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Ganotra GK, Wade RC. Prediction of Drug-Target Binding Kinetics by Comparative Binding Energy Analysis. ACS Med Chem Lett 2018; 9:1134-1139. [PMID: 30429958 PMCID: PMC6231175 DOI: 10.1021/acsmedchemlett.8b00397] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/04/2018] [Indexed: 12/02/2022] Open
Abstract
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A growing
consensus is emerging that optimizing the drug–target
affinity alone under equilibrium conditions does not necessarily translate
into higher potency in vivo and that instead binding kinetic parameters
should be optimized to ensure better efficacy. Therefore, in silico
methods are needed to predict the kinetic parameters and the mechanistic
determinants of drug–protein binding. Here we demonstrate the
application of COMparative BINding Energy (COMBINE) analysis to derive
quantitative structure–kinetics relationships (QSKRs) for the
dissociation rate constants (koff) of
inhibitors of heat shock protein 90 (HSP90) and HIV-1 protease. We
derived protein-specific scoring functions by correlating koff rate constants with a subset of weighted
interaction energy components determined from the energy-minimized
structures of drug–protein complexes. As the QSKRs derived
for these sets of chemically diverse compounds have good predictive
ability and provide insights into important drug–protein interactions
for optimizing koff, COMBINE analysis
offers a promising approach for binding kinetics-guided lead optimization.
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Affiliation(s)
- Gaurav K. Ganotra
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Rebecca C. Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, 69118 Heidelberg, Germany
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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2
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Teruya K, Hattori Y, Shimamoto Y, Kobayashi K, Sanjoh A, Nakagawa A, Yamashita E, Akaji K. Structural basis for the development of SARS 3CL protease inhibitors from a peptide mimic to an aza-decaline scaffold. Biopolymers 2016; 106:391-403. [PMID: 26572934 PMCID: PMC7159131 DOI: 10.1002/bip.22773] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/22/2015] [Accepted: 11/02/2015] [Indexed: 02/03/2023]
Abstract
Design of inhibitors against severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CL(pro) ) is a potentially important approach to fight against SARS. We have developed several synthetic inhibitors by structure-based drug design. In this report, we reveal two crystal structures of SARS 3CL(pro) complexed with two new inhibitors based on our previous work. These structures combined with six crystal structures complexed with a series of related ligands reported by us are collectively analyzed. To these eight complexes, the structural basis for inhibitor binding was analyzed by the COMBINE method, which is a chemometrical analysis optimized for the protein-ligand complex. The analysis revealed that the first two latent variables gave a cumulative contribution ratio of r(2) = 0.971. Interestingly, scores using the second latent variables for each complex were strongly correlated with root mean square deviations (RMSDs) of side-chain heavy atoms of Met(49) from those of the intact crystal structure of SARS-3CL(pro) (r = 0.77) enlarging the S2 pocket. The substantial contribution of this side chain (∼10%) for the explanation of pIC50 s was dependent on stereochemistry and the chemical structure of the ligand adapted to the S2 pocket of the protease. Thus, starting from a substrate mimic inhibitor, a design for a central scaffold for a low molecular weight inhibitor was evaluated to develop a further potent inhibitor. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 391-403, 2016.
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Affiliation(s)
- Kenta Teruya
- Department of NeurochemistryTohoku University Graduate School of MedicineAoba‐Ku Sendai980‐8575Japan
| | - Yasunao Hattori
- Department of Medicinal ChemistryKyoto Pharmaceutical UniversityYamashina‐KuKyoto607‐8412Japan
| | - Yasuhiro Shimamoto
- Department of Medicinal ChemistryKyoto Pharmaceutical UniversityYamashina‐KuKyoto607‐8412Japan
| | - Kazuya Kobayashi
- Department of Medicinal ChemistryKyoto Pharmaceutical UniversityYamashina‐KuKyoto607‐8412Japan
| | | | - Atsushi Nakagawa
- Institute for Protein Research, Osaka UniversitySuitaOsaka565‐0871Japan
| | - Eiki Yamashita
- Institute for Protein Research, Osaka UniversitySuitaOsaka565‐0871Japan
| | - Kenichi Akaji
- Department of Medicinal ChemistryKyoto Pharmaceutical UniversityYamashina‐KuKyoto607‐8412Japan
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3
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Abia D, Bastolla U, Chacón P, Fábrega C, Gago F, Morreale A, Tramontano A. In memoriam. Proteins 2010; 78:iii-viii. [DOI: 10.1002/prot.22660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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4
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Rao H, Yang G, Tan N, Li P, Li Z, Li X. Prediction of HIV-1 Protease Inhibitors Using Machine Learning Approaches. ACTA ACUST UNITED AC 2009. [DOI: 10.1002/qsar.200960021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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5
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Henrich S, Feierberg I, Wang T, Blomberg N, Wade RC. Comparative binding energy analysis for binding affinity and target selectivity prediction. Proteins 2009; 78:135-53. [DOI: 10.1002/prot.22579] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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6
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Gil-Redondo R, Klett J, Gago F, Morreale A. gCOMBINE: A graphical user interface to perform structure-based comparative binding energy (COMBINE) analysis on a set of ligand-receptor complexes. Proteins 2009; 78:162-72. [DOI: 10.1002/prot.22543] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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Kuzmanovski I, Novič M, Trpkovska M. Automatic adjustment of the relative importance of different input variables for optimization of counter-propagation artificial neural networks. Anal Chim Acta 2009; 642:142-7. [DOI: 10.1016/j.aca.2009.01.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Revised: 11/25/2008] [Accepted: 01/19/2009] [Indexed: 10/21/2022]
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8
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Dezi C, Brea J, Alvarado M, Raviña E, Masaguer CF, Loza MI, Sanz F, Pastor M. Multistructure 3D-QSAR studies on a series of conformationally constrained butyrophenones docked into a new homology model of the 5-HT2A receptor. J Med Chem 2007; 50:3242-55. [PMID: 17579386 DOI: 10.1021/jm070277a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present study is part of a long-term research project aiming to gain insight into the mechanism of action of atypical antipsychotics. Here we describe a 3D-QSAR study carried out on a series of butyrophenones with affinity for the serotonin-2A receptor, aligned by docking into the binding site of a receptor model. The series studied has two peculiarities: (i) all the compounds have a chiral center and can be represented by two enantiomeric structures, and (ii) many of the structures can bind the receptor in two alternative orientations, posing the problem of how to select a single representative structure for every compound. We have used an original solution consisting of the simultaneous use of multiple structures, representing different configurations, binding conformations, and positions. The final model showed good statistical quality (n = 426, r2 = 0.84, q2LOO = 0.81) and its interpretation provided useful information, not obtainable from the simple inspection of the ligand-receptor complexes.
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Affiliation(s)
- Cristina Dezi
- Research Unit on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, Dr. Aiguader 88, E-08003 Barcelona, Spain
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9
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Wade RC, Henrich S, Wang T. Using 3D protein structures to derive 3D-QSARs. DRUG DISCOVERY TODAY. TECHNOLOGIES 2004; 1:241-246. [PMID: 24981491 DOI: 10.1016/j.ddtec.2004.11.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The three-dimensional structures of proteins are being solved apace, yet this information is often underused in quantitative structure-activity relationship (QSAR) studies. Here, we describe and compare methods for exploiting protein structures to derive 3D-QSARs. These methods can facilitate molecular design and lead optimization and should increasingly become a standard component of the drug designer's repertoire.:
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Affiliation(s)
- Rebecca C Wade
- Molecular and Cellular Modeling Group, EML Research, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany.
| | - Stefan Henrich
- Molecular and Cellular Modeling Group, EML Research, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany
| | - Ting Wang
- Molecular and Cellular Modeling Group, EML Research, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany
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Murcia M, Ortiz AR. Virtual screening with flexible docking and COMBINE-based models. Application to a series of factor Xa inhibitors. J Med Chem 2004; 47:805-20. [PMID: 14761183 DOI: 10.1021/jm030137a] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A two-step, fully automatic virtual screening procedure consisting of flexible docking followed by activity prediction by COMparative BINding Energy (COMBINE) analysis is presented. This novel approach has been successfully applied, as an example with medicinal chemistry interest, to a recently reported series of 133 factor Xa (fXa)(1) inhibitors whose activities encompass 4 orders of magnitude. The docking algorithm is linked to the COMBINE analysis program and used to derive independent regression models of the 133 inhibitors docked within three different fXa structures (PDB entries 1fjs, 1f0r, and 1xka), so as to explore the effect of receptor conformation on the overall results. Reliable docking conformations and predictive regression models requiring eight latent variables could be derived for two of the fXa structures, with the best model achieving a Q(2) of 0.63 and a standard deviation of errors of prediction (SDEP) of 0.51 (leave-one-out). The two-step procedure was then employed to screen a designed virtual library of 112 ligands, containing both active and inactive compounds. While docking energies alone could show a good performance for selecting hits, including structurally diverse ones, inclusion of COMBINE analysis regression models provided improved rankings for the identification of structurally related molecules in external sets. In our best case, a recognition rate of approximately 80% of known binders at approximately 15% false positives rate was achieved, corresponding to an enrichment factor of approximately 450% over random.
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Affiliation(s)
- Marta Murcia
- Department of Physiology & Biophysics, Mount Sinai School of Medicine, New York University, One Gustave Levy Place, Box 1218, New York, New York 10029, USA
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11
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Kmunícek J, Bohác M, Luengo S, Gago F, Wade RC, Damborský J. Comparative binding energy analysis of haloalkane dehalogenase substrates: modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations. J Comput Aided Mol Des 2003; 17:299-311. [PMID: 14635723 DOI: 10.1023/a:1026159215220] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We evaluate the applicability of automated molecular docking techniques and quantum mechanical calculations to the construction of a set of structures of enzyme-substrate complexes for use in Comparative binding energy (COMBINE) analysis to obtain 3D structure-activity relationships. The data set studied consists of the complexes of eighteen substrates docked within the active site of haloalkane dehalogenase (DhlA) from Xanthobacter autotrophicus GJ10. The results of the COMBINE analysis are compared with previously reported data obtained for the same dataset from modelled complexes that were based on an experimentally determined structure of the DhlA-dichloroethane complex. The quality of fit and the internal predictive power of the two COMBINE models are comparable, but better external predictions are obtained with the new approach. Both models show a similar composition of the principal components. Small differences in the relative contributions that are assigned to important residues for explaining binding affinity differences can be directly linked to structural differences in the modelled enzyme-substrate complexes: (i) rotation of all substrates in the active site about their longitudinal axis, (ii) repositioning of the ring of epihalohydrines and the halogen substituents of 1,2-dihalopropanes, and (iii) altered conformation of the long-chain molecules (halobutanes and halohexanes). For external validation, both a novel substrate not included in the training series and two different mutant proteins were used. The results obtained can be useful in the future to guide the rational engineering of substrate specificity in DhlA and other related enzymes.
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Affiliation(s)
- Jan Kmunícek
- National Centre for Biomolecular Research, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
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12
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Kiralj R, Ferreira MMC. A priori molecular descriptors in QSAR: a case of HIV-1 protease inhibitors. II. Molecular graphics and modeling. J Mol Graph Model 2003; 21:499-515. [PMID: 12676237 DOI: 10.1016/s1093-3263(02)00202-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Molecular graphics and modeling methods illustrated the chemical background of the a priori approach from part I, and visualized steric and electronic enzyme-inhibitor relationships at qualitative and quantitative level for 34 and its derivatives. The enzyme-inhibitor electron density overlap occurs at 1.5-5.5A cut-off distance, beyond van der Waals radii. Derivatives of 34 exhibit linear relationships between biological activity, molecular size and number of intermolecular interactions.
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Affiliation(s)
- Rudolf Kiralj
- Instituto de Química, Universidade Estadual de Campinas, Campinas, SP, Brazil
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Kiralj R, Ferreira MMC. A priori molecular descriptors in QSAR: a case of HIV-1 protease inhibitors. I. The chemometric approach. J Mol Graph Model 2003; 21:435-48. [PMID: 12543139 DOI: 10.1016/s1093-3263(02)00201-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A quantitative structure-activity relationship (QSAR) study on 48 peptidic HIV-1 protease inhibitors was performed. Fourteen a priori molecular descriptors were used to build QSAR models. Hierarchical cluster analysis (HCA), principal component analysis (PCA) and partial least squares (PLS) regression were employed. PLS models with 32/16 (model I) and 48/0 (model II) molecules in the training/external validation set were constructed. The a priori molecular descriptors were related to two energetic variables using PLS. HCA and PCA on data from model II classified the inhibitors as slightly, moderately and highly active; three principal components, the chemical nature of which has been highlighted, are enough to describe the enzyme-inhibitor binding. Model I (r(2)=0.91, q(2)=0.84) is comparable to literature models obtained by various QSAR softwares, which justified the use of a priori descriptors.
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Affiliation(s)
- Rudolf Kiralj
- Instituto de Química, Universidade Estadual de Campinas, Campinas, SP 13083-970, Brazil
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14
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Kmunícek J, Luengo S, Gago F, Ortiz AR, Wade RC, Damborský J. Comparative binding energy analysis of the substrate specificity of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. Biochemistry 2001; 40:8905-17. [PMID: 11467952 DOI: 10.1021/bi010464p] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Comparative binding energy (COMBINE) analysis was conducted for 18 substrates of the haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 (DhlA): 1-chlorobutane, 1-chlorohexane, dichloromethane, 1,2-dichloroethane, 1,2-dichloropropane, 2-chloroethanol, epichlorohydrine, 2-chloroacetonitrile, 2-chloroacetamide, and their brominated analogues. The purpose of the COMBINE analysis was to identify the amino acid residues determining the substrate specificity of the haloalkane dehalogenase. This knowledge is essential for the tailoring of this enzyme for biotechnological applications. Complexes of the enzyme with these substrates were modeled and then refined by molecular mechanics energy minimization. The intermolecular enzyme-substrate energy was decomposed into residue-wise van der Waals and electrostatic contributions and complemented by surface area dependent and electrostatic desolvation terms. Partial least-squares projection to latent structures analysis was then used to establish relationships between the energy contributions and the experimental apparent dissociation constants. A model containing van der Waals and electrostatic intermolecular interaction energy contributions calculated using the AMBER force field explained 91% (73% cross-validated) of the quantitative variance in the apparent dissociation constants. A model based on van der Waals intermolecular contributions from AMBER and electrostatic interactions derived from the Poisson-Boltzmann equation explained 93% (74% cross-validated) of the quantitative variance. COMBINE models predicted correctly the change in apparent dissociation constants upon single-point mutation of DhlA for six enzyme-substrate complexes. The amino acid residues contributing most significantly to the substrate specificity of DhlA were identified; they include Asp124, Trp125, Phe164, Phe172, Trp175, Phe222, Pro223, and Leu263. These residues are suitable targets for modification by site-directed mutagenesis.
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Affiliation(s)
- J Kmunícek
- National Centre for Biomolecular Research, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
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