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He X, Walker B, Man VH, Ren P, Wang J. Recent progress in general force fields of small molecules. Curr Opin Struct Biol 2022; 72:187-193. [PMID: 34942567 PMCID: PMC8860847 DOI: 10.1016/j.sbi.2021.11.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 09/10/2021] [Accepted: 11/16/2021] [Indexed: 02/03/2023]
Abstract
Recent advances in computational hardware and free energy algorithms enable a broader application of molecular simulation of binding interactions between receptors and small-molecule ligands. The underlying molecular mechanics force fields (FFs) for small molecules have also achieved advancements in accuracy, user-friendliness, and speed during the past several years (2018-2020). Besides the expansion of chemical space coverage of ligand-like molecules among major popular classical additive FFs and polarizable FFs, new charge models have been proposed for better accuracy and transferability, new chemical perception of avoiding predefined atom types have been applied, and new automated parameterization toolkits, including machine learning approaches, have been developed for users' convenience.
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Affiliation(s)
- Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Brandon Walker
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Viet H. Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, USA,Corresponding authors: Pengyu Ren (), Junmei Wang ()
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA,Corresponding authors: Pengyu Ren (), Junmei Wang ()
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Burai Patrascu M, Pottel J, Pinus S, Bezanson M, Norrby PO, Moitessier N. From desktop to benchtop with automated computational workflows for computer-aided design in asymmetric catalysis. Nat Catal 2020. [DOI: 10.1038/s41929-020-0468-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Wei W, Champion C, Barigye SJ, Liu Z, Labute P, Moitessier N. Use of Extended-Hückel Descriptors for Rapid and Accurate Predictions of Conjugated Torsional Energy Barriers. J Chem Inf Model 2020; 60:3534-3545. [DOI: 10.1021/acs.jcim.0c00440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wanlei Wei
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal H3A 0B8, Québec, Canada
| | - Candide Champion
- Chemical Computing Group Incorporation, 1010 Sherbrooke St. W., Montreal H3A 2R7, Québec, Canada
| | - Stephen J. Barigye
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal H3A 0B8, Québec, Canada
| | - Zhaomin Liu
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal H3A 0B8, Québec, Canada
| | - Paul Labute
- Chemical Computing Group Incorporation, 1010 Sherbrooke St. W., Montreal H3A 2R7, Québec, Canada
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal H3A 0B8, Québec, Canada
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Champion C, Barigye SJ, Wei W, Liu Z, Labute P, Moitessier N. Atom Type Independent Modeling of the Conformational Energy of Benzylic, Allylic, and Other Bonds Adjacent to Conjugated Systems. J Chem Inf Model 2019; 59:4750-4763. [PMID: 31589815 DOI: 10.1021/acs.jcim.9b00581] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Applications of computational methods to predict binding affinities for protein/drug complexes are routinely used in structure-based drug discovery. Applications of these methods often rely on empirical force fields (FFs) and their associated parameter sets and atom types. However, it is widely accepted that FFs cannot accurately cover the entire chemical space of drug-like molecules, due to the restrictive cost of parametrization and the poor transferability of existing parameters. To address these limitations, initiatives have been carried out to develop more transferable methods, in order to allow for more rigorous descriptions of any drug-like molecule. We have previously reported H-TEQ, a method which does not rely on atom types and incorporates well established chemical principles to assign parameters to organic molecules. The previous implementation of H-TEQ (a torsional barrier prediction method) only covered saturated and lone pair containing molecules; here, we report our efforts to incorporate conjugated systems into our model. The next step was the evaluation of the introduction of unsaturations. The developed model (H-TEQ3.0) has been validated on a wide variety of molecules containing heteroaromatic groups, alkyls, and fused ring systems. Our method performs on par with one of the most commonly used FFs (GAFF2), without relying on atom types or any prior parametrization.
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Affiliation(s)
- Candide Champion
- Department of Chemistry , McGill University , 801 Sherbrooke Street W. , Montréal , QC , Canada H3A 0B8
| | - Stephen J Barigye
- Department of Chemistry , McGill University , 801 Sherbrooke Street W. , Montréal , QC , Canada H3A 0B8
| | - Wanlei Wei
- Department of Chemistry , McGill University , 801 Sherbrooke Street W. , Montréal , QC , Canada H3A 0B8
| | - Zhaomin Liu
- Department of Chemistry , McGill University , 801 Sherbrooke Street W. , Montréal , QC , Canada H3A 0B8
| | - Paul Labute
- Chemical Computing Group Inc. , 1010 Sherbrooke Street W. , Montréal , QC , Canada H3A 2R7
| | - Nicolas Moitessier
- Department of Chemistry , McGill University , 801 Sherbrooke Street W. , Montréal , QC , Canada H3A 0B8
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Wei W, Champion C, Liu Z, Barigye SJ, Labute P, Moitessier N. Torsional Energy Barriers of Biaryls Could Be Predicted by Electron Richness/Deficiency of Aromatic Rings; Advancement of Molecular Mechanics toward Atom-Type Independence. J Chem Inf Model 2019; 59:4764-4777. [PMID: 31430147 DOI: 10.1021/acs.jcim.9b00585] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Biaryl molecules are ubiquitous pharmacophores found in natural products and pharmaceuticals. In spite of this, existing molecular mechanics force fields are unable to accurately reproduce their torsional energy profiles, except for a few well-parametrized cases. This effectively limits the ability of structure-based drug design methods to correctly identify hits involving biaryls with confidence (e.g., during virtual screening, employing docking and/or molecular dynamics simulations). Continuing in our endeavor to quantify organic chemistry principles, we showed that the torsional energy profile of biaryl compounds could be computed on-the-fly based on the electron richness/deficiency of the aromatic rings. This method, called H-TEQ 4.0, was developed using a set of 131 biaryls. It was subsequently validated on a separate set of 100 diverse biaryls, including multisubstituted, bicyclic and tricyclic druglike molecules, and produced an average root-mean-square error (RMSE) of 0.95 kcal·mol-1. For comparison, GAFF2 produced an RMSE of 3.88 kcal·mol-1, owing to problems associated with the transferability of torsion parameters. The success of H-TEQ 4.0 provided further evidence that force fields could transition to become atom-type independent, providing that the correct chemical principles are used. Overall, this method solved the problem of transferability of biaryl torsion parameters, while simultaneously improving the overall accuracy of the force field.
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Affiliation(s)
- Wanlei Wei
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montréal , Quebec , Canada H3A 0B8
| | - Candide Champion
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montréal , Quebec , Canada H3A 0B8
| | - Zhaomin Liu
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montréal , Quebec , Canada H3A 0B8
| | - Stephen J Barigye
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montréal , Quebec , Canada H3A 0B8
| | - Paul Labute
- Chemical Computing Group Inc. , 1010 Sherbrooke Street West , Montréal , Quebec , Canada H3A 2R7
| | - Nicolas Moitessier
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montréal , Quebec , Canada H3A 0B8
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Liu Z, Barigye SJ, Shahamat M, Labute P, Moitessier N. Atom Types Independent Molecular Mechanics Method for Predicting the Conformational Energy of Small Molecules. J Chem Inf Model 2018; 58:194-205. [PMID: 29253333 DOI: 10.1021/acs.jcim.7b00645] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We previously implemented a well-known qualitative chemical principle into an accurate quantitative model computing relative potential energies of conformers. According to this principle, hyperconjugation strength correlates with electronegativity of donors and acceptors. While this earlier version of our model applies to σ bonds, lone pairs, disregarded in this earlier version, also have a major impact on the conformational preferences of molecules. Among the well-established principles used by organic chemists to rationalize some organic chemical behaviors are the anomeric effect, the alpha effect, basicity, and nucleophilicity. These effects are directly related to the presence of lone pairs. We report herein our effort to incorporate lone pairs into our model to extend its applicability domain to any saturated small molecules. The developed model H-TEQ 2 has been validated on a wide variety of molecules from polyaromatic molecules to carbohydrates and molecules with high heteroatoms/carbon ratios. Interestingly, this method, in contrast to common force field-based methods, does not rely on atom types and is virtually applicable to any organic molecules.
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Affiliation(s)
- Zhaomin Liu
- Department of Chemistry, McGill University , 801 Sherbrooke Street W., Montréal, QC, Canada H3A 0B8
| | - Stephen J Barigye
- Department of Chemistry, McGill University , 801 Sherbrooke Street W., Montréal, QC, Canada H3A 0B8
| | - Moeed Shahamat
- Department of Chemistry, McGill University , 801 Sherbrooke Street W., Montréal, QC, Canada H3A 0B8
| | - Paul Labute
- Chemical Computing Group Inc. , 1010 Sherbrooke Street W., Montréal, QC, Canada H3A 2R7
| | - Nicolas Moitessier
- Department of Chemistry, McGill University , 801 Sherbrooke Street W., Montréal, QC, Canada H3A 0B8
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Burai Patrascu M, Malek-Adamian E, Damha MJ, Moitessier N. Accurately Modeling the Conformational Preferences of Nucleosides. J Am Chem Soc 2017; 139:13620-13623. [PMID: 28899099 DOI: 10.1021/jacs.7b07436] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Mihai Burai Patrascu
- Department of Chemistry, McGill University, 801
Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Elise Malek-Adamian
- Department of Chemistry, McGill University, 801
Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Masad J. Damha
- Department of Chemistry, McGill University, 801
Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801
Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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Wu X, Dai C, Fang S, Li H, Wu Y, Sun X, Zhao M. The effect of hydroxyl on the solution behavior of a quaternary ammonium gemini surfactant. Phys Chem Chem Phys 2017; 19:16047-16056. [DOI: 10.1039/c7cp00131b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The influence of the introduction of a hydroxyl group into the system is studied at the macro and micro levels.
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Affiliation(s)
- Xuepeng Wu
- School of Petroleum Engineering
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum (East China)
- Qingdao
- China
| | - Caili Dai
- School of Petroleum Engineering
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum (East China)
- Qingdao
- China
| | - Sisi Fang
- School of Petroleum Engineering
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum (East China)
- Qingdao
- China
| | - Hao Li
- School of Petroleum Engineering
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum (East China)
- Qingdao
- China
| | - Yining Wu
- School of Petroleum Engineering
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum (East China)
- Qingdao
- China
| | - Xin Sun
- School of Petroleum Engineering
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum (East China)
- Qingdao
- China
| | - Mingwei Zhao
- School of Petroleum Engineering
- State Key Laboratory of Heavy Oil Processing
- China University of Petroleum (East China)
- Qingdao
- China
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