2 = 0.713) while the model with deltaSrot was unsuccessful. The prediction for a training inhibitor by the deltaElig model also showed good agreement with experimental activity. These results suggest that the conformational flexibility of HIV-1 protease inhibitors directly contributes to the enzyme inhibition.
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Affiliation(s)
- Keigo Gohda
- Computer-Aided Molecular Modeling Research Center Kansai (CAMM Kansai), 2-8-20-404, Mikagehonmachi, Higashinada-ku Kobe 658-0046, Japan.
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11
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Thorsteinsdottir HB, Schwede T, Zoete V, Meuwly M. How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding. Proteins 2006; 65:407-23. [PMID: 16941468 DOI: 10.1002/prot.21096] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The influence of possible inaccuracies that can arise during homology modeling of protein structures used for ligand binding studies were investigated with the molecular mechanics generalized Born surface area (MM-GBSA) method. For this, a family of well-characterized HIV-I protease-inhibitor complexes was used. Validation of MM-GBSA led to a correlation coefficient ranging from 0.72 to 0.93 between calculated and experimental binding free energies DeltaG. All calculated DeltaG values were based on molecular dynamics simulations with explicit solvent. Errors introduced into the protein structure through misplacement of side-chains during rotamer modeling led to a correlation coefficient between DeltaG(calc) and DeltaG(exp) of 0.75 compared with 0.90 for the correctly placed side chains. This is in contrast to homology models for members of the retroviral protease family with template structures ranging in sequence identity between 32% and 51%. For these protein models, the correlation coefficients vary between 0.84 and 0.87, which is considerably closer to the original protein (0.90). It is concluded that HIV-I low sequence identity with the template structure still allows creating sufficiently reliable homology models to be used for ligand-binding studies, although placement of the rotamers is a critical step during the modeling.
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12
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Sharma GVM, Jyothi Y, Lakshmi PS. Efficient Room‐Temperature Synthesis of Tri‐ and Tetrasubstituted Imidazoles Catalyzed by ZrCl4. SYNTHETIC COMMUN 2006. [DOI: 10.1080/00397910600773825] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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13
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Todorov NP, Buenemann CL, Alberts IL. De novo ligand design to an ensemble of protein structures. Proteins 2006; 64:43-59. [PMID: 16555306 DOI: 10.1002/prot.20928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We describe a combinatorial method for de novo ligand design to an ensemble of receptor structures. Receptor conformations, protonation states, and structural water molecules are considered consistently within the framework of de novo ligand design. The method relies on Monte Carlo optimization to search the space of ligand structures, conformations, and rigid-body movements as well as receptor models. The method is applied to an ensemble of HIV protease and human collagenase receptor models. Ligand structures generated de novo exhibit the correct hydrogen-bonding pattern in the core of the active site, with hydrophobic groups extending into the receptor S1 and S1' pocket space. Furthermore, it is shown that known ligands are recovered in the correct binding mode and in the native, most tightly binding receptor model.
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Affiliation(s)
- N P Todorov
- De Novo Pharmaceuticals Ltd., Compass House, Cambridge, United Kingdom
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14
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Wong FF, Chen CY, Chen TH, Huang JJ, Fang HP, Yeh MY. Synthesis of 3alpha-hydroxy-21-(1'-imidazolyl)-3beta-methoxyl-methyl-5alpha-pregnan-20-one via lithium imidazole with 17alpha-acetylbromopregnanone. Steroids 2006; 71:77-82. [PMID: 16246385 DOI: 10.1016/j.steroids.2005.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Revised: 06/15/2005] [Accepted: 08/17/2005] [Indexed: 12/01/2022]
Abstract
The synthesis of biologically active 3alpha-hydroxyl-21-(1'-imidazolyl)-3beta-methoxymethyl-5alpha-pregnan-20-one was accomplished in six steps. The key steps were the improvement of stereoselectivity for acetyl isomers in C-17 and the introduction of imidazole into the core structure by use of lithium imidazole. This latter key step provided the desired product in 82% yield without the formation of 1,3-disubstituted imidazolium salt as impurity, which is generally observed in traditional method.
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Affiliation(s)
- Fung Fuh Wong
- Environmental Resource Management Research Center, National Cheng Kung University, No. 500, Sec. 3, An-Ming Rd., Tainan City, Taiwan 709, ROC.
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15
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Bombek S, Požgan F, Kočevar M, Polanc S. A simple and efficient synthesis of 2-imidazolin-2-ones. NEW J CHEM 2005. [DOI: 10.1039/b502719e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Zoete V, Michielin O, Karplus M. Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors. J Comput Aided Mol Des 2004; 17:861-80. [PMID: 15124934 DOI: 10.1023/b:jcam.0000021882.99270.4c] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SASbur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, deltaGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC5o without reparametrization.
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Affiliation(s)
- V Zoete
- Laboratoire de Chimie Biophysique, Institut de Science et d'Ingénierie Supramoléculaires, Université Louis Pasteur, 8 allée Gaspard Monge, BP 70028 Strasbourg Cedex, France
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17
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18
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Jenwitheesuk E, Samudrala R. Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations. BMC STRUCTURAL BIOLOGY 2003; 3:2. [PMID: 12675950 PMCID: PMC154089 DOI: 10.1186/1472-6807-3-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2002] [Accepted: 04/01/2003] [Indexed: 11/23/2022]
Abstract
BACKGROUND The accurate prediction of enzyme-substrate interaction energies is one of the major challenges in computational biology. This study describes the improvement of protein-ligand binding energy prediction by incorporating protein flexibility through the use of molecular dynamics (MD) simulations. RESULTS Docking experiments were undertaken using the program AutoDock for twenty-five HIV-1 protease-inhibitor complexes determined by x-ray crystallography. Protein-rigid docking without any dynamics produced a low correlation of 0.38 between the experimental and calculated binding energies. Correlations improved significantly for all time scales of MD simulations of the receptor-ligand complex. The highest correlation coefficient of 0.87 between the experimental and calculated energies was obtained after 0.1 picoseconds of dynamics simulation. CONCLUSION Our results indicate that relaxation of protein complexes by MD simulation is useful and necessary to obtain binding energies that are representative of the experimentally determined values.
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Affiliation(s)
- Ekachai Jenwitheesuk
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Clinical Microbiology, Faculty of Medical Technology, Mahidol University, Bangkok, Thailand
| | - Ram Samudrala
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
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19
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Chen X, Wang W. Chapter 32. The use of bioisosteric groups in lead optimization. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2003. [DOI: 10.1016/s0065-7743(03)38033-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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20
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Breslin HJ, Miskowski TA, Kukla MJ, Leister WH, De Winter HL, Gauthier DA, Somers MVF, Peeters DCG, Roevens PWM. Design, synthesis, and tripeptidyl peptidase II inhibitory activity of a novel series of (S)-2,3-dihydro-2-(4-alkyl-1H-imidazol-2-yl)-1H-indoles. J Med Chem 2002; 45:5303-10. [PMID: 12431057 DOI: 10.1021/jm0202831] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Butabindide, 1, was previously reported as a potent inhibitor (IC50 = 7 nM) of the serine protease enzyme tripeptidyl peptidase II (TPPII), an endogenous protease that degrades cholecystokinin-8 (CCK-8). We found that 1 has some inherent chemical instability, yielding diketopiperazine 2 fairly readily under mimicked physiological conditions. We therefore prepared imidazoles 3, which are void of 1's inherent instability, and have found that our novel analogues maintained comparable TPPII inhibitory activity (e.g.,for 3c, IC50 = 4 nM) as 1.
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Affiliation(s)
- Henry J Breslin
- Johnson & Johnson Pharmaceutical Research & Development, L.L.C., Welsh and McKean Roads, P.O. Box 776, Spring House, Pennsylvania 19477-0776, USA.
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21
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Zoete V, Michielin O, Karplus M. Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility. J Mol Biol 2002; 315:21-52. [PMID: 11771964 DOI: 10.1006/jmbi.2001.5173] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The flexibility of different regions of HIV-1 protease was examined by using a database consisting of 73 X-ray structures that differ in terms of sequence, ligands or both. The root-mean-square differences of the backbone for the set of structures were shown to have the same variation with residue number as those obtained from molecular dynamics simulations, normal mode analyses and X-ray B-factors. This supports the idea that observed structural changes provide a measure of the inherent flexibility of the protein, although specific interactions between the protease and the ligand play a secondary role. The results suggest that the potential energy surface of the HIV-1 protease is characterized by many local minima with small energetic differences, some of which are sampled by the different X-ray structures of the HIV-1 protease complexes. Interdomain correlated motions were calculated from the structural fluctuations and the results were also in agreement with molecular dynamics simulations and normal mode analyses. Implications of the results for the drug-resistance engendered by mutations are discussed briefly.
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Affiliation(s)
- V Zoete
- Laboratoire de Chimie Biophysique, Institut Le Bel, Université Louis Pasteur, 4 rue Blaise Pascal, Strasbourg, 67000, France
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22
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Garg R, Gupta SP, Gao H, Babu MS, Debnath AK, Hansch C. Comparative Quantitative Structureminus signActivity Relationship Studies on Anti-HIV Drugs. Chem Rev 1999; 99:3525-3602. [PMID: 11849030 DOI: 10.1021/cr9703358] [Citation(s) in RCA: 204] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rajni Garg
- Department of Chemistry, Pomona College, Claremont, California 91711, Departments of Chemistry and Pharmacy, Birla Institute of Technology and Science, Pilani 333031, India, Pharmacia & Upjohn, 301 Henrietta Street, Kalamazoo, Michigan 49007, and Biochemical Virology Laboratory, Lindsley F. Kimball Research Institute of The New York Blood Center, 310 E. 67th Street, New York, New York 10021
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23
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Abstract
[formula: see text] A series of simple heterocyclic HIV-1 protease inhibitors were developed on the basis of size, shape, and electronic complementarity to the active site of the enzyme. The C2-symmetric heterocycles do not contain a transition-state isostere nor are they active site directed irreversible inhibitors; thus, they represent the success of a new design strategy. The first generation heterocycles inhibit the protease in the micromolar range, whereas control compounds show no bioactivity at the same concentrations.
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Affiliation(s)
- P W Baures
- Department of Chemistry, Kansas State University, Manhattan 66506, USA.
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25
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Abstract
A fast and reliable evaluation of the binding energy from a single conformation of a molecular complex is an important practical task. Knowledge-based scoring schemes may not be sufficiently general and transferable, while molecular dynamics or Monte Carlo calculations with explicit solvent are too computationally expensive for many applications. Recently, several empirical schemes using finite difference Poisson-Boltzmann electrostatics to predict energies for particular types of complexes were proposed. Here, an improved empirical binding energy function has been derived and validated on three different types of complexes: protein-small ligand, protein-peptide and protein-protein. The function uses the boundary element algorithm to evaluate the electrostatic solvation energy. We show that a single set of parameters can predict the relative binding energies of the heterogeneous validation set of complexes with 2.5 kcal/mol accuracy. We also demonstrate that global optimization of the ligand and of the flexible side-chains of the receptor improves the accuracy of the evaluation.
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Affiliation(s)
- M Schapira
- Skirball Institute of Biomolecular Medicine, Structural Biology, New York University Medical Center, 540 First Avenue, New York, NY 10016, USA
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26
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27
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Marrone TJ, Resat H, Hodge CN, Chang CH, McCammon JA. Solvation studies of DMP323 and A76928 bound to HIV protease: analysis of water sites using grand canonical Monte Carlo simulations. Protein Sci 1998; 7:573-9. [PMID: 9541388 PMCID: PMC2143944 DOI: 10.1002/pro.5560070305] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We examine the water solvation of the complex of the inhibitors DMP323 and A76928 bound to HIV-1 protease through grand canonical Monte Carlo simulations, and demonstrate the ability of this method to reproduce crystal waters and effectively predict water positions not seen in the DMP323 or A76928 structures. The simulation method is useful for identifying structurally important waters that may not be resolved in the crystal structures. It can also be used to identify water positions around a putative drug candidate docked into a binding pocket. Knowledge of these water positions may be useful in designing drugs to utilize them as bridging groups or displace them in the binding pocket. In addition, the method should be useful in finding water sites in homology models of enzymes for which crystal structures are unavailable.
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Affiliation(s)
- T J Marrone
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla 92093-0365, USA
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Towards understanding ligand specificity of retroviral proteases. Implications for the design of human immunodeficiency virus type 1 and 2 protease inhibitors. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0166-1280(97)00121-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Thompson SK, Halbert SM, Bossard MJ, Tomaszek TA, Levy MA, Zhao B, Smith WW, Abdel-Meguid SS, Janson CA, D'Alessio KJ, McQueney MS, Amegadzie BY, Hanning CR, DesJarlais RL, Briand J, Sarkar SK, Huddleston MJ, Ijames CF, Carr SA, Garnes KT, Shu A, Heys JR, Bradbeer J, Zembryki D, Lee-Rykaczewski L, James IE, Lark MW, Drake FH, Gowen M, Gleason JG, Veber DF. Design of potent and selective human cathepsin K inhibitors that span the active site. Proc Natl Acad Sci U S A 1997; 94:14249-54. [PMID: 9405598 PMCID: PMC24926 DOI: 10.1073/pnas.94.26.14249] [Citation(s) in RCA: 104] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Potent and selective active-site-spanning inhibitors have been designed for cathepsin K, a cysteine protease unique to osteoclasts. They act by mechanisms that involve tight binding intermediates, potentially on a hydrolytic pathway. X-ray crystallographic, MS, NMR spectroscopic, and kinetic studies of the mechanisms of inhibition indicate that different intermediates or transition states are being represented that are dependent on the conditions of measurement and the specific groups flanking the carbonyl in the inhibitor. The species observed crystallographically are most consistent with tetrahedral intermediates that may be close approximations of those that occur during substrate hydrolysis. Initial kinetic studies suggest the possibility of irreversible and reversible active-site modification. Representative inhibitors have demonstrated antiresorptive activity both in vitro and in vivo and therefore are promising leads for therapeutic agents for the treatment of osteoporosis. Expansion of these inhibitor concepts can be envisioned for the many other cysteine proteases implicated for therapeutic intervention.
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Affiliation(s)
- S K Thompson
- Department of Medicinal Chemistry, SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406, USA
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Towler EM, Thompson SK, Tomaszek T, Debouck C. Identification of a loop outside the active site cavity of the human immunodeficiency virus proteases which confers inhibitor specificity. Biochemistry 1997; 36:5128-33. [PMID: 9136873 DOI: 10.1021/bi962729j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have investigated the inhibitor specificity for the proteases of the human immunodeficiency viruses, types 1 and 2. Using a series of related inhibitors, the P1' side chain was confirmed to play a significant role in determining both the absolute and relative affinity for the enzymes. To further define the residues in the enzymes responsible for the difference in affinity, chimeric proteins were constructed in which domains of the respective proteases were exchanged at the genetic level. The results of these studies demonstrated that inhibitor affinity is conferred by a combination of the active site residues (32, 47, and 82) along with a loop comprised of residues 31 and 33-37, which lies outside of the active site cavity. These results are discussed in terms of existing structural data.
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Affiliation(s)
- E M Towler
- Department of Molecular Genetics, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406, USA
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Abstract
A method is described to dock a ligand into a binding site in a protein on the basis of the complementarity of the intermolecular atomic contacts. Docking is performed by maximization of a complementarity function that is dependent on atomic contact surface area and the chemical properties of the contacting atoms. The generality and simplicity of the complementarity function ensure that a wide range of chemical structures can be handled. The ligand and the protein are treated as rigid bodies, but displacement of a small number of residues lining the ligand binding site can be taken into account. The method can assist in the design of improved ligands by indicating what changes in complementarity may occur as a result of the substitution of an atom in the ligand. The capabilities of the method are demonstrated by application to 14 protein-ligand complexes of known crystal structure.
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Affiliation(s)
- V Sobolev
- Department of Plant Genetics, Weizmann Institute of Science, Rehovot, Israel
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Wallqvist A, Jernigan RL, Covell DG. A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design. Protein Sci 1995; 4:1881-903. [PMID: 8528086 PMCID: PMC2143230 DOI: 10.1002/pro.5560040923] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The interface between protein receptor-ligand complexes has been studied with respect to their binary interatomic interactions. Crystal structure data have been used to catalogue surfaces buried by atoms from each member of a bound complex and determine a statistical preference for pairs of amino-acid atoms. A simple free energy model of the receptor-ligand system is constructed from these atom-atom preferences and used to assess the energetic importance of interfacial interactions. The free energy approximation of binding strength in this model has a reliability of about +/- 1.5 kcal/mol, despite limited knowledge of the unbound states. The main utility of such a scheme lies in the identification of important stabilizing atomic interactions across the receptor-ligand interface. Thus, apart from an overall hydrophobic attraction (Young L, Jernigan RL, Covell DG, 1994, Protein Sci 3:717-729), a rich variety of specific interactions is observed. An analysis of 10 HIV-1 protease inhibitor complexes is presented that reveals a common binding motif comprised of energetically important contacts with a rather limited set of atoms. Design improvements to existing HIV-1 protease inhibitors are explored based on a detailed analysis of this binding motif.
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Affiliation(s)
- A Wallqvist
- Frederick Cancer Research and Development Center, National Cancer Institute, Frederick, Maryland 21702, USA
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Chapter 15. Antiviral Agents. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 1995. [DOI: 10.1016/s0065-7743(08)60928-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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