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Tan SL, Lee SM, Lo KM, Otero-de-la-Roza A, Tiekink ERT. Experimental and computational evidence for a stabilising C–Cl(lone-pair)⋯π(chelate-ring) interaction. CrystEngComm 2021. [DOI: 10.1039/d0ce01478h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Stabilising C–Cl(lone-pair)⋯π(chelate ring) interactions are described.
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Affiliation(s)
- Sang Loon Tan
- Research Centre for Crystalline Materials
- School of Science and Technology
- Sunway University
- 47500 Bandar Sunway
- Malaysia
| | - See Mun Lee
- Research Centre for Crystalline Materials
- School of Science and Technology
- Sunway University
- 47500 Bandar Sunway
- Malaysia
| | - Kong Mun Lo
- Research Centre for Crystalline Materials
- School of Science and Technology
- Sunway University
- 47500 Bandar Sunway
- Malaysia
| | - A. Otero-de-la-Roza
- Departamento de Química Física y Analítica
- Facultad de Química
- Universidad de Oviedo
- 33006 Oviedo
- Spain
| | - Edward R. T. Tiekink
- Research Centre for Crystalline Materials
- School of Science and Technology
- Sunway University
- 47500 Bandar Sunway
- Malaysia
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2
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Gu C, Cai J, Fan X, Bian Y, Yang X, Xia Q, Sun C, Jiang X. Theoretical investigation of AhR binding property with relevant structural requirements for AhR-mediated toxicity of polybrominated diphenyl ethers. CHEMOSPHERE 2020; 249:126554. [PMID: 32213394 DOI: 10.1016/j.chemosphere.2020.126554] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 06/10/2023]
Abstract
Polybrominated diphenyl ethers (PBDEs) are more frequently suspected with the induction of toxicity via signal transduction pathway of cytosolic aryl hydrocarbon receptor (AhR), the initial binding to which is assumed to be an essential prerequisite during the ligand-dependent activation. However, the AhR binding property and associated toxicity of PBDEs is yet to be clearly known for lacking insights into the structural requirements at molecular level. To understand the AhR binding property of PBDEs, the ligand binding domain (LBD) of AhR was simulatively developed on homologous protein after basic validation of geometrical rationality and the binding interaction profile was visually described using molecular docking approach. For AhR binding, the offset or edge-on π-π stackings with aromatic motifs including Phe289, Phe345 and His285 were shown to be structurally required whereas the electrostatic attraction validated for AhR binding to dioxins might be less effective for 2,2',3,4,4'-pentabromodiphenyl ether (BDE-85). Besides the demands of less steric hindrance from alanines and weak formulation of hydrogen bonds, the dispersion force through large contact and polarization of S-π electrons seemed to be impactful when BDE-85 were closer to Cys327, Met334 or Met342. With theoretical computation of AhR binding energies, the more significant correlativity with bioassays was derived especially for the lowly/moderately brominated congeners, and could be used to predict the AhR binding affinity on certain degree. The informative results would thus not only help well understand the molecular basis of AhR-mediated toxicity but give an approach for accelerative evaluation of AhR binding and toxicity of PBDEs.
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Affiliation(s)
- Chenggang Gu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China.
| | - Jun Cai
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China; University of the Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Xiuli Fan
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China; University of the Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yongrong Bian
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Xinglun Yang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China
| | - Qiying Xia
- Shandong Province Key Laboratory of Soil Conservation and Environmental Protection, Linyi University, Linyi, 276005, PR China.
| | - Cheng Sun
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing, 210023, PR China
| | - Xin Jiang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China.
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Kula K, Dobosz J, Jasiński R, Kącka-Zych A, Łapczuk-Krygier A, Mirosław B, Demchuk OM. [3+2] Cycloaddition of diaryldiazomethanes with (E)-3,3,3-trichloro-1-nitroprop-1-ene: An experimental, theoretical and structural study. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127473] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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4
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Amsharov KY, Holzwarth J, Roshchyna K, Sharapa DI, Hampel F, Hirsch A. Synthesis, Structural Characterization, and Crystal Packing of the Elusive Pentachlorinated Azafullerene C 59 NCl 5. Chemistry 2017; 23:9014-9017. [PMID: 28464445 DOI: 10.1002/chem.201700802] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Indexed: 11/07/2022]
Abstract
We report on the synthesis and the structure elucidation of the elusive azafullerene pentachloride C59 NCl5 , which was obtained by high temperature halogenation of (C59 N)2 . The exceptionally strong host-guest interaction of the title compound in the solid is discussed.
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Affiliation(s)
- Konstantin Yu Amsharov
- Lehrstuhl für Organische Chemie II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestrasse 42, 91054, Erlangen, Germany
| | - Johannes Holzwarth
- Lehrstuhl für Organische Chemie II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestrasse 42, 91054, Erlangen, Germany
| | - Kateryna Roshchyna
- Lehrstuhl für Organische Chemie II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestrasse 42, 91054, Erlangen, Germany
| | - Dmitry I Sharapa
- Computer-Chemie-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nägelsbachstrasse 25, 91052, Erlangen, Germany
| | - Frank Hampel
- Lehrstuhl für Organische Chemie II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestrasse 42, 91054, Erlangen, Germany
| | - Andreas Hirsch
- Lehrstuhl für Organische Chemie II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestrasse 42, 91054, Erlangen, Germany
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5
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McNeece AJ, Mokhtarzadeh CC, Moore CE, Rheingold AL, Figueroa JS. Nickel bis- m-terphenylisocyanide dihalide complexes formed from 1,2-alkyl dihalides: probing for isolable β-haloalkyl complexes of square planar nickel. J COORD CHEM 2016. [DOI: 10.1080/00958972.2016.1172702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Andrew J. McNeece
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | | | - Curtis E. Moore
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Arnold L. Rheingold
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Joshua S. Figueroa
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
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6
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Schicke O, Faure B, Carissan Y, Giorgi M, Jalila Simaan A, Réglier M. Synthesis and Characterization of a Dinuclear Copper Complex Bearing a Hydrophobic Cavity as a Model for Copper‐Containing Monooxygenases. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Olivier Schicke
- Aix Marseille Université, Centrale Marseille, CNRS, ISM2 UMR 7313, 13397 Marseille, France http://ism2.univ‐amu.fr/pages‐bleues/index2.htm
| | - Bruno Faure
- Aix Marseille Université, Centrale Marseille, CNRS, ISM2 UMR 7313, 13397 Marseille, France http://ism2.univ‐amu.fr/pages‐bleues/index2.htm
| | - Yannick Carissan
- Aix Marseille Université, Centrale Marseille, CNRS, ISM2 UMR 7313, 13397 Marseille, France http://ism2.univ‐amu.fr/pages‐bleues/index2.htm
| | - Michel Giorgi
- Aix Marseille Université, Spectropole, CNRS, FR1739, 13397 Marseille, France
| | - Ariane Jalila Simaan
- Aix Marseille Université, Centrale Marseille, CNRS, ISM2 UMR 7313, 13397 Marseille, France http://ism2.univ‐amu.fr/pages‐bleues/index2.htm
| | - Marius Réglier
- Aix Marseille Université, Centrale Marseille, CNRS, ISM2 UMR 7313, 13397 Marseille, France http://ism2.univ‐amu.fr/pages‐bleues/index2.htm
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7
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The Bright Future of Unconventional σ/π-Hole Interactions. Chemphyschem 2015; 16:2496-517. [DOI: 10.1002/cphc.201500314] [Citation(s) in RCA: 475] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 01/25/2023]
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8
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Cadoni E, Ferino G, Pitzanti P, Secci F, Fattuoni C, Nicolò F, Bruno G. Halogen and Hydrogen Bonding Benzothiophene Diol Derivatives: A Study Using ab initio Calculations and X-Ray Crystal Structure Measurements. ChemistryOpen 2015; 4:161-8. [PMID: 25969814 PMCID: PMC4420588 DOI: 10.1002/open.201402087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Indexed: 12/03/2022] Open
Abstract
The aim of this study is to describe and compare the supramolecular interactions, in the solid state, of chloro-, bromo-, and iodobenzothiophene diols. The compounds were obtained through organo-catalyzed reactions starting from 3-substituted halobenzothiophene carbaldehydes. Energies of the noncovalent interactions were obtained by density functional theory calculations. Bond distances and angles were found to be in accordance with those determined by X-ray structure analysis. anti-Bromobenzothiophene derivatives showed strong halogen⋅⋅⋅π interactions between bromine and the heterocyclic phenyl ring, corresponding to an energy of 7.5 kcal mol(-1). syn-Bromo and syn-iodo derivatives appeared to be isostructural, showing X⋅⋅⋅O (carbonyl) interactions, π stacking, and formation of extended hydrogen bonding networks. In contrast, the chloro derivatives displayed no halogen bonding interactions.
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Affiliation(s)
- Enzo Cadoni
- Dipartimento di Scienze Chimiche, Università degli Studi di Cagliari, Cittadella Universitaria di MonserratoSS 554, Bivio per Sestu, 90042, Monserrato, CA, Italy
| | - Giulio Ferino
- Dipartimento di Scienze Chimiche, Università degli Studi di Cagliari, Cittadella Universitaria di MonserratoSS 554, Bivio per Sestu, 90042, Monserrato, CA, Italy
| | - Patrizia Pitzanti
- Dipartimento di Scienze Chimiche, Università degli Studi di Cagliari, Cittadella Universitaria di MonserratoSS 554, Bivio per Sestu, 90042, Monserrato, CA, Italy
| | - Francesco Secci
- Dipartimento di Scienze Chimiche, Università degli Studi di Cagliari, Cittadella Universitaria di MonserratoSS 554, Bivio per Sestu, 90042, Monserrato, CA, Italy
| | - Claudia Fattuoni
- Dipartimento di Scienze Chimiche, Università degli Studi di Cagliari, Cittadella Universitaria di MonserratoSS 554, Bivio per Sestu, 90042, Monserrato, CA, Italy
| | - Francesco Nicolò
- Dipartimento di Scienze Chimiche, Università degli Studi di MessinaSalita Sperone 31, Villaggio S. Agata, 98166, Messina, Italy
| | - Giuseppe Bruno
- Dipartimento di Scienze Chimiche, Università degli Studi di MessinaSalita Sperone 31, Villaggio S. Agata, 98166, Messina, Italy
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Carpenter AE, McNeece AJ, Barnett BR, Estrada AL, Mokhtarzadeh CC, Moore CE, Rheingold AL, Perrin CL, Figueroa JS. Direct Observation of β-Chloride Elimination from an Isolable β-Chloroalkyl Complex of Square-Planar Nickel. J Am Chem Soc 2014; 136:15481-4. [DOI: 10.1021/ja508956q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alex E. Carpenter
- Department of Chemistry and
Biochemistry, University of California, San Diego, 9500 Gilman
Drive, Mail Code 0358, La Jolla, California 92093-0358, United States
| | - Andrew J. McNeece
- Department of Chemistry and
Biochemistry, University of California, San Diego, 9500 Gilman
Drive, Mail Code 0358, La Jolla, California 92093-0358, United States
| | - Brandon R. Barnett
- Department of Chemistry and
Biochemistry, University of California, San Diego, 9500 Gilman
Drive, Mail Code 0358, La Jolla, California 92093-0358, United States
| | - Alexander L. Estrada
- Department of Chemistry and
Biochemistry, University of California, San Diego, 9500 Gilman
Drive, Mail Code 0358, La Jolla, California 92093-0358, United States
| | - Charles C. Mokhtarzadeh
- Department of Chemistry and
Biochemistry, University of California, San Diego, 9500 Gilman
Drive, Mail Code 0358, La Jolla, California 92093-0358, United States
| | - Curtis E. Moore
- Department of Chemistry and
Biochemistry, University of California, San Diego, 9500 Gilman
Drive, Mail Code 0358, La Jolla, California 92093-0358, United States
| | - Arnold L. Rheingold
- Department of Chemistry and
Biochemistry, University of California, San Diego, 9500 Gilman
Drive, Mail Code 0358, La Jolla, California 92093-0358, United States
| | - Charles L. Perrin
- Department of Chemistry and
Biochemistry, University of California, San Diego, 9500 Gilman
Drive, Mail Code 0358, La Jolla, California 92093-0358, United States
| | - Joshua S. Figueroa
- Department of Chemistry and
Biochemistry, University of California, San Diego, 9500 Gilman
Drive, Mail Code 0358, La Jolla, California 92093-0358, United States
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Fradera X, Kazemier B, Carswell E, Cooke A, Oubrie A, Hamilton W, Dempster M, Krapp S, Nagel S, Jestel A. High-resolution crystal structures of factor XIa coagulation factor in complex with nonbasic high-affinity synthetic inhibitors. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:404-8. [PMID: 22505407 PMCID: PMC3325807 DOI: 10.1107/s1744309112009037] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Accepted: 02/29/2012] [Indexed: 01/18/2023]
Abstract
Factor XI (FXI) is a key enzyme in the coagulation pathway and an attractive target for the development of anticoagulant drugs. A small number of high-resolution crystal structures of FXIa in complex with small synthetic inhibitors have been published to date. All of these ligands have a basic P1 group and bind exclusively in the nonprime side of the active site of FXIa. Here, two structures of FXIa in complex with nonbasic inhibitors that occupy both the prime and nonprime sides of the active site are presented. These new structures could be valuable in the design and optimization of new FXIa synthethic inhibitors.
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Affiliation(s)
- Xavier Fradera
- Merck Research Laboratories, MSD, Newhouse, Lanarkshire ML1 5SH, Scotland.
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11
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Ichihara O, Barker J, Law RJ, Whittaker M. Compound Design by Fragment-Linking. Mol Inform 2011; 30:298-306. [PMID: 27466947 DOI: 10.1002/minf.201000174] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 02/14/2010] [Indexed: 12/21/2022]
Abstract
The linking together of two fragment compounds that bind to distinct protein sub-sites can lead to a superadditivity of binding affinities, in which the binding free energy of the linked fragments exceeds the simple sum of the binding energies of individual fragments (linking coefficient E<1). However, a review of the literature shows that such events are relatively rare and, in the majority of the cases, linking coefficients are far from optimal being much greater than 1. It is critical to design a linker that does not disturb the original binding poses of each fragment in order to achieve successful linking. However, such an ideal linker is often difficult to design and even more difficult to actually synthesize. We suggest that the chance of achieving successful fragment linking can be significantly improved by choosing a fragment pair that consists of one fragment that binds by strong H-bonds (or non-classical equivalents) and a second fragment that is more tolerant of changes in binding mode (hydrophobic or vdW binders). We also propose that the fragment molecular orbital (FMO) calculations can be used to analyse the nature of the binding interactions of the fragment hits for the selection of fragments for evolution, merging and linking in order to optimize the chance of success.
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Affiliation(s)
- Osamu Ichihara
- Evotec (UK) Ltd, 114 Milton Park, Abingdon, OXON, OX14 4SA, UK phone: +44(0)1235 441238
| | - John Barker
- Evotec (UK) Ltd, 114 Milton Park, Abingdon, OXON, OX14 4SA, UK phone: +44(0)1235 441238
| | - Richard J Law
- Evotec (UK) Ltd, 114 Milton Park, Abingdon, OXON, OX14 4SA, UK phone: +44(0)1235 441238
| | - Mark Whittaker
- Evotec (UK) Ltd, 114 Milton Park, Abingdon, OXON, OX14 4SA, UK phone: +44(0)1235 441238.
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Mazanetz MP, Ichihara O, Law RJ, Whittaker M. Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method. J Cheminform 2011; 3:2. [PMID: 21219630 PMCID: PMC3032746 DOI: 10.1186/1758-2946-3-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 01/10/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The reliable and robust estimation of ligand binding affinity continues to be a challenge in drug design. Many current methods rely on molecular mechanics (MM) calculations which do not fully explain complex molecular interactions. Full quantum mechanical (QM) computation of the electronic state of protein-ligand complexes has recently become possible by the latest advances in the development of linear-scaling QM methods such as the ab initio fragment molecular orbital (FMO) method. This approximate molecular orbital method is sufficiently fast that it can be incorporated into the development cycle during structure-based drug design for the reliable estimation of ligand binding affinity. Additionally, the FMO method can be combined with approximations for entropy and solvation to make it applicable for binding affinity prediction for a broad range of target and chemotypes. RESULTS We applied this method to examine the binding affinity for a series of published cyclin-dependent kinase 2 (CDK2) inhibitors. We calculated the binding affinity for 28 CDK2 inhibitors using the ab initio FMO method based on a number of X-ray crystal structures. The sum of the pair interaction energies (PIE) was calculated and used to explain the gas-phase enthalpic contribution to binding. The correlation of the ligand potencies to the protein-ligand interaction energies gained from FMO was examined and was seen to give a good correlation which outperformed three MM force field based scoring functions used to appoximate the free energy of binding. Although the FMO calculation allows for the enthalpic component of binding interactions to be understood at the quantum level, as it is an in vacuo single point calculation, the entropic component and solvation terms are neglected. For this reason a more accurate and predictive estimate for binding free energy was desired. Therefore, additional terms used to describe the protein-ligand interactions were then calculated to improve the correlation of the FMO derived values to experimental free energies of binding. These terms were used to account for the polar and non-polar solvation of the molecule estimated by the Poisson-Boltzmann equation and the solvent accessible surface area (SASA), respectively, as well as a correction term for ligand entropy. A quantitative structure-activity relationship (QSAR) model obtained by Partial Least Squares projection to latent structures (PLS) analysis of the ligand potencies and the calculated terms showed a strong correlation (r2 = 0.939, q2 = 0.896) for the 14 molecule test set which had a Pearson rank order correlation of 0.97. A training set of a further 14 molecules was well predicted (r2 = 0.842), and could be used to obtain meaningful estimations of the binding free energy. CONCLUSIONS Our results show that binding energies calculated with the FMO method correlate well with published data. Analysis of the terms used to derive the FMO energies adds greater understanding to the binding interactions than can be gained by MM methods. Combining this information with additional terms and creating a scaled model to describe the data results in more accurate predictions of ligand potencies than the absolute values obtained by FMO alone.
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Affiliation(s)
- Michael P Mazanetz
- Evotec (UK) limited, 114 Milton Park, Abingdon, Oxfordshire, OX14 4SA, UK
| | - Osamu Ichihara
- Evotec (UK) limited, 114 Milton Park, Abingdon, Oxfordshire, OX14 4SA, UK
| | - Richard J Law
- Evotec (UK) limited, 114 Milton Park, Abingdon, Oxfordshire, OX14 4SA, UK
| | - Mark Whittaker
- Evotec (UK) limited, 114 Milton Park, Abingdon, Oxfordshire, OX14 4SA, UK
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Wallnoefer HG, Fox T, Liedl KR, Tautermann CS. Dispersion dominated halogen–π interactions: energies and locations of minima. Phys Chem Chem Phys 2010; 12:14941-9. [DOI: 10.1039/c0cp00607f] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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