1
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SAMPL6 host–guest blind predictions using a non equilibrium alchemical approach. J Comput Aided Mol Des 2018; 32:965-982. [DOI: 10.1007/s10822-018-0151-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/10/2018] [Indexed: 02/07/2023]
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2
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Cardelli C, Barducci A, Procacci P. Lipid tempering simulation of model biological membranes on parallel platforms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1480-1488. [DOI: 10.1016/j.bbamem.2018.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/10/2018] [Accepted: 04/25/2018] [Indexed: 11/17/2022]
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3
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Kilburg D, Gallicchio E. Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes. Front Mol Biosci 2018; 5:22. [PMID: 29568737 PMCID: PMC5852065 DOI: 10.3389/fmolb.2018.00022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/21/2018] [Indexed: 01/24/2023] Open
Abstract
The computational modeling of peptide inhibitors to target protein-protein binding interfaces is growing in interest as these are often too large, too shallow, and too feature-less for conventional small molecule compounds. Here, we present a rare successful application of an alchemical binding free energy method for the calculation of converged absolute binding free energies of a series of protein-peptide complexes. Specifically, we report the binding free energies of a series of cyclic peptides derived from the LEDGF/p75 protein to the integrase receptor of the HIV1 virus. The simulations recapitulate the effect of mutations relative to the wild-type binding motif of LEDGF/p75, providing structural, energetic and dynamical interpretations of the observed trends. The equilibration and convergence of the calculations are carefully analyzed. Convergence is aided by the adoption of a single-decoupling alchemical approach with implicit solvation, which circumvents the convergence difficulties of conventional double-decoupling protocols. We hereby present the single-decoupling methodology and critically evaluate its advantages and limitations. We also discuss some of the challenges and potential pitfalls of binding free energy calculations for complex molecular systems which have generally limited their applicability to the quantitative study of protein-peptide binding equilibria.
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Affiliation(s)
- Denise Kilburg
- Department of Chemistry, Brooklyn College, Brooklyn, NY, United States.,Ph.D. Program in Chemistry, The Graduate Center, City University of New York, New York, NY, United States
| | - Emilio Gallicchio
- Department of Chemistry, Brooklyn College, Brooklyn, NY, United States.,Ph.D. Program in Chemistry, The Graduate Center, City University of New York, New York, NY, United States.,Ph.D. Program in Biochemistry, The Graduate Center, City University of New York, New York, NY, United States
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4
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Giovannelli E, Procacci P, Cardini G, Pagliai M, Volkov V, Chelli R. Binding Free Energies of Host–Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Theoretical Framework. J Chem Theory Comput 2017; 13:5874-5886. [DOI: 10.1021/acs.jctc.7b00594] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Edoardo Giovannelli
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Piero Procacci
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Gianni Cardini
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Marco Pagliai
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Victor Volkov
- Interdisciplinary
Biomedical Research Center, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, U.K
| | - Riccardo Chelli
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
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5
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Alchemical determination of drug-receptor binding free energy: Where we stand and where we could move to. J Mol Graph Model 2017; 71:233-241. [DOI: 10.1016/j.jmgm.2016.11.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/24/2016] [Accepted: 11/29/2016] [Indexed: 01/05/2023]
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6
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Weininger U, Modig K, Geitner AJ, Schmidpeter PAM, Koch JR, Akke M. Dynamics of Aromatic Side Chains in the Active Site of FKBP12. Biochemistry 2016; 56:334-343. [DOI: 10.1021/acs.biochem.6b01157] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ulrich Weininger
- Department
of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O.
Box 124, SE-22100 Lund, Sweden
- Institute
of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, D-06120 Halle (Saale), Germany
| | - Kristofer Modig
- Department
of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O.
Box 124, SE-22100 Lund, Sweden
| | - Anne-Juliane Geitner
- Laboratorium
für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Philipp A. M. Schmidpeter
- Laboratorium
für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Johanna R. Koch
- Laboratorium
für Biochemie, Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Mikael Akke
- Department
of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P.O.
Box 124, SE-22100 Lund, Sweden
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7
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Procacci P. Hybrid MPI/OpenMP Implementation of the ORAC Molecular Dynamics Program for Generalized Ensemble and Fast Switching Alchemical Simulations. J Chem Inf Model 2016; 56:1117-21. [PMID: 27231982 DOI: 10.1021/acs.jcim.6b00151] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a new release (6.0β) of the ORAC program [Marsili et al. J. Comput. Chem. 2010, 31, 1106-1116] with a hybrid OpenMP/MPI (open multiprocessing message passing interface) multilevel parallelism tailored for generalized ensemble (GE) and fast switching double annihilation (FS-DAM) nonequilibrium technology aimed at evaluating the binding free energy in drug-receptor system on high performance computing platforms. The production of the GE or FS-DAM trajectories is handled using a weak scaling parallel approach on the MPI level only, while a strong scaling force decomposition scheme is implemented for intranode computations with shared memory access at the OpenMP level. The efficiency, simplicity, and inherent parallel nature of the ORAC implementation of the FS-DAM algorithm, project the code as a possible effective tool for a second generation high throughput virtual screening in drug discovery and design. The code, along with documentation, testing, and ancillary tools, is distributed under the provisions of the General Public License and can be freely downloaded at www.chim.unifi.it/orac .
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Affiliation(s)
- Piero Procacci
- Department of Chemistry, University of Florence , Sesto Fiorentino, 50019, Italy
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8
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De Vivo M, Masetti M, Bottegoni G, Cavalli A. Role of Molecular Dynamics and Related Methods in Drug Discovery. J Med Chem 2016; 59:4035-61. [DOI: 10.1021/acs.jmedchem.5b01684] [Citation(s) in RCA: 538] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Marco De Vivo
- Laboratory
of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
- IAS-5/INM-9 Computational
Biomedicine Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Matteo Masetti
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
| | - Giovanni Bottegoni
- CompuNet, Istituto
Italiano di Tecnologia, Via Morego
30, 16163 Genova, Italy
- BiKi Technologies
srl, Via XX Settembre 33/10, 16121 Genova, Italy
| | - Andrea Cavalli
- Department
of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro
6, I-40126 Bologna, Italy
- CompuNet, Istituto
Italiano di Tecnologia, Via Morego
30, 16163 Genova, Italy
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9
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Nerattini F, Chelli R, Procacci P. II. Dissociation free energies in drug–receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands. Phys Chem Chem Phys 2016; 18:15005-18. [DOI: 10.1039/c5cp05521k] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fast switch double annihilation method (FS-DAM) provides an effective mean to the compute the binding free energies in drug-receptor systems. Here we present an application to the FK506-related ligands of the FKBP12 protein.
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10
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Procacci P. I. Dissociation free energies of drug–receptor systems via non-equilibrium alchemical simulations: a theoretical framework. Phys Chem Chem Phys 2016; 18:14991-5004. [DOI: 10.1039/c5cp05519a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this contribution I critically discuss the alchemical approach for evaluating binding free energies in drug–receptor systems, placing this methodology into the broader context of non-equilibrium thermodynamics.
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11
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Sandberg RB, Banchelli M, Guardiani C, Menichetti S, Caminati G, Procacci P. Efficient Nonequilibrium Method for Binding Free Energy Calculations in Molecular Dynamics Simulations. J Chem Theory Comput 2015; 11:423-35. [DOI: 10.1021/ct500964e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Robert B. Sandberg
- Department
of Chemistry, State University of New York at Binghamton, Binghamton, New York 13902, United States
| | | | - Carlo Guardiani
- Department
of Physics, University of Cagliari, 09124 Cagliari, Italy
- IOM Institute, CNR, 09042 Cagliari, Italy
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