201
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Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design. Biochim Biophys Acta Gen Subj 2014; 1850:966-971. [PMID: 25196360 DOI: 10.1016/j.bbagen.2014.08.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 08/26/2014] [Accepted: 08/28/2014] [Indexed: 11/24/2022]
Abstract
BACKGROUND Non-nucleoside inhibitors of HIV reverse transcriptase are an important component of treatment against HIV infection. Novel inhibitors are sought that increase potency against variants that contain the Tyr181Cys mutation. METHODS Molecular dynamics based free energy perturbation simulations have been run to study factors that contribute to protein-ligand binding, and the results are compared with those from previous Monte Carlo based simulations and activity data. RESULTS Predictions of protein-ligand binding modes are very consistent for the two simulation methods; the accord is attributed to the use of an enhanced sampling protocol. The Tyr181Cys binding pocket supports large, hydrophobic substituents, which is in good agreement with experiment. CONCLUSIONS Although some discrepancies exist between the results of the two simulation methods and experiment, free energy perturbation simulations can be used to rapidly test small molecules for gains in binding affinity. GENERAL SIGNIFICANCE Free energy perturbation methods show promise in providing fast, reliable and accurate data that can be used to complement experiment in lead optimization projects. This article is part of a Special Issue entitled "Recent developments of molecular dynamics".
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202
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Vilseck J, Tirado-Rives J, Jorgensen WL. Evaluation of CM5 Charges for Condensed-Phase Modeling. J Chem Theory Comput 2014; 10:2802-2812. [PMID: 25061445 PMCID: PMC4095915 DOI: 10.1021/ct500016d] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Indexed: 11/30/2022]
Abstract
The recently developed Charge Model 5 (CM5) is tested for its utility in condensed-phase simulations. The CM5 approach, which derives partial atomic charges from Hirshfeld population analyses, provides excellent results for gas-phase dipole moments and is applicable to all elements of the periodic table. Herein, the adequacy of scaled CM5 charges for use in modeling aqueous solutions has been evaluated by computing free energies of hydration (ΔGhyd) for 42 neutral organic molecules via Monte Carlo statistical mechanics. An optimal scaling factor for the CM5 charges was determined to be 1.27, resulting in a mean unsigned error (MUE) of 1.1 kcal/mol for the free energies of hydration. Testing for an additional 20 molecules gave an MUE of 1.3 kcal/mol. The high precision of the results is confirmed by free energy calculations using both sequential perturbations and complete molecular annihilation. Performance for specific functional groups is discussed; sulfur-containing molecules yield the largest errors. In addition, the scaling factor of 1.27 is shown to be appropriate for CM5 charges derived from a variety of density functional methods and basis sets. Though the average errors from the 1.27*CM5 results are only slightly lower than those using 1.14*CM1A charges, the broader applicability and easier access to CM5 charges via the Gaussian program are additional attractive features. The 1.27*CM5 charge model can be used for an enormous variety of applications in conjunction with many fixed-charge force fields and molecular modeling programs.
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Affiliation(s)
- Jonah
Z. Vilseck
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L. Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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203
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Mobley DL, Guthrie JP. FreeSolv: a database of experimental and calculated hydration free energies, with input files. J Comput Aided Mol Des 2014. [PMID: 24928188 DOI: 10.1007/s10822-014-9747-x.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz .
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Affiliation(s)
- David L Mobley
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, 147 Bison Modular, Irvine, CA, 92697, USA,
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204
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Mobley DL, Guthrie JP. FreeSolv: a database of experimental and calculated hydration free energies, with input files. J Comput Aided Mol Des 2014; 28:711-20. [PMID: 24928188 DOI: 10.1007/s10822-014-9747-x] [Citation(s) in RCA: 224] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 05/03/2014] [Indexed: 12/14/2022]
Abstract
This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz .
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Affiliation(s)
- David L Mobley
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, 147 Bison Modular, Irvine, CA, 92697, USA,
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205
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Hansen N, van Gunsteren WF. Practical Aspects of Free-Energy Calculations: A Review. J Chem Theory Comput 2014; 10:2632-47. [PMID: 26586503 DOI: 10.1021/ct500161f] [Citation(s) in RCA: 289] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Free-energy calculations in the framework of classical molecular dynamics simulations are nowadays used in a wide range of research areas including solvation thermodynamics, molecular recognition, and protein folding. The basic components of a free-energy calculation, that is, a suitable model Hamiltonian, a sampling protocol, and an estimator for the free energy, are independent of the specific application. However, the attention that one has to pay to these components depends considerably on the specific application. Here, we review six different areas of application and discuss the relative importance of the three main components to provide the reader with an organigram and to make nonexperts aware of the many pitfalls present in free energy calculations.
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Affiliation(s)
- Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart , D-70569 Stuttgart, Germany.,Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , CH-8093 Zürich, Switzerland
| | - Wilfred F van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH , CH-8093 Zürich, Switzerland
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206
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Jämbeck JPM, Lyubartsev AP. Update to the General Amber Force Field for Small Solutes with an Emphasis on Free Energies of Hydration. J Phys Chem B 2014; 118:3793-804. [DOI: 10.1021/jp4111234] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Joakim P. M. Jämbeck
- Division of Physical Chemistry,
Arrhenius Laboratory, Stockholm University, Stockholm SE-10691, Sweden
| | - Alexander P. Lyubartsev
- Division of Physical Chemistry,
Arrhenius Laboratory, Stockholm University, Stockholm SE-10691, Sweden
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207
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Götz AW, Bucher D, Lindert S, McCammon JA. Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields. J Chem Theory Comput 2014; 10:1631-1637. [PMID: 24803868 PMCID: PMC3986234 DOI: 10.1021/ct401049q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Indexed: 11/29/2022]
Abstract
The description of aggregation processes with molecular dynamics simulations is a playground for testing biomolecular force fields, including a new generation of force fields that explicitly describe electronic polarization. In this work, we study a system consisting of 50 glycyl-l-alanine (Gly-Ala) dipeptides in solution with 1001 water molecules. Neutron diffraction experiments have shown that at this concentration, Gly-Ala aggregates into large clusters. However, general-purpose force fields in combination with established water models can fail to correctly describe this aggregation process, highlighting important deficiencies in how solute-solute and solute-solvent interactions are parametrized in these force fields. We found that even for the fully polarizable AMOEBA force field, the degree of association is considerably underestimated. Instead, a fixed point-charge approach based on the newly developed IPolQ scheme [Cerutti et al. J. Phys. Chem.2013, 117, 2328] allows for the correct modeling of the dipeptide aggregation in aqueous solution. This result should stimulate interest in novel fitting schemes that aim to improve the description of the solvent polarization effect within both explicitly polarizable and fixed point-charge frameworks.
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Affiliation(s)
- Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States ; Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Denis Bucher
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States ; Department of Pharmacology, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States ; Howard Hughes Medical Institute, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093, United States
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208
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Vanommeslaeghe K, Guvench O, MacKerell AD. Molecular mechanics. Curr Pharm Des 2014; 20:3281-92. [PMID: 23947650 PMCID: PMC4026342 DOI: 10.2174/13816128113199990600] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/07/2013] [Indexed: 11/22/2022]
Abstract
Molecular Mechanics (MM) force fields are the methods of choice for protein simulations, which are essential in the study of conformational flexibility. Given the importance of protein flexibility in drug binding, MM is involved in most if not all Computational Structure-Based Drug Discovery (CSBDD) projects. This paper introduces the reader to the fundamentals of MM, with a special emphasis on how the target data used in the parametrization of force fields determine their strengths and weaknesses. Variations and recent developments such as polarizable force fields are discussed. The paper ends with a brief overview of common force fields in CSBDD.
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Affiliation(s)
- Kenno Vanommeslaeghe
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St, HSF-II Rm 633, Baltimore, MD 21201; tel: 410-706-7442; fax: 410-706-5017
| | - Olgun Guvench
- Department of Pharmaceutical Sciences, University of New England College of Pharmacy, 716 Stevens Ave, Portland, ME 04103
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St, HSF-II Rm 633, Baltimore, MD 21201; tel: 410-706-7442; fax: 410-706-5017
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209
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Christ CD, Fox T. Accuracy Assessment and Automation of Free Energy Calculations for Drug Design. J Chem Inf Model 2013; 54:108-20. [DOI: 10.1021/ci4004199] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Clara D. Christ
- Department of Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, 88397 Germany
| | - Thomas Fox
- Department of Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, 88397 Germany
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210
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Chen IJ, Foloppe N. Tackling the conformational sampling of larger flexible compounds and macrocycles in pharmacology and drug discovery. Bioorg Med Chem 2013; 21:7898-920. [DOI: 10.1016/j.bmc.2013.10.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 09/29/2013] [Accepted: 10/04/2013] [Indexed: 02/01/2023]
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211
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Could MM-GBSA be accurate enough for calculation of absolute protein/ligand binding free energies? J Mol Graph Model 2013; 46:41-51. [DOI: 10.1016/j.jmgm.2013.09.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 09/06/2013] [Accepted: 09/07/2013] [Indexed: 11/20/2022]
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212
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Wickstrom L, He P, Gallicchio E, Levy RM. Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process. J Chem Theory Comput 2013; 9:3136-3150. [PMID: 25147485 DOI: 10.1021/ct400003r] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Host-guest inclusion complexes are useful models for understanding the structural and energetic aspects of molecular recognition. Due to their small size relative to much larger protein-ligand complexes, converged results can be obtained rapidly for these systems thus offering the opportunity to more reliably study fundamental aspects of the thermodynamics of binding. In this work, we have performed a large scale binding affinity survey of 57 β-cyclodextrin (CD) host guest systems using the binding energy distribution analysis method (BEDAM) with implicit solvation (OPLS-AA/AGBNP2). Converged estimates of the standard binding free energies are obtained for these systems by employing techniques such as parallel Hamitionian replica exchange molecular dynamics, conformational reservoirs and multistate free energy estimators. Good agreement with experimental measurements is obtained in terms of both numerical accuracy and affinity rankings. Overall, average effective binding energies reproduce affinity rank ordering better than the calculated binding affinities, even though calculated binding free energies, which account for effects such as conformational strain and entropy loss upon binding, provide lower root mean square errors when compared to measurements. Interestingly, we find that binding free energies are superior rank order predictors for a large subset containing the most flexible guests. The results indicate that, while challenging, accurate modeling of reorganization effects can lead to ligand design models of superior predictive power for rank ordering relative to models based only on ligand-receptor interaction energies.
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Affiliation(s)
- Lauren Wickstrom
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854 ; Department of Chemistry, Lehman College, The City University of New York, Bronx, NY 10468
| | - Peng He
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Emilio Gallicchio
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - Ronald M Levy
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
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213
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Dunbar JB, Smith RD, Damm-Ganamet KL, Ahmed A, Esposito EX, Delproposto J, Chinnaswamy K, Kang YN, Kubish G, Gestwicki JE, Stuckey JA, Carlson HA. CSAR data set release 2012: ligands, affinities, complexes, and docking decoys. J Chem Inf Model 2013; 53:1842-52. [PMID: 23617227 PMCID: PMC3753885 DOI: 10.1021/ci4000486] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
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A major goal in drug design is the
improvement of computational
methods for docking and scoring. The Community Structure Activity
Resource (CSAR) has collected several data sets from industry and
added in-house data sets that may be used for this purpose (www.csardock.org). CSAR has currently obtained data from Abbott, GlaxoSmithKline,
and Vertex and is working on obtaining data from several others. Combined
with our in-house projects, we are providing a data set consisting
of 6 protein targets, 647 compounds with biological affinities, and
82 crystal structures. Multiple congeneric series are available for
several targets with a few representative crystal structures of each
of the series. These series generally contain a few inactive compounds,
usually not available in the literature, to provide an upper bound
to the affinity range. The affinity ranges are typically 3–4
orders of magnitude per series. For our in-house projects, we have
had compounds synthesized for biological testing. Affinities were
measured by Thermofluor, Octet RED, and isothermal titration calorimetry
for the most soluble. This allows the direct comparison of the biological
affinities for those compounds, providing a measure of the variance
in the experimental affinity. It appears that there can be considerable
variance in the absolute value of the affinity, making the prediction
of the absolute value ill-defined. However, the relative rankings
within the methods are much better, and this fits with the observation
that predicting relative ranking is a more tractable problem computationally.
For those in-house compounds, we also have measured the following
physical properties: logD, logP, thermodynamic solubility, and pKa. This data set also provides a substantial
decoy set for each target consisting of diverse conformations covering
the entire active site for all of the 58 CSAR-quality crystal structures.
The CSAR data sets (CSAR-NRC HiQ and the 2012 release) provide substantial,
publically available, curated data sets for use in parametrizing and
validating docking and scoring methods.
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Affiliation(s)
- James B Dunbar
- Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, Michigan 48109-1065, USA.
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214
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Affiliation(s)
- Riccardo Baron
- Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112-5820;
| | - J. Andrew McCammon
- Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology, and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093-0365;
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215
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Extended solvent-contact model for protein solvation: test cases for dipeptides. J Mol Graph Model 2013; 42:50-9. [PMID: 23548585 DOI: 10.1016/j.jmgm.2013.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 02/08/2013] [Accepted: 02/13/2013] [Indexed: 11/22/2022]
Abstract
Solvation effects are critically important in the structural stabilization and functional optimization of proteins. Here, we propose a new solvation free energy function for proteins, and test its applicability in predicting the solvation free energies of dipeptides. The present solvation model involves the improvement of the previous solvent-contact model assuming that the molecular solvation free energy could be given by the sum over the individual atomic contributions. In addition to the existing solvent-contact term, the modified solvation free energy function includes the self-solvation term that reflects the effects of intramolecular interactions in the solute molecule on solute-solvent interactions. Four kinds of atomic parameters should be determined in this solvation model: atomic fragmental volume, maximum atomic occupancy, atomic solvation, and atomic self-solvation parameters. All of these parameters for 16 atom types are optimized with a standard genetic algorithm in such a way to minimize the difference between the solvation free energies of dipeptides obtained from high-level quantum chemical calculations and those predicted by the solvation free energy function. The solvation free energies of dipeptides estimated from the new solvation model are in good agreement with the quantum chemical results. Therefore, the optimized solvation free energy function is expected to be useful for examining the structural and energetic features of proteins in aqueous solution.
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216
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Mobley DL, Klimovich PV. Perspective: Alchemical free energy calculations for drug discovery. J Chem Phys 2012; 137:230901. [PMID: 23267463 PMCID: PMC3537745 DOI: 10.1063/1.4769292] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/15/2012] [Indexed: 02/06/2023] Open
Abstract
Computational techniques see widespread use in pharmaceutical drug discovery, but typically prove unreliable in predicting trends in protein-ligand binding. Alchemical free energy calculations seek to change that by providing rigorous binding free energies from molecular simulations. Given adequate sampling and an accurate enough force field, these techniques yield accurate free energy estimates. Recent innovations in alchemical techniques have sparked a resurgence of interest in these calculations. Still, many obstacles stand in the way of their routine application in a drug discovery context, including the one we focus on here, sampling. Sampling of binding modes poses a particular challenge as binding modes are often separated by large energy barriers, leading to slow transitions. Binding modes are difficult to predict, and in some cases multiple binding modes may contribute to binding. In view of these hurdles, we present a framework for dealing carefully with uncertainty in binding mode or conformation in the context of free energy calculations. With careful sampling, free energy techniques show considerable promise for aiding drug discovery.
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Affiliation(s)
- David L Mobley
- Department of Chemistry, University of New Orleans, 2000 Lakeshore Drive, New Orleans, Louisiana 70148, USA.
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217
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Close intramolecular sulfur–oxygen contacts: modified force field parameters for improved conformation generation. J Comput Aided Mol Des 2012; 26:1195-205. [DOI: 10.1007/s10822-012-9610-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 09/20/2012] [Indexed: 11/26/2022]
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