1
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Di Paco G, Macchiagodena M, Procacci P. Identification of Potential Inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations. ChemMedChem 2024; 19:e202400095. [PMID: 38456332 DOI: 10.1002/cmdc.202400095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/09/2024]
Abstract
We have assembled a computational pipeline based on virtual screening, docking techniques, and nonequilibrium molecular dynamics simulations, with the goal of identifying possible inhibitors of the SARS-CoV-2 NSP13 helicase, catalyzing by ATP hydrolysis the unwinding of double or single-stranded RNA in the viral replication process inside the host cell. The druggable sites for broad-spectrum inhibitors are represented by the RNA binding sites at the 5' entrance and 3' exit of the central channel, a structural motif that is highly conserved across coronaviruses. Potential binders were first generated using structure-based ligand techniques. Their potency was estimated by using four popular docking scoring functions. Common docking hits for NSP13 were finally tested using advanced nonequilibrium alchemical techniques for binding free energy calculations on a high-performing parallel cluster. Four potential NSP13 inhibitors with potency from submicrimolar to nanomolar were finally identified.
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Affiliation(s)
- Giorgio Di Paco
- Dipartimento di Chimica "Ugo Schiff", Universit'a degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Marina Macchiagodena
- Dipartimento di Chimica "Ugo Schiff", Universit'a degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Piero Procacci
- Dipartimento di Chimica "Ugo Schiff", Universit'a degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
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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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Procacci P, Guarnieri G. SAMPL9 blind predictions using nonequilibrium alchemical approaches. J Chem Phys 2022; 156:164104. [PMID: 35490003 DOI: 10.1063/5.0086640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We present our blind predictions for the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL), ninth challenge, focusing on the binding of WP6 (carboxy-pillar[6]arene) with ammonium/diammonium cationic guests. Host-guest binding free energies have been calculated using the recently developed virtual double system single box approach, based on the enhanced sampling of the bound and unbound end-states followed by fast switching nonequilibrium alchemical simulations [M. Macchiagodena et al., J. Chem. Theory Comput. 16, 7160 (2020)]. As far as Pearson and Kendall coefficients are concerned, performances were acceptable and, in general, better than those we submitted for calixarenes, cucurbituril-like open cavitand, and beta-cyclodextrines in previous SAMPL host-guest challenges, confirming the reliability of nonequilibrium approaches for absolute binding free energy calculations. In comparison with previous submissions, we found a rather large mean signed error that we attribute to the way the finite charge correction was addressed through the assumption of a neutralizing background plasma.
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Affiliation(s)
- Piero Procacci
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Guido Guarnieri
- ENEA, Portici Research Centre, DTE-ICT-HPC, P.le E. Fermi, 1, I-80055 Portici, NA, Italy
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4
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Procacci P, Macchiagodena M. On the NS-DSSB unidirectional estimates in the SAMPL6 SAMPLing challenge. J Comput Aided Mol Des 2021; 35:1055-1065. [PMID: 34625885 PMCID: PMC8523005 DOI: 10.1007/s10822-021-00419-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 09/27/2021] [Indexed: 12/03/2022]
Abstract
In the context of the recent SAMPL6 SAMPLing challenge (Rizzi et al. 2020 in J Comput Aided Mol Des 34:601–633) aimed at assessing convergence properties and reproducibility of molecular dynamics binding free energy methodologies, we propose a simple explanation of the severe errors observed in the nonequilibrium switch double-system-single-box (NS-DSSB) approach when using unidirectional estimates. At the same time, we suggest a straightforward and minimal modification of the NS-DSSB protocol for obtaining reliable unidirectional estimates for the process where the ligand is decoupled in the bound state and recoupled in the bulk.
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Affiliation(s)
- Piero Procacci
- Department of Chemistry, University of Florence, Via Lastruccia n. 3, 50019, Sesto Fiorentino, FI, Italy.
| | - Marina Macchiagodena
- Department of Chemistry, University of Florence, Via Lastruccia n. 3, 50019, Sesto Fiorentino, FI, Italy
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5
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Hurst T, Chen SJ. Deciphering nucleotide modification-induced structure and stability changes. RNA Biol 2021; 18:1920-1930. [PMID: 33586616 DOI: 10.1080/15476286.2021.1882179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nucleotide modification in RNA controls a bevy of biological processes, including RNA degradation, gene expression, and gene editing. In turn, misregulation of modified nucleotides is associated with a host of chronic diseases and disorders. However, the molecular mechanisms driving these processes remain poorly understood. To partially address this knowledge gap, we used alchemical and temperature replica exchange molecular dynamics (TREMD) simulations on an RNA duplex and an analogous hairpin to probe the structural effects of modified and/or mutant nucleotides. The simulations successfully predict the modification/mutation-induced relative free energy change for complementary duplex formation, and structural analyses highlight mechanisms driving stability changes. Furthermore, TREMD simulations for a hairpin-forming RNA with and without modification provide reliable estimations of the energy landscape. Illuminating the impact of methylated and/or mutated nucleotides on the structure-function relationship and the folding energy landscape, the simulations provide insights into modification-induced alterations to the folding mechanics of the hairpin. The results here may be biologically significant as hairpins are widespread structure motifs that play critical roles in gene expression and regulation. Specifically, the tetraloop of the probed hairpin is phylogenetically abundant, and the stem mirrors a miRNA seed region whose modification has been implicated in epilepsy pathogenesis.
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Affiliation(s)
- Travis Hurst
- Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
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6
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Procacci P, Guarnieri G. SAMPL7 blind predictions using nonequilibrium alchemical approaches. J Comput Aided Mol Des 2021; 35:37-47. [PMID: 33392950 DOI: 10.1007/s10822-020-00365-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/27/2020] [Indexed: 11/24/2022]
Abstract
In the context of the SAMPL7 challenge, we computed, employing a non-equilibrium (NE) alchemical technique, the standard binding free energy of two series of host-guest systems, involving as a host the Isaac's TrimerTrip, a Cucurbituril-like open cavitand, and the Gilson's Cyclodextrin derivatives. The adopted NE alchemy combines enhanced sampling molecular dynamics simulations with driven fast out-of-equilibrium alchemical trajectories to recover the free energy via the Jarzynski and Crooks NE theorems. The GAFF2 non-polarizable force field was used for the parametrization. Performances were acceptable and similar in accuracy to those we submitted for Gibb's Deep Cavity Cavitands in the previous SAMPL6 host-guest challenge, confirming the reliability of the computational approach and exposing, in some cases, some important deficiencies of the GAFF2 non-polarizable force field.
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Affiliation(s)
- Piero Procacci
- University of Florence, Department of Chemistry, 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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7
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Procacci P. Methodological uncertainties in drug-receptor binding free energy predictions based on classical molecular dynamics. Curr Opin Struct Biol 2020; 67:127-134. [PMID: 33220532 DOI: 10.1016/j.sbi.2020.08.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/02/2020] [Accepted: 08/02/2020] [Indexed: 12/13/2022]
Abstract
Computational approaches are becoming an essential tool in modern drug design and discovery, with fast compound triaging using a combination of machine learning and docking techniques followed by molecular dynamics binding free energies assessment using alchemical techniques. The traditional MD-based alchemical free energy perturbation (FEP) method faces severe sampling issues that may limits its reliability in automated workflows. Here we review the major sources of uncertainty in FEP protocols for drug discovery, showing how the sampling problem can be effectively tackled by switching to nonequilibrium alchemical techniques.
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Affiliation(s)
- Piero Procacci
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, dVia della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
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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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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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10
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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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11
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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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12
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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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13
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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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14
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Wang X, Tu X, Deng B, Zhang JZH, Sun Z. BAR-based optimum adaptive steered MD for configurational sampling. J Comput Chem 2019; 40:1270-1289. [PMID: 30762879 DOI: 10.1002/jcc.25784] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/05/2018] [Accepted: 01/06/2019] [Indexed: 11/08/2022]
Abstract
The equilibrium and nonequilibrium adaptive alchemical free energy simulation methods optimum Bennett's acceptance ratio and optimum crooks' equation (OCE), based on the statistically optimal bidirectional reweighting estimator named Bennett's Acceptance Ratio or Crooks' equation, perform initial sampling in the staging alchemical transformation and then determine the importance rank of different states via the time-derivative of the variance. The method is proven to give speedups compared with the equal time rule. In the current work, we extend the time derivative of variance guided adaptive sampling method to the configurational space, falling in the term of steered MD (SMD). The SMD approach biasing physically meaningful collective variable (CV) such as one dihedral or one distance to pulling the system from one conformational state to another. By minimizing the variance of the free energy differences along the pathway in an optimized way, a new type of adaptive SMD (ASMD) is introduced. As exhibits in the alchemical case, this adaptive sampling method outperforms the traditional equal-time SMD in nonequilibrium stratification. Also, the method gives much more efficient calculation of potential of mean force than the selection criterion-based ASMD scheme, which is proven to be more efficient than traditional SMD. The OCE workflow is periodicity-of-CV dependent while ASMD is not. The performance is demonstrated in a dihedral flipping case and two distance pulling cases, accounting for periodic and nonperiodic CVs, respectively. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.,Institute of Computational Science, Università della Svizzera italiana (USI), CH-6900, Lugano, Ticino, Switzerland
| | - Xingzhao Tu
- Institute of Organic Chemistry, University of Leipzig, Leipzig 04103, Germany
| | - Boming Deng
- Laboratory of Oil Analysis, Beijing Hangfengkewei Equipment Technology Co., Ltd., Beijing 100141, China
| | - John Z H Zhang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Department of Chemistry, New York University, New York, New York, 10003
| | - Zhaoxi Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.,Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Juelich, Jülich 52425, Germany
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15
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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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16
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Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD. Overview of the SAMPL6 host-guest binding affinity prediction challenge. J Comput Aided Mol Des 2018; 32:937-963. [PMID: 30415285 PMCID: PMC6301044 DOI: 10.1007/s10822-018-0170-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/07/2018] [Indexed: 10/27/2022]
Abstract
Accurately predicting the binding affinities of small organic molecules to biological macromolecules can greatly accelerate drug discovery by reducing the number of compounds that must be synthesized to realize desired potency and selectivity goals. Unfortunately, the process of assessing the accuracy of current computational approaches to affinity prediction against binding data to biological macromolecules is frustrated by several challenges, such as slow conformational dynamics, multiple titratable groups, and the lack of high-quality blinded datasets. Over the last several SAMPL blind challenge exercises, host-guest systems have emerged as a practical and effective way to circumvent these challenges in assessing the predictive performance of current-generation quantitative modeling tools, while still providing systems capable of possessing tight binding affinities. Here, we present an overview of the SAMPL6 host-guest binding affinity prediction challenge, which featured three supramolecular hosts: octa-acid (OA), the closely related tetra-endo-methyl-octa-acid (TEMOA), and cucurbit[8]uril (CB8), along with 21 small organic guest molecules. A total of 119 entries were received from ten participating groups employing a variety of methods that spanned from electronic structure and movable type calculations in implicit solvent to alchemical and potential of mean force strategies using empirical force fields with explicit solvent models. While empirical models tended to obtain better performance than first-principle methods, it was not possible to identify a single approach that consistently provided superior results across all host-guest systems and statistical metrics. Moreover, the accuracy of the methodologies generally displayed a substantial dependence on the system considered, emphasizing the need for host diversity in blind evaluations. Several entries exploited previous experimental measurements of similar host-guest systems in an effort to improve their physical-based predictions via some manner of rudimentary machine learning; while this strategy succeeded in reducing systematic errors, it did not correspond to an improvement in statistical correlation. Comparison to previous rounds of the host-guest binding free energy challenge highlights an overall improvement in the correlation obtained by the affinity predictions for OA and TEMOA systems, but a surprising lack of improvement regarding root mean square error over the past several challenge rounds. The data suggests that further refinement of force field parameters, as well as improved treatment of chemical effects (e.g., buffer salt conditions, protonation states), may be required to further enhance predictive accuracy.
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Affiliation(s)
- 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
| | - Steven Murkli
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - John N McNeill
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Wei Yao
- Department of Chemistry, Tulane University, Louisiana, LA, 70118, USA
| | - Matthew Sullivan
- Department of Chemistry, Tulane University, Louisiana, LA, 70118, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Michael W Chiu
- Qualcomm Institute, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Bruce C Gibb
- Department of Chemistry, Tulane University, Louisiana, LA, 70118, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, California, 92697, USA.
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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17
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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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18
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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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19
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Wang X, Tu X, Zhang JZH, Sun Z. BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification. Phys Chem Chem Phys 2018; 20:2009-2021. [PMID: 29299568 DOI: 10.1039/c7cp07573a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Following the previously proposed equilibrate-state sampling based adaptive sampling regime Optimum Bennett Acceptance Ratio (OBAR), we introduce its nonequilibrium extension, the Optimum Crooks' Equation (OCE) in the current work. The efficiency of the NonEquilibrium Work (NEW) stratification is improved by adaptively manipulating the significance of each nonequilibrium realization followed by importance sampling. As is exhibited in the equilibrium case, the nonequilibrium extension outperforms the simple equal time rule used in nonequilibrium stratification in the sense of minimizing the total variance of the free energy estimate. The speedup of this non-equal time rule is more than 1-fold. The Time Derivative of total Variance (TDV) proposed for the OBAR criterion is extended to determine the importance of each nonequilibrium transformation, which is linearly dependent on the variance. The TDV in the nonequilibrium case gives a totally different importance rank from the standard errors of the free energy differences and OBAR TDV due to the duration of nonequilibrium pulling being added into the OCE equation. The performance of the OCE workflow is demonstrated in the solvation of several small molecules with a series of lambda increments and relaxation times between successive perturbations. To the best of our knowledge, such a nonequilibrium adaptive sampling regime in alchemical transformation is unprecedented.
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Affiliation(s)
- Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
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20
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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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21
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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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22
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Procacci P, Chelli R. Statistical Mechanics of Ligand–Receptor Noncovalent Association, Revisited: Binding Site and Standard State Volumes in Modern Alchemical Theories. J Chem Theory Comput 2017; 13:1924-1933. [DOI: 10.1021/acs.jctc.6b01192] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Piero Procacci
- Department of Chemistry, University of Florence, Via Lastruccia
n. 3, Sesto
Fiorentino I-50019, Italy
| | - Riccardo Chelli
- Department of Chemistry, University of Florence, Via Lastruccia
n. 3, Sesto
Fiorentino I-50019, Italy
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23
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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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24
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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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