DFFR: A New Method for High-Throughput Recalibration of Automatic Force-Fields for Drugs.


Journal

Journal of chemical theory and computation
ISSN: 1549-9626
Titre abrégé: J Chem Theory Comput
Pays: United States
ID NLM: 101232704

Informations de publication

Date de publication:
13 Oct 2020
Historique:
pubmed: 29 8 2020
medline: 2 7 2021
entrez: 29 8 2020
Statut: ppublish

Résumé

We present drug force-field recalibration (DFFR), a new method for refining of automatic force-fields used to represent small drugs in docking and molecular dynamics simulations. The method is based on fine-tuning of torsional terms to obtain ensembles that reproduce observables derived from reference data. DFFR is fast and flexible and can be easily automatized for a high-throughput regime, making it useful in drug-design projects. We tested the performance of the method in a few model systems and also in a variety of druglike molecules using reference data derived from: (i) density functional theory coupled to a self-consistent reaction field (DFT/SCRF) calculations on highly populated conformers and (ii) enhanced sampling quantum mechanical/molecular mechanics (QM/MM) where the drug is reproduced at the QM level, while the solvent is represented by classical force-fields. Extension of the method to include other sources of reference data is discussed.

Identifiants

pubmed: 32856910
doi: 10.1021/acs.jctc.0c00306
doi:

Substances chimiques

Pharmaceutical Preparations 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

6598-6608

Auteurs

David Moreno (D)

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.

Sanja Zivanovic (S)

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.

Francesco Colizzi (F)

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.

Adam Hospital (A)

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.

Juan Aranda (J)

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.

Robert Soliva (R)

Nostrum Biodiscovery, Nexus II Building, Barcelona 08034, Spain.

Modesto Orozco (M)

Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain.
Departament de Bioquímica i Biomedicina, Facultat de Biologia, Universitat de Barcelona, Barcelona E08028, Spain.

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Classifications MeSH