1
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Lagardère L, Maurin L, Adjoua O, El Hage K, Monmarché P, Piquemal JP, Hénin J. Lambda-ABF: Simplified, Portable, Accurate, and Cost-Effective Alchemical Free-Energy Computation. J Chem Theory Comput 2024; 20:4481-4498. [PMID: 38805379 DOI: 10.1021/acs.jctc.3c01249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
We introduce the lambda-Adaptive Biasing Force (lambda-ABF) method for the computation of alchemical free-energy differences. We propose a software implementation and showcase it on biomolecular systems. The method arises from coupling multiple-walker adaptive biasing force with λ-dynamics. The sampling of the alchemical variable is continuous and converges toward a uniform distribution, making manual optimization of the λ schedule unnecessary. Contrary to most other approaches, alchemical free-energy estimates are obtained immediately without any postprocessing. Free diffusion of λ improves orthogonal relaxation compared to fixed-λ thermodynamic integration or free-energy perturbation. Furthermore, multiple walkers provide generic orthogonal space coverage with minimal user input and negligible computational overhead. We show that our high-performance implementations coupling the Colvars library with NAMD and Tinker-HP can address real-world cases including ligand-receptor binding with both fixed-charge and polarizable models, with a demonstrably richer sampling than fixed-λ methods. The implementation is fully open-source, publicly available, and readily usable by practitioners of current alchemical methods. Thanks to the portable Colvars library, lambda-ABF presents a unified user interface regardless of the back-end (NAMD, Tinker-HP, or any software to be interfaced in the future), sparing users the effort of learning multiple interfaces. Finally, the Colvars Dashboard extension of the visual molecular dynamics (VMD) software provides an interactive monitoring and diagnostic tool for lambda-ABF simulations.
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Affiliation(s)
- Louis Lagardère
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
- Sorbonne Université, Institut Parisien de Chimie Physique et Théorique, FR2622 CNRS, 75005 Paris, France
- Qubit Pharmaceuticals, 29 rue du Faubourg Saint Jacques, 75014 Paris, France
| | - Lise Maurin
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
- Sorbonne Université, Laboratoire Jacques-Louis Lions, UMR 7589 CNRS, 75005 Paris, France
| | - Olivier Adjoua
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
| | - Krystel El Hage
- Qubit Pharmaceuticals, 29 rue du Faubourg Saint Jacques, 75014 Paris, France
| | - Pierre Monmarché
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
- Sorbonne Université, Laboratoire Jacques-Louis Lions, UMR 7589 CNRS, 75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, Paris 75005, France
- Qubit Pharmaceuticals, 29 rue du Faubourg Saint Jacques, 75014 Paris, France
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, Université Paris Cité, CNRS, UPR 9080, 75005 Paris, France
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2
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Karrenbrock M, Rizzi V, Procacci P, Gervasio FL. Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations. J Phys Chem B 2024; 128:1595-1605. [PMID: 38323915 DOI: 10.1021/acs.jpcb.3c06516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Alchemical transformations can be used to quantitatively estimate absolute binding free energies at a reasonable computational cost. However, most of the approaches currently in use require knowledge of the correct (crystallographic) pose. In this paper, we present a combined Hamiltonian replica exchange nonequilibrium alchemical method that allows us to reliably calculate absolute binding free energies, even when starting from suboptimal initial binding poses. Performing a preliminary Hamiltonian replica exchange enhances the sampling of slow degrees of freedom of the ligand and the target, allowing the system to populate the correct binding pose when starting from an approximate docking pose. We apply the method on 6 ligands of the first bromodomain of the BRD4 bromodomain-containing protein. For each ligand, we start nonequilibrium alchemical transformations from both the crystallographic pose and the top-scoring docked pose that are often significantly different. We show that the method produces statistically equivalent binding free energies, making it a useful tool for computational drug discovery pipelines.
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Affiliation(s)
- Maurice Karrenbrock
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, Switzerland
| | - Valerio Rizzi
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, Switzerland
| | - Piero Procacci
- Chemistry Department, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Francesco Luigi Gervasio
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CH-1206 Geneva, Switzerland
- Chemistry Department, University College London (UCL), WC1E 6BT London, U.K
- Swiss Bioinformatics Institute, University of Geneva, CH-1206 Geneva, Switzerland
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3
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Sun Z, Wang M, He Q, Liu Z. Molecular Modeling of Ionic Liquids: Force‐Field Validation and Thermodynamic Perspective from Large‐Scale Fast‐Growth Solvation Free Energy Calculations. ADVANCED THEORY AND SIMULATIONS 2022. [DOI: 10.1002/adts.202200274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zhaoxi Sun
- Beijing National Laboratory for Molecular Sciences College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
| | - Mao Wang
- NCS Testing Technology Co., Ltd. No. 13, Gaoliangqiao Xiejie Beijing 100081 China
| | - Qiaole He
- AI Department of Enzymaster (Ningbo) Bio‐Engineering Co., Ltd. North Century Avenue 333 Ningbo 315100 China
| | - Zhirong Liu
- Beijing National Laboratory for Molecular Sciences College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
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4
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Paiva VDA, Gomes IDS, Monteiro CR, Mendonça MV, Martins PM, Santana CA, Gonçalves-Almeida V, Izidoro SC, Melo-Minardi RCD, Silveira SDA. Protein structural bioinformatics: An overview. Comput Biol Med 2022; 147:105695. [DOI: 10.1016/j.compbiomed.2022.105695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/27/2022]
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5
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Di Pasquale N, Davidchack RL. Cleaving Method for Molecular Crystals and Its Application to Calculation of the Surface Free Energy of Crystalline β-d-Mannitol at Room Temperature. J Phys Chem A 2022; 126:2134-2141. [PMID: 35324191 PMCID: PMC9007450 DOI: 10.1021/acs.jpca.2c00604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
![]()
Calculation
of the surface free energy (SFE) is an important application
of the thermodynamic integration (TI) methodology, which was mainly
employed for atomic crystals (such as Lennard–Jones or metals).
In this work, we present the calculation of the SFE of a molecular
crystal using the cleaving technique which we implemented in the LAMMPS
molecular dynamics package. We apply this methodology to a crystal
of β-d-mannitol at room temperature and report the
results for two types of force fields belonging to the GROMOS family:
all atoms and united atoms. The results show strong dependence on
the type of force field used, highlighting the need for the development
of better force fields to model the surface properties of molecular
crystals. In particular, we observe that the united-atoms force field,
despite its higher degree of coarse graining compared to the all-atoms
force field, produces SFE results in better agreement with the experimental
results from inverse gas chromatography measurements.
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Affiliation(s)
- Nicodemo Di Pasquale
- School of Mathematics and Actuarial Science, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | - Ruslan L Davidchack
- School of Mathematics and Actuarial Science, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
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6
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Bergazin TD, Tielker N, Zhang Y, Mao J, Gunner MR, Francisco K, Ballatore C, Kast SM, Mobley DL. Evaluation of log P, pK a, and log D predictions from the SAMPL7 blind challenge. J Comput Aided Mol Des 2021; 35:771-802. [PMID: 34169394 PMCID: PMC8224998 DOI: 10.1007/s10822-021-00397-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/05/2021] [Indexed: 12/16/2022]
Abstract
The Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenges focuses the computational modeling community on areas in need of improvement for rational drug design. The SAMPL7 physical property challenge dealt with prediction of octanol-water partition coefficients and pKa for 22 compounds. The dataset was composed of a series of N-acylsulfonamides and related bioisosteres. 17 research groups participated in the log P challenge, submitting 33 blind submissions total. For the pKa challenge, 7 different groups participated, submitting 9 blind submissions in total. Overall, the accuracy of octanol-water log P predictions in the SAMPL7 challenge was lower than octanol-water log P predictions in SAMPL6, likely due to a more diverse dataset. Compared to the SAMPL6 pKa challenge, accuracy remains unchanged in SAMPL7. Interestingly, here, though macroscopic pKa values were often predicted with reasonable accuracy, there was dramatically more disagreement among participants as to which microscopic transitions produced these values (with methods often disagreeing even as to the sign of the free energy change associated with certain transitions), indicating far more work needs to be done on pKa prediction methods.
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Affiliation(s)
| | - Nicolas Tielker
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Yingying Zhang
- Department of Physics, The Graduate Center, City University of New York, New York, 10016, USA
| | - Junjun Mao
- Department of Physics, City College of New York, New York, 10031, USA
| | - M R Gunner
- Department of Physics, The Graduate Center, City University of New York, New York, 10016, USA.,Department of Physics, City College of New York, New York, 10031, USA
| | - Karol Francisco
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, Ja Jolla, CA, 92093-0756, USA
| | - Carlo Ballatore
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, Ja Jolla, CA, 92093-0756, USA
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA. .,Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
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7
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Huai Z, Shen Z, Sun Z. Binding Thermodynamics and Interaction Patterns of Inhibitor-Major Urinary Protein-I Binding from Extensive Free-Energy Calculations: Benchmarking AMBER Force Fields. J Chem Inf Model 2020; 61:284-297. [PMID: 33307679 DOI: 10.1021/acs.jcim.0c01217] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mouse major urinary protein (MUP) plays a key role in the pheromone communication system. The one-end-closed β-barrel of MUP-I forms a small, deep, and hydrophobic central cavity, which could accommodate structurally diverse ligands. Previous computational studies employed old protein force fields and short simulation times to determine the binding thermodynamics or investigated only a small number of structurally similar ligands, which resulted in sampled regions far from the experimental structure, nonconverged sampling outcomes, and limited understanding of the possible interaction patterns that the cavity could produce. In this work, extensive end-point and alchemical free-energy calculations with advanced protein force fields were performed to determine the binding thermodynamics of a series of MUP-inhibitor systems and investigate the inter- and intramolecular interaction patterns. Three series of inhibitors with a total of 14 ligands were simulated. We independently simulated the MUP-inhibitor complexes under two advanced AMBER force fields. Our benchmark test showed that the advanced AMBER force fields including AMBER19SB and AMBER14SB provided better descriptions of the system, and the backbone root-mean-square deviation (RMSD) was significantly lowered compared with previous computational studies with old protein force fields. Surprisingly, although the latest AMBER force field AMBER19SB provided better descriptions of various observables, it neither improved the binding thermodynamics nor lowered the backbone RMSD compared with the previously proposed and widely used AMBER14SB. The older but widely used AMBER14SB actually achieved better performance in the prediction of binding affinities from the alchemical and end-point free-energy calculations. We further analyzed the protein-ligand interaction networks to identify important residues stabilizing the bound structure. Six residues including PHE38, LEU40, PHE90, ALA103, LEU105, and TYR120 were found to contribute the most significant part of protein-ligand interactions, and 10 residues were found to provide favorable interactions stabilizing the bound state. The two AMBER force fields gave extremely similar interaction networks, and the secondary structures also showed similar behavior. Thus, the intra- and intermolecular interaction networks described with the two AMBER force fields are similar. Therefore, AMBER14SB could still be the default option in free-energy calculations to achieve highly accurate binding thermodynamics and interaction patterns.
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Affiliation(s)
- Zhe Huai
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Zhaoxi Shen
- Institute of Applied Physics and Materials Engineering, University of Macau, Avenida da Universidade, Taipa, Macau 999078, China
| | - Zhaoxi Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
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8
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Macchiagodena M, Pagliai M, Karrenbrock M, Guarnieri G, Iannone F, Procacci P. Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease. J Chem Theory Comput 2020; 16:7160-7172. [PMID: 33090785 PMCID: PMC8015232 DOI: 10.1021/acs.jctc.0c00634] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In the context of drug-receptor binding affinity calculations using molecular dynamics techniques, we implemented a combination of Hamiltonian replica exchange (HREM) and a novel nonequilibrium alchemical methodology, called virtual double-system single-box, with increased accuracy, precision, and efficiency with respect to the standard nonequilibrium approaches. The method has been applied for the determination of absolute binding free energies of 16 newly designed noncovalent ligands of the main protease (3CLpro) of SARS-CoV-2. The core structures of 3CLpro ligands were previously identified using a multimodal structure-based ligand design in combination with docking techniques. The calculated binding free energies for four additional ligands with known activity (either for SARS-CoV or SARS-CoV-2 main protease) are also reported. The nature of binding in the 3CLpro active site and the involved residues besides the CYS-HYS catalytic dyad have been thoroughly characterized by enhanced sampling simulations of the bound state. We have identified several noncongeneric compounds with predicted low micromolar activity for 3CLpro inhibition, which may constitute possible lead compounds for the development of antiviral agents in Covid-19 treatment.
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Affiliation(s)
- Marina Macchiagodena
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Marco Pagliai
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Maurice Karrenbrock
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Guido Guarnieri
- ENEA, Portici Research Centre, DTE-ICT-HPC P.le E. Fermi, 1, I-80055 Portici (NA), Italy
| | - Francesco Iannone
- ENEA, Portici Research Centre, DTE-ICT-HPC P.le E. Fermi, 1, I-80055 Portici (NA), Italy
| | - Piero Procacci
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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9
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Plazinska A, Plazinski W. Chirality Effects in Biomolecular Systems: Calculation of the Relative Free Energies by Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:5424-5436. [PMID: 32937074 DOI: 10.1021/acs.jcim.0c00605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Chirality plays an essential role in chemical and biological sciences. At the molecular level, the effects associated with this phenomenon can be studied by using the well-established technique of molecular dynamics simulations. In this work, we present several approaches suited for the molecular dynamics-based free energy calculation in chiral systems. In particular, we have proposed and tested the following strategies relying on the application of general, enhanced sampling methods: (i) biased sampling in the two-dimensional space, along the coordinates defined by the values of the selected torsional angles; (ii) biased sampling in the one- or two-dimensional space, along the path-based coordinate(s); (iii) rational alteration of the system's Hamiltonian in order to enable the interconversion between stereoisomers and reweighting the biased distribution of configurations; (iv) using the free energy landscape generated within approaches (i) or (ii) as time-independent bias in order to further improve sampling efficiency and simultaneously account for multiple chiral centers. All approaches have been tested on a set of model compounds (fenoterol, fructofuranose, and bromochlorofluoromethane), demonstrating the good performance but also some differences in the range of their applicabilities.
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Affiliation(s)
- Anita Plazinska
- Department of Biopharmacy, Medical University of Lublin, Chodzki 4a, 20-093 Lublin, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
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10
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Macchiagodena M, Pagliai M, Andreini C, Rosato A, Procacci P. Upgraded AMBER Force Field for Zinc-Binding Residues and Ligands for Predicting Structural Properties and Binding Affinities in Zinc-Proteins. ACS OMEGA 2020; 5:15301-15310. [PMID: 32637803 PMCID: PMC7331063 DOI: 10.1021/acsomega.0c01337] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/13/2020] [Indexed: 05/08/2023]
Abstract
We developed a novel force field in the context of AMBER parameterization for glutamate and aspartate zinc(II)-binding residues. The interaction between the zinc ion and the coordinating atoms is represented by a spherical nonbonded parameterization. The polarization effect due to the zinc ion has been taken into account by redefining the atomic charges on the residues through accurate quantum mechanical calculations. The new zinc-binding ASP and GLU residues, along with the CYS and HIS zinc-binding residues, parameterized in a recent work [Macchiagodena M.;J. Chem. Inf. Model.2019, 59, 3803-3816], allow users to reliably simulate 96% of the Zn-proteins available in the Protein Data Bank. The upgraded force field for zinc(II)-bound residues has been tested performing molecular dynamics simulations with an explicit solvent and comparing the structural information with experimental data for five different proteins binding zinc(II) with GLU, ASP, HIS, and CYS. We further validated our approach by evaluating the binding free energy of (R)-2-benzyl-3-nitropropanoic acid to carboxypeptidase A using a recently developed nonequilibrium alchemical method. We demonstrated that in this setting it is crucial to take into account polarization effects also on the metal-bound inhibitor.
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Affiliation(s)
- Marina Macchiagodena
- Dipartimento
di Chimica “Ugo Schiff”, Università
degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Marco Pagliai
- Dipartimento
di Chimica “Ugo Schiff”, Università
degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudia Andreini
- Dipartimento
di Chimica “Ugo Schiff”, Università
degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic
Resonance Center (CERM), Università
degli Studi di Firenze, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Antonio Rosato
- Dipartimento
di Chimica “Ugo Schiff”, Università
degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
- Magnetic
Resonance Center (CERM), Università
degli Studi di Firenze, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Piero Procacci
- Dipartimento
di Chimica “Ugo Schiff”, Università
degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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11
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Procacci P. A remark on the efficiency of the double-system/single-box nonequilibrium approach in the SAMPL6 SAMPLing challenge. J Comput Aided Mol Des 2020; 34:635-639. [PMID: 32277315 DOI: 10.1007/s10822-020-00312-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/30/2020] [Indexed: 11/25/2022]
Abstract
The alchemical nonequilibrium switching technique was one of several methods in the top tier of performance in the recent SAMPL6 SAMPLing challenge in both accuracy and efficiency. In this paper, in the context of nonequilibrium alchemical switching, we compare the efficiency of the double-system/single-box (DSSB) approach (used in the SAMPL6 challenges) to the standard single-system/double-box method (SSDB). Exploiting the Crooks theorem in a simple but effective test case, we analytically show that the DSSB approach is almost twice as efficient as SSDB for slow near-equilibrium switching but it gives basically no gain over the conventional SSDB approach when the variance of the work distribution exceeds few [Formula: see text], with the potential of producing artifacts and entanglements if not judiciously implemented.
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Affiliation(s)
- Piero Procacci
- Department of Chemistry, University of Florence, Via Lastruccia n. 3, 50019, Sesto Fiorentino, FI, Italy.
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12
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Işık M, Bergazin TD, Fox T, Rizzi A, Chodera JD, Mobley DL. Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge. J Comput Aided Mol Des 2020; 34:335-370. [PMID: 32107702 PMCID: PMC7138020 DOI: 10.1007/s10822-020-00295-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
Abstract
The SAMPL Challenges aim to focus the biomolecular and physical modeling community on issues that limit the accuracy of predictive modeling of protein-ligand binding for rational drug design. In the SAMPL5 log D Challenge, designed to benchmark the accuracy of methods for predicting drug-like small molecule transfer free energies from aqueous to nonpolar phases, participants found it difficult to make accurate predictions due to the complexity of protonation state issues. In the SAMPL6 log P Challenge, we asked participants to make blind predictions of the octanol-water partition coefficients of neutral species of 11 compounds and assessed how well these methods performed absent the complication of protonation state effects. This challenge builds on the SAMPL6 p[Formula: see text] Challenge, which asked participants to predict p[Formula: see text] values of a superset of the compounds considered in this log P challenge. Blind prediction sets of 91 prediction methods were collected from 27 research groups, spanning a variety of quantum mechanics (QM) or molecular mechanics (MM)-based physical methods, knowledge-based empirical methods, and mixed approaches. There was a 50% increase in the number of participating groups and a 20% increase in the number of submissions compared to the SAMPL5 log D Challenge. Overall, the accuracy of octanol-water log P predictions in SAMPL6 Challenge was higher than cyclohexane-water log D predictions in SAMPL5, likely because modeling only the neutral species was necessary for log P and several categories of method benefited from the vast amounts of experimental octanol-water log P data. There were many highly accurate methods: 10 diverse methods achieved RMSE less than 0.5 log P units. These included QM-based methods, empirical methods, and mixed methods with physical modeling supported with empirical corrections. A comparison of physical modeling methods showed that QM-based methods outperformed MM-based methods. The average RMSE of the most accurate five MM-based, QM-based, empirical, and mixed approach methods based on RMSE were 0.92 ± 0.13, 0.48 ± 0.06, 0.47 ± 0.05, and 0.50 ± 0.06, respectively.
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Affiliation(s)
- Mehtap Işık
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, 10065, USA.
| | | | - Thomas Fox
- Computational Chemistry, Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach, Germany
| | - Andrea Rizzi
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, 10065, USA
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
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13
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Procacci P, Guarnieri G. SAMPL6 blind predictions of water-octanol partition coefficients using nonequilibrium alchemical approaches. J Comput Aided Mol Des 2019; 34:371-384. [PMID: 31624982 DOI: 10.1007/s10822-019-00233-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 10/03/2019] [Indexed: 12/13/2022]
Abstract
In this paper, we compute, by means of a non equilibrium alchemical technique, the water-octanol partition coefficients (LogP) for a series of drug-like compounds in the context of the SAMPL6 challenge initiative. Our blind predictions are based on three of the most popular non-polarizable force fields, CGenFF, GAFF2, and OPLS-AA and are critically compared to other MD-based predictions produced using free energy perturbation or thermodynamic integration approaches with stratification. The proposed non-equilibrium method emerges has a reliable tool for LogP prediction, systematically being among the top performing submissions in all force field classes for at least two among the various indicators such as the Pearson or the Kendall correlation coefficients or the mean unsigned error. Contrarily to the widespread equilibrium approaches, that yielded apparently very disparate results in the SAMPL6 challenge, all our independent prediction sets, irrespective of the adopted force field and of the adopted estimate (unidirectional or bidirectional) are, mutually, from moderately to strongly correlated.
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Affiliation(s)
- Piero Procacci
- Department of Chemistry, University of Florence, Via Lastruccia n. 3, 50019, Sesto Fiorentino, FI, Italy.
| | - Guido Guarnieri
- ENEA, Portici Research Centre, DTE-ICT-HPC, P.le E. Fermi, 1, 80055, Portici, NA, Italy
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14
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Procacci P. Accuracy, precision, and efficiency of nonequilibrium alchemical methods for computing free energies of solvation. I. Bidirectional approaches. J Chem Phys 2019; 151:144113. [DOI: 10.1063/1.5120615] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Piero Procacci
- Department of Chemistry, University of Florence, Florence, Italy
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15
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Procacci P. Precision and computational efficiency of nonequilibrium alchemical methods for computing free energies of solvation. II. Unidirectional estimates. J Chem Phys 2019; 151:144115. [DOI: 10.1063/1.5120616] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Piero Procacci
- Department of Chemistry, University of Florence, Florence, Italy
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16
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Procacci P. Solvation free energies via alchemical simulations: let's get honest about sampling, once more. Phys Chem Chem Phys 2019; 21:13826-13834. [PMID: 31211310 DOI: 10.1039/c9cp02808k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Free energy perturbation (FEP) approaches with stratification have seen widespread and increasing use in computational studies of biologically relevant molecules. However, when the molecular systems are characterized by a complex conformational free energy landscape, the assessment of convergence remains a concern for many practitioners. The sampling problem in FEP has been authoritatively addressed in a recent perspective paper [D. Mobley, J. Comput.-Aided Mol. Des., 2012, 26, 93], incisively entitled "Let's get honest about sampling". Here, I return to the issue of sampling in the determination of the octanol-water partition coefficient for a synthetic precursor of kinase inhibitors that has been included in the recent extension of the SAMPL6 blind challenge of log P coefficients. I will show that even for this simple compound, whose conformational space is essentially dictated by two sp3 rotable bonds connecting rigid planar units, canonical sampling using standard techniques can be surprisingly hard to achieve. I will also show how the conformational sampling problem can be effectively bypassed using unidirectional and bidirectional nonequilibrium work methods, reliably recovering the solvation energy with minimal methodological uncertainty.
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17
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Pagliai M, Funghi G, Vassetti D, Procacci P, Chelli R, Cardini G. Imidazole in Aqueous Solution: Hydrogen Bond Interactions and Structural Reorganization with Concentration. J Phys Chem B 2019; 123:4055-4064. [DOI: 10.1021/acs.jpcb.9b01611] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Pagliai
- Dipartimento di Chimica ”Ugo Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Giada Funghi
- Dipartimento di Chimica ”Ugo Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Dario Vassetti
- Dipartimento di Chimica ”Ugo Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Piero Procacci
- Dipartimento di Chimica ”Ugo Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Riccardo Chelli
- Dipartimento di Chimica ”Ugo Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Gianni Cardini
- Dipartimento di Chimica ”Ugo Schiff”, Università degli Studi di Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
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18
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Vassetti D, Pagliai M, Procacci P. Assessment of GAFF2 and OPLS-AA General Force Fields in Combination with the Water Models TIP3P, SPCE, and OPC3 for the Solvation Free Energy of Druglike Organic Molecules. J Chem Theory Comput 2019; 15:1983-1995. [DOI: 10.1021/acs.jctc.8b01039] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Dario Vassetti
- Department of Chemistry, University of Florence, Via Lastruccia n. 3, Sesto Fiorentino, I-50019 Italy
| | - Marco Pagliai
- Department of Chemistry, University of Florence, Via Lastruccia n. 3, Sesto Fiorentino, I-50019 Italy
| | - Piero Procacci
- Department of Chemistry, University of Florence, Via Lastruccia n. 3, Sesto Fiorentino, I-50019 Italy
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Wang M, Mei Y, Ryde U. Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations. J Chem Theory Comput 2018; 14:6613-6622. [DOI: 10.1021/acs.jctc.8b00685] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Meiting Wang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
- NYU−ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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20
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Loeffler HH, Bosisio S, Duarte Ramos Matos G, Suh D, Roux B, Mobley DL, Michel J. Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages. J Chem Theory Comput 2018; 14:5567-5582. [PMID: 30289712 DOI: 10.1021/acs.jctc.8b00544] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alchemical free energy calculations are an increasingly important modern simulation technique to calculate free energy changes on binding or solvation. Contemporary molecular simulation software such as AMBER, CHARMM, GROMACS, and SOMD include support for the method. Implementation details vary among those codes, but users expect reliability and reproducibility, i.e., for a given molecular model and set of force field parameters, comparable free energy differences should be obtained within statistical bounds regardless of the code used. Relative alchemical free energy (RAFE) simulation is increasingly used to support molecule discovery projects, yet the reproducibility of the methodology has been less well tested than its absolute counterpart. Here we present RAFE calculations of hydration free energies for a set of small organic molecules and demonstrate that free energies can be reproduced to within about 0.2 kcal/mol with the aforementioned codes. Absolute alchemical free energy simulations have been carried out as a reference. Achieving this level of reproducibility requires considerable attention to detail and package-specific simulation protocols, and no universally applicable protocol emerges. The benchmarks and protocols reported here should be useful for the community to validate new and future versions of software for free energy calculations.
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Affiliation(s)
- Hannes H Loeffler
- Science & Technology Facilities Council , Daresbury, Warrington WA4 4AD , United Kingdom
| | - Stefano Bosisio
- EaStCHEM School of Chemistry , University of Edinburgh , David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
| | | | - Donghyuk Suh
- University of Chicago , Chicago , Illinois 60637 , United States
| | - Benoit Roux
- University of Chicago , Chicago , Illinois 60637 , United States
| | - David L Mobley
- Departments of Pharmaceutical Sciences and Chemistry , University of California , Irvine , California 92697 , United States
| | - Julien Michel
- EaStCHEM School of Chemistry , University of Edinburgh , David Brewster Road , Edinburgh EH9 3FJ , United Kingdom
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21
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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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22
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Procacci P. Myeloid Cell Leukemia 1 Inhibition: An in Silico Study Using Non-equilibrium Fast Double Annihilation Technology. J Chem Theory Comput 2018; 14:3890-3902. [DOI: 10.1021/acs.jctc.8b00305] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Piero Procacci
- Department of Chemistry, University of Florence, Via Lastruccia No. 3, Sesto Fiorentino I-50019, Italy
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23
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Remsing RC, Weeks JD. Alchemical free energy calculations and umbrella sampling with local molecular field theory. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1142/s0219633618400035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Understanding the thermodynamic driving forces underlying any chemical process requires a description of the underlying free energy surface. However, computation of free energies is difficult, often requiring advanced sampling techniques. Moreover, these computations can be further complicated by the evaluation of any long-ranged interactions in the system of interest, such as Coulomb interactions in charged and polar media. Local molecular field theory is a promising approach to avoid many of the conceptual and computational difficulties associated with long-ranged interactions. We present frameworks for performing alchemical free energy calculations and non-Boltzmann sampling with local molecular field theory. We demonstrate that local molecular field theory can be used to perform these free energy calculations with accuracy comparable to traditional methodologies while eliminating the need for explicit treatment of long-ranged interactions in simulations.
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Affiliation(s)
- Richard C. Remsing
- Institute for Computational Molecular Science, Department of Chemistry, Temple University, Philadelphia, PA 19122, USA
| | - John D. Weeks
- Institute for Physical Science and Technology, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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24
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Li PF, Jia XY, Wang MT, Mei Y. Comparison of Accuracy and Convergence Rate between Equilibrium and Nonequilibrium Alchemical Transformations for Calculation of Relative Binding Free Energy. CHINESE J CHEM PHYS 2017. [DOI: 10.1063/1674-0068/30/cjcp1711204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Peng-fei Li
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - Xiang-yu Jia
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Mei-ting Wang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman OK 73019, USA
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25
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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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26
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Giovannelli E, Cioni M, Procacci P, Cardini G, Pagliai M, Volkov V, Chelli R. Binding Free Energies of Host–Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Illustrative Calculations and Numerical Validation. J Chem Theory Comput 2017; 13:5887-5899. [DOI: 10.1021/acs.jctc.7b00595] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Edoardo Giovannelli
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Matteo Cioni
- 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
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Riccardo Chelli
- Interdisciplinary
Biomedical Research Center, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, U.K
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Wang M, Li P, Jia X, Liu W, Shao Y, Hu W, Zheng J, Brooks BR, Mei Y. Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level. J Chem Inf Model 2017; 57:2476-2489. [DOI: 10.1021/acs.jcim.7b00001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Meiting Wang
- State Key Laboratory
of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - Pengfei Li
- State Key Laboratory
of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - Xiangyu Jia
- State Key Laboratory
of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - Wei Liu
- State Key Laboratory
of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
| | - Yihan Shao
- Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman Oklahoma 73019, United States
| | - Wenxin Hu
- The Computer
Center, School of Computer Science and Software Engineering, East China Normal University, Shanghai 200062, China
| | - Jun Zheng
- The Computer
Center, School of Computer Science and Software Engineering, East China Normal University, Shanghai 200062, China
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Institutes of Health, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Ye Mei
- State Key Laboratory
of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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28
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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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29
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Watkins AM, Bonneau R, Arora PS. Modeling and Design of Peptidomimetics to Modulate Protein-Protein Interactions. Methods Mol Biol 2017; 1561:291-307. [PMID: 28236245 DOI: 10.1007/978-1-4939-6798-8_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We describe a modular approach to identify and inhibit protein-protein interactions (PPIs) that are mediated by protein secondary and tertiary structures with rationally designed peptidomimetics. Our analysis begins with entries of high-resolution complexes in the Protein Data Bank and utilizes conformational sampling, scoring, and design capabilities of advanced biomolecular modeling software to develop peptidomimetics.
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Affiliation(s)
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, 29 Washington Place, Brown Bldg., Room 360, New York, NY, USA.
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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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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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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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33
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Procacci P. Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures. J Chem Phys 2015; 142:154117. [DOI: 10.1063/1.4918558] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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34
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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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