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Amezcua M, Setiadi J, Ge Y, Mobley DL. An overview of the SAMPL8 host-guest binding challenge. J Comput Aided Mol Des 2022; 36:707-734. [PMID: 36229622 PMCID: PMC9596595 DOI: 10.1007/s10822-022-00462-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022]
Abstract
The SAMPL series of challenges aim to focus the community on specific modeling challenges, while testing and hopefully driving progress of computational methods to help guide pharmaceutical drug discovery. In this study, we report on the results of the SAMPL8 host–guest blind challenge for predicting absolute binding affinities. SAMPL8 focused on two host–guest datasets, one involving the cucurbituril CB8 (with a series of common drugs of abuse) and another involving two different Gibb deep-cavity cavitands. The latter dataset involved a previously featured deep cavity cavitand (TEMOA) as well as a new variant (TEETOA), both binding to a series of relatively rigid fragment-like guests. Challenge participants employed a reasonably wide variety of methods, though many of these were based on molecular simulations, and predictive accuracy was mixed. As in some previous SAMPL iterations (SAMPL6 and SAMPL7), we found that one approach to achieve greater accuracy was to apply empirical corrections to the binding free energy predictions, taking advantage of prior data on binding to these hosts. Another approach which performed well was a hybrid MD-based approach with reweighting to a force matched QM potential. In the cavitand challenge, an alchemical method using the AMOEBA-polarizable force field achieved the best success with RMSE less than 1 kcal/mol, while another alchemical approach (ATM/GAFF2-AM1BCC/TIP3P/HREM) had RMSE less than 1.75 kcal/mol. The work discussed here also highlights several important lessons; for example, retrospective studies of reference calculations demonstrate the sensitivity of predicted binding free energies to ethyl group sampling and/or guest starting pose, providing guidance to help improve future studies on these systems.
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Affiliation(s)
- Martin Amezcua
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Jeffry Setiadi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yunhui Ge
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, 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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2
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Reif MM, Zacharias M. Improving the Potential of Mean Force and Nonequilibrium Pulling Simulations by Simultaneous Alchemical Modifications. J Chem Theory Comput 2022; 18:3873-3893. [PMID: 35653503 DOI: 10.1021/acs.jctc.1c01194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present an approach combining alchemical modifications and physical-pathway methods to calculate absolute binding free energies. The employed physical-pathway method is either a stratified umbrella sampling to calculate a potential of mean force or nonequilibrium pulling. We devised two basic approaches: the simultaneous approach (S-approach), where, along the physical unbinding pathway, an alchemical transformation of ligand-protein interactions is installed and deinstalled, and the prior-plus-simultaneous approach (PPS-approach), where, prior to the physical-pathway simulation, an alchemical transformation of ligand-protein interactions is installed in the binding site and deinstalled during the physical-pathway simulation. Using a mutant of T4 lysozyme with a benzene ligand as an example, we show that installation and deinstallation of soft-core interactions concurrent with physical ligand unbinding (S-approach) allow successful potential of mean force calculations and nonequilibrium pulling simulations despite the problems posed by the occluded nature of the lysozyme binding pocket. Good agreement between the potential of the mean-force-based S-approach and double decoupling simulations as well as a remarkable efficiency and accuracy of the nonequilibrium-pulling-based S-approach is found. The latter turned out to be more compute-efficient than the potential of mean force calculation by approximately 70%. Furthermore, we illustrate the merits of reducing ligand-protein interactions prior to potential of mean force calculations using the murine double minute homologue protein MDM2 with a p53-derived peptide ligand (PPS-approach). Here, the problem of breaking strong interactions in the binding pocket is transferred to a prior alchemical transformation that reduces the free-energy barrier between the bound and unbound state in the potential of mean force. Besides, disentangling physical ligand displacement from the deinstallation of ligand-protein interactions was seen to allow a more uniform sampling of distance histograms in the umbrella sampling. In the future, physical ligand unbinding combined with simultaneous alchemical modifications may prove useful in the calculation of protein-protein binding free energies, where sampling problems posed by multiple, possibly sticky interactions and potential steric clashes can thus be reduced.
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Affiliation(s)
- Maria M Reif
- Center for Protein Assemblies (CPA), Physics Department, Chair of Theoretical Biophysics (T38), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, Garching 85748, Germany
| | - Martin Zacharias
- Center for Protein Assemblies (CPA), Physics Department, Chair of Theoretical Biophysics (T38), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, Garching 85748, Germany
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3
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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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Sun Z, Liu Z. BAR‐Based Multi‐Dimensional Nonequilibrium Pulling for Indirect Construction of QM/MM Free Energy Landscapes: Varying the QM Region. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202100185] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Zhaoxi Sun
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
| | - Zhirong Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
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5
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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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Amezcua M, El Khoury L, Mobley DL. SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations. J Comput Aided Mol Des 2021; 35:1-35. [PMID: 33392951 PMCID: PMC8121194 DOI: 10.1007/s10822-020-00363-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/24/2020] [Indexed: 12/15/2022]
Abstract
The SAMPL challenges focus on testing and driving progress of computational methods to help guide pharmaceutical drug discovery. However, assessment of methods for predicting binding affinities is often hampered by computational challenges such as conformational sampling, protonation state uncertainties, variation in test sets selected, and even lack of high quality experimental data. SAMPL blind challenges have thus frequently included a component focusing on host-guest binding, which removes some of these challenges while still focusing on molecular recognition. Here, we report on the results of the SAMPL7 blind prediction challenge for host-guest affinity prediction. In this study, we focused on three different host-guest categories-a familiar deep cavity cavitand series which has been featured in several prior challenges (where we examine binding of a series of guests to two hosts), a new series of cyclodextrin derivatives which are monofunctionalized around the rim to add amino acid-like functionality (where we examine binding of two guests to a series of hosts), and binding of a series of guests to a new acyclic TrimerTrip host which is related to previous cucurbituril hosts. Many predictions used methods based on molecular simulations, and overall success was mixed, though several methods stood out. As in SAMPL6, we find that one strategy for achieving reasonable accuracy here was to make empirical corrections to binding predictions based on previous data for host categories which have been studied well before, though this can be of limited value when new systems are included. Additionally, we found that alchemical free energy methods using the AMOEBA polarizable force field had considerable success for the two host categories in which they participated. The new TrimerTrip system was also found to introduce some sampling problems, because multiple conformations may be relevant to binding and interconvert only slowly. Overall, results in this challenge tentatively suggest that further investigation of polarizable force fields for these challenges may be warranted.
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Affiliation(s)
- Martin Amezcua
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Léa El Khoury
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, 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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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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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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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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10
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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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