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Suruzhon M, Bodnarchuk MS, Ciancetta A, Viner R, Wall ID, Essex JW. Sensitivity of Binding Free Energy Calculations to Initial Protein Crystal Structure. J Chem Theory Comput 2021; 17:1806-1821. [PMID: 33534995 DOI: 10.1021/acs.jctc.0c00972] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Binding free energy calculations using alchemical free energy (AFE) methods are widely considered to be the most rigorous tool in the computational drug discovery arsenal. Despite this, the calculations suffer from accuracy, precision, and reproducibility issues. In this publication, we perform a high-throughput study of more than a thousand AFE calculations, utilizing over 220 μs of total sampling time, on three different protein systems to investigate the impact of the initial crystal structure on the resulting binding free energy values. We also consider the influence of equilibration time and discover that the initial crystal structure can have a significant effect on free energy values obtained at short timescales that can manifest itself as a free energy difference of more than 1 kcal/mol. At longer timescales, these differences are largely overtaken by important rare events, such as torsional ligand motions, typically resulting in a much higher uncertainty in the obtained values. This work emphasizes the importance of rare event sampling and long-timescale dynamics in free energy calculations even for routinely performed alchemical perturbations. We conclude that an optimal protocol should not only concentrate computational resources on achieving convergence in the alchemical coupling parameter (λ) space but also on longer simulations and multiple repeats.
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Affiliation(s)
- Miroslav Suruzhon
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
| | | | | | - Russell Viner
- Syngenta, Jealott's Hill International Research Centre, Bracknell RG42 6EY, U.K
| | - Ian D Wall
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
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Schindler CEM, Baumann H, Blum A, Böse D, Buchstaller HP, Burgdorf L, Cappel D, Chekler E, Czodrowski P, Dorsch D, Eguida MKI, Follows B, Fuchß T, Grädler U, Gunera J, Johnson T, Jorand Lebrun C, Karra S, Klein M, Knehans T, Koetzner L, Krier M, Leiendecker M, Leuthner B, Li L, Mochalkin I, Musil D, Neagu C, Rippmann F, Schiemann K, Schulz R, Steinbrecher T, Tanzer EM, Unzue Lopez A, Viacava Follis A, Wegener A, Kuhn D. Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects. J Chem Inf Model 2020; 60:5457-5474. [PMID: 32813975 DOI: 10.1021/acs.jcim.0c00900] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Accurate ranking of compounds with regards to their binding affinity to a protein using computational methods is of great interest to pharmaceutical research. Physics-based free energy calculations are regarded as the most rigorous way to estimate binding affinity. In recent years, many retrospective studies carried out both in academia and industry have demonstrated its potential. Here, we present the results of large-scale prospective application of the FEP+ method in active drug discovery projects in an industry setting at Merck KGaA, Darmstadt, Germany. We compare these prospective data to results obtained on a new diverse, public benchmark of eight pharmaceutically relevant targets. Our results offer insights into the challenges faced when using free energy calculations in real-life drug discovery projects and identify limitations that could be tackled by future method development. The new public data set we provide to the community can support further method development and comparative benchmarking of free energy calculations.
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Affiliation(s)
| | - Hannah Baumann
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Andreas Blum
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Dietrich Böse
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | | | - Lars Burgdorf
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | | | - Eugene Chekler
- EMD Serono Research and Development Institute Inc., 45A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Paul Czodrowski
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Dieter Dorsch
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | | | - Bruce Follows
- EMD Serono Research and Development Institute Inc., 45A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Thomas Fuchß
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Ulrich Grädler
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Jakub Gunera
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Theresa Johnson
- EMD Serono Research and Development Institute Inc., 45A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Catherine Jorand Lebrun
- EMD Serono Research and Development Institute Inc., 45A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Srinivasa Karra
- EMD Serono Research and Development Institute Inc., 45A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Markus Klein
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Tim Knehans
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Lisa Koetzner
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Mireille Krier
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | | | | | - Liwei Li
- EMD Serono Research and Development Institute Inc., 45A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Igor Mochalkin
- EMD Serono Research and Development Institute Inc., 45A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Djordje Musil
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Constantin Neagu
- EMD Serono Research and Development Institute Inc., 45A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | | | - Kai Schiemann
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Robert Schulz
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany.,Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2+4, 14195 Berlin, Germany
| | | | - Eva-Maria Tanzer
- EMD Serono Research and Development Institute Inc., 45A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | | | - Ariele Viacava Follis
- EMD Serono Research and Development Institute Inc., 45A Middlesex Turnpike, Billerica, Massachusetts 01821, United States
| | - Ansgar Wegener
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - Daniel Kuhn
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
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Cappel D, Hall ML, Lenselink EB, Beuming T, Qi J, Bradner J, Sherman W. Relative Binding Free Energy Calculations Applied to Protein Homology Models. J Chem Inf Model 2016; 56:2388-2400. [PMID: 28024402 PMCID: PMC5777225 DOI: 10.1021/acs.jcim.6b00362] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A significant challenge and potential high-value application of computer-aided drug design is the accurate prediction of protein-ligand binding affinities. Free energy perturbation (FEP) using molecular dynamics (MD) sampling is among the most suitable approaches to achieve accurate binding free energy predictions, due to the rigorous statistical framework of the methodology, correct representation of the energetics, and thorough treatment of the important degrees of freedom in the system (including explicit waters). Recent advances in sampling methods and force fields coupled with vast increases in computational resources have made FEP a viable technology to drive hit-to-lead and lead optimization, allowing for more efficient cycles of medicinal chemistry and the possibility to explore much larger chemical spaces. However, previous FEP applications have focused on systems with high-resolution crystal structures of the target as starting points-something that is not always available in drug discovery projects. As such, the ability to apply FEP on homology models would greatly expand the domain of applicability of FEP in drug discovery. In this work we apply a particular implementation of FEP, called FEP+, on congeneric ligand series binding to four diverse targets: a kinase (Tyk2), an epigenetic bromodomain (BRD4), a transmembrane GPCR (A2A), and a protein-protein interaction interface (BCL-2 family protein MCL-1). We apply FEP+ using both crystal structures and homology models as starting points and find that the performance using homology models is generally on a par with the results when using crystal structures. The robustness of the calculations to structural variations in the input models can likely be attributed to the conformational sampling in the molecular dynamics simulations, which allows the modeled receptor to adapt to the "real" conformation for each ligand in the series. This work exemplifies the advantages of using all-atom simulation methods with full system flexibility and offers promise for the general application of FEP to homology models, although additional validation studies should be performed to further understand the limitations of the method and the scenarios where FEP will work best.
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Affiliation(s)
- Daniel Cappel
- Schrödinger GmbH, Dynamostraße 13, 68165 Mannheim, Germany
| | - Michelle Lynn Hall
- Schrodinger Inc., 120 W 45th Street, New York, New York 10036, United States
| | - Eelke B. Lenselink
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Thijs Beuming
- Schrodinger Inc., 120 W 45th Street, New York, New York 10036, United States
| | - Jun Qi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, LC-2210, Boston, Massachusetts 02215, United States
| | - James Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, LC-2210, Boston, Massachusetts 02215, United States
| | - Woody Sherman
- Schrodinger Inc., 120 W 45th Street, New York, New York 10036, United States
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Hudson BD, Shimpukade B, Milligan G, Ulven T. The molecular basis of ligand interaction at free fatty acid receptor 4 (FFA4/GPR120). J Biol Chem 2014; 289:20345-58. [PMID: 24860101 PMCID: PMC4106347 DOI: 10.1074/jbc.m114.561449] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The long-chain fatty acid receptor FFA4 (previously GPR120) is receiving substantial interest as a novel target for the treatment of metabolic and inflammatory disease. This study examines for the first time the detailed mode of binding of both long-chain fatty acid and synthetic agonist ligands at FFA4 by integrating molecular modeling, receptor mutagenesis, and ligand structure-activity relationship approaches in an iterative format. In doing so, residues required for binding of fatty acid and synthetic agonists to FFA4 have been identified. This has allowed for the refinement of a well validated model of the mode of ligand-FFA4 interaction that will be invaluable in the identification of novel ligands and the future development of this receptor as a therapeutic target. The model reliably predicted the effects of substituent variations on agonist potency, and it was also able to predict the qualitative effect of binding site mutations in the majority of cases.
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Affiliation(s)
- Brian D Hudson
- From the Molecular Pharmacology Group, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom and
| | - Bharat Shimpukade
- the Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Graeme Milligan
- From the Molecular Pharmacology Group, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom and
| | - Trond Ulven
- the Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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Bharadwaj VS, Dean AM, Maupin CM. Insights into the Glycyl Radical Enzyme Active Site of Benzylsuccinate Synthase: A Computational Study. J Am Chem Soc 2013; 135:12279-88. [DOI: 10.1021/ja404842r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Vivek S. Bharadwaj
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden,
Colorado 80401, United States
| | - Anthony M. Dean
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden,
Colorado 80401, United States
| | - C. Mark Maupin
- Chemical and Biological Engineering Department, Colorado School of Mines, 1500 Illinois Street, Golden,
Colorado 80401, United States
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