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Miñarro-Lleonar M, Ruiz-Carmona S, Alvarez-Garcia D, Schmidtke P, Barril X. Development of an Automatic Pipeline for Participation in the CELPP Challenge. Int J Mol Sci 2022; 23:ijms23094756. [PMID: 35563148 PMCID: PMC9105952 DOI: 10.3390/ijms23094756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/01/2022] Open
Abstract
The prediction of how a ligand binds to its target is an essential step for Structure-Based Drug Design (SBDD) methods. Molecular docking is a standard tool to predict the binding mode of a ligand to its macromolecular receptor and to quantify their mutual complementarity, with multiple applications in drug design. However, docking programs do not always find correct solutions, either because they are not sampled or due to inaccuracies in the scoring functions. Quantifying the docking performance in real scenarios is essential to understanding their limitations, managing expectations and guiding future developments. Here, we present a fully automated pipeline for pose prediction validated by participating in the Continuous Evaluation of Ligand Pose Prediction (CELPP) Challenge. Acknowledging the intrinsic limitations of the docking method, we devised a strategy to automatically mine and exploit pre-existing data, defining—whenever possible—empirical restraints to guide the docking process. We prove that the pipeline is able to generate predictions for most of the proposed targets as well as obtain poses with low RMSD values when compared to the crystal structure. All things considered, our pipeline highlights some major challenges in the automatic prediction of protein–ligand complexes, which will be addressed in future versions of the pipeline.
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Affiliation(s)
- Marina Miñarro-Lleonar
- Pharmacy Faculty, University of Barcelona, Av. de Joan XXIII 27-31, 08028 Barcelona, Spain;
| | | | - Daniel Alvarez-Garcia
- GAIN Therapeutics, Parc Cientific de Barcelona, Baldiri i Reixac 10, 08029 Barcelona, Spain;
| | - Peter Schmidtke
- Discngine S.A.S., 79 Avenue Ledru Rollin, 75012 Paris, France;
| | - Xavier Barril
- Pharmacy Faculty, University of Barcelona, Av. de Joan XXIII 27-31, 08028 Barcelona, Spain;
- GAIN Therapeutics, Parc Cientific de Barcelona, Baldiri i Reixac 10, 08029 Barcelona, Spain;
- Catalan Institute for Research and Advanced Studies (ICREA), Passeig de Lluis Companys 23, 08010 Barcelona, Spain
- Correspondence:
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Alvarez-Garcia D, Schmidtke P, Cubero E, Barril X. Extracting Atomic Contributions to Binding Free Energy Using Molecular Dynamics Simulations with Mixed Solvents (MDmix). Curr Drug Discov Technol 2022; 19:62-68. [PMID: 34951392 PMCID: PMC9906626 DOI: 10.2174/1570163819666211223162829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/28/2021] [Accepted: 10/05/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Mixed solvents MD (MDmix) simulations have proved to be a useful and increasingly accepted technique with several applications in structure-based drug discovery. One of the assumptions behind the methodology is the transferability of free energy values from the simulated cosolvent molecules to larger drug-like molecules. However, the binding free energy maps (ΔGbind) calculated for the different moieties of the cosolvent molecules (e.g. a hydroxyl map for the ethanol) are largely influenced by the rest of the solvent molecule and do not reflect the intrinsic affinity of the moiety in question. As such, they are hardly transferable to different molecules. METHOD To achieve transferable energies, we present here a method for decomposing the molecular binding free energy into accurate atomic contributions. RESULT We demonstrate with two qualitative visual examples how the corrected energy maps better match known binding hotspots and how they can reveal hidden hotspots with actual drug design potential. CONCLUSION Atomic decomposition of binding free energies derived from MDmix simulations provides transferable and quantitative binding free energy maps.
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Affiliation(s)
- Daniel Alvarez-Garcia
- Gain Therapeutics, Parc Cientific de Barcelona, Baldiri Reixac 10, 08029 Barcelona, Spain
| | - Peter Schmidtke
- Facultat de Farmacia, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain;,Current address: Discngine, 79 Avenue Ledru Rollin, 75012 Paris, France;
| | - Elena Cubero
- Gain Therapeutics, Parc Cientific de Barcelona, Baldiri Reixac 10, 08029 Barcelona, Spain
| | - Xavier Barril
- Gain Therapeutics, Parc Cientific de Barcelona, Baldiri Reixac 10, 08029 Barcelona, Spain;,Facultat de Farmacia, Universitat de Barcelona, Av. Joan XXIII 27-31, 08028 Barcelona, Spain;,Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain,Address correspondence to this author at the Gain Therapeutics, Parc Cientific de Barcelona, Baldiri Reixac 10, 08029 Barcelona, Spain; E-mail:
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Arcon JP, Defelipe LA, Modenutti CP, López ED, Alvarez-Garcia D, Barril X, Turjanski AG, Martí MA. Molecular Dynamics in Mixed Solvents Reveals Protein–Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions. J Chem Inf Model 2017; 57:846-863. [DOI: 10.1021/acs.jcim.6b00678] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Juan Pablo Arcon
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Lucas A. Defelipe
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Carlos P. Modenutti
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Elias D. López
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | | | - Xavier Barril
- Institut
de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat
de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Adrián G. Turjanski
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
| | - Marcelo A. Martí
- Departamento
de Química Biológica e IQUIBICEN-CONICET, Facultad de
Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, C1428EHA Ciudad de Buenos Aires, Argentina
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Alvarez-Garcia D, Barril X. Molecular Simulations with Solvent Competition Quantify Water Displaceability and Provide Accurate Interaction Maps of Protein Binding Sites. J Med Chem 2014; 57:8530-9. [DOI: 10.1021/jm5010418] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Daniel Alvarez-Garcia
- Departament
de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Gran Via de les Corts Catalanes,
585, 08007 Barcelona, Spain
| | - Xavier Barril
- Departament
de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Gran Via de les Corts Catalanes,
585, 08007 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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Alvarez-Garcia D, Barril X. Relationship between Protein Flexibility and Binding: Lessons for Structure-Based Drug Design. J Chem Theory Comput 2014; 10:2608-14. [DOI: 10.1021/ct500182z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Alvarez-Garcia
- Departament
de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Xavier Barril
- Departament
de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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