1
|
Gilson MK, Kurtzman T. Free Energy Density of a Fluid and Its Role in Solvation and Binding. J Chem Theory Comput 2024; 20:2871-2887. [PMID: 38536144 PMCID: PMC11197885 DOI: 10.1021/acs.jctc.3c01173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
The concept that a fluid has a position-dependent free energy density appears in the literature but has not been fully developed or accepted. We set this concept on an unambiguous theoretical footing via the following strategy. First, we set forth four desiderata that should be satisfied by any definition of the position-dependent free energy density, f(R), in a system comprising only a fluid and a rigid solute: its volume integral, plus the fixed internal energy of the solute, should be the system free energy; it deviates from its bulk value, fbulk, near a solute but should asymptotically approach fbulk with increasing distance from the solute; it should go to zero where the solvent density goes to zero; and it should be well-defined in the most general case of a fluid made up of flexible molecules with an arbitrary interaction potential. Second, we use statistical thermodynamics to formulate a definition of the free energy density that satisfies these desiderata. Third, we show how any free energy density satisfying the desiderata may be used to analyze molecular processes in solution. In particular, because the spatial integral of f(R) equals the free energy of the system, it can be used to compute free energy changes that result from the rearrangement of solutes as well as the forces exerted on the solutes by the solvent. This enables the use of a thermodynamic analysis of water in protein binding sites to inform ligand design. Finally, we discuss related literature and address published concerns regarding the thermodynamic plausibility of a position-dependent free energy density. The theory presented here has applications in theoretical and computational chemistry and may be further generalizable beyond fluids, such as to solids and macromolecules.
Collapse
Affiliation(s)
- Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, and Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA, 92093, USA
| | - Tom Kurtzman
- PhD Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, New York, 10016, USA; Department of Chemistry, Lehman College, The City University of New York, Bronx, New York, 10468, USA
| |
Collapse
|
2
|
Kaczor AA, Zięba A, Matosiuk D. The application of WaterMap-guided structure-based virtual screening in novel drug discovery. Expert Opin Drug Discov 2024; 19:73-83. [PMID: 37807912 DOI: 10.1080/17460441.2023.2267015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/02/2023] [Indexed: 10/10/2023]
Abstract
INTRODUCTION Nowadays, it is widely accepted that water molecules play a key role in binding a ligand to a molecular target. Neglecting water molecules in the process of molecular recognition was the result of several failures of the structure-based drug discovery campaigns. The application of WaterMap, in particular WaterMap-guided molecular docking, enables the reasonably accurate and quick description of the location and energetics of water molecules at the ligand-protein interface. AREAS COVERED In this review, the authors shortly discuss the importance of water in drug design and discovery and provide a brief overview of the computational approaches used to predict the solvent-related effects for the purposes of presenting WaterMap in the context of other available techniques and tools. A concise description of WaterMap concept is followed by the presentation of WaterMap-assisted virtual screening literature published between 2013 and 2023. EXPERT OPINION In recent years, WaterMap software has been extensively used to support structure-based drug design, in particular structure-based virtual screening. Indeed, it is a useful tool to rescore docking results considering water molecules in the binding pocket. Although WaterMap allows for the consideration of the dynamic behavior of water molecules in the binding site, for best accuracy, its application in conjunction with other techniques such as molecular mechanics-generalized Born surface area of FEP (Free Energy Perturbation) is recommended.
Collapse
Affiliation(s)
- Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Lublin, Poland
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Agata Zięba
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Lublin, Poland
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Lublin, Poland
| |
Collapse
|
3
|
Xu H. The slow but steady rise of binding free energy calculations in drug discovery. J Comput Aided Mol Des 2023; 37:67-74. [PMID: 36469232 DOI: 10.1007/s10822-022-00494-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
Binding free energy calculations are increasingly used in drug discovery research to predict protein-ligand binding affinities and to prioritize candidate drug molecules accordingly. It has taken decades of collective effort to transform this academic concept into a technology adopted by the pharmaceutical and biotech industry. Having personally witnessed and taken part in this transformation, here I recount the (incomplete) list of problems that had to be solved to make this computational tool practical and suggest areas of future development.
Collapse
Affiliation(s)
- Huafeng Xu
- Roivant Discovery, 151 West 42nd Street, New York, NY, 10036, USA.
| |
Collapse
|
4
|
Ahmed M, Ganesan A, Barakat K. Leveraging structural and 2D-QSAR to investigate the role of functional group substitutions, conserved surface residues and desolvation in triggering the small molecule-induced dimerization of hPD-L1. BMC Chem 2022; 16:49. [PMID: 35761353 PMCID: PMC9238240 DOI: 10.1186/s13065-022-00842-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 06/21/2022] [Indexed: 12/02/2022] Open
Abstract
Small molecules are rising as a new generation of immune checkpoints’ inhibitors, with compounds targeting the human Programmed death-ligand 1 (hPD-L1) protein are pioneering this area of research. Promising examples include the recently disclosed compounds from Bristol-Myers-Squibb (BMS). These molecules bind specifically to hPD-L1 through a unique mode of action. They induce dimerization between two hPD-L1 monomers through the hPD-1 binding interface in each monomer, thereby inhibiting the PD-1/PD-L1 axis. While the recently reported crystal structures of such small molecules bound to hPD-L1 reveal valuable insights regarding their molecular interactions, there is still limited information about the dynamics driving this unusual complex formation. The current study provides an in-depth computational structural analysis to study the interactions of five small molecule compounds in complex with hPD-L1. By employing a combination of molecular dynamic simulations, binding energy calculations and computational solvent mapping techniques, our analyses quantified the dynamic roles of different hydrophilic and lipophilic residues at the surface of hPD-L1 in mediating these interactions. Furthermore, ligand-based analyses, including Free-Wilson 2D-QSAR was conducted to quantify the impact of R-group substitutions at different sites of the phenoxy-methyl biphenyl core. Our results emphasize the importance of a terminal phenyl ring that must be present in any hPD-L1 small molecule inhibitor. This phenyl moiety overlaps with a very unfavorable hydration site, which can explain the ability of such small molecules to trigger hPD-L1 dimerization.
Collapse
Affiliation(s)
- Marawan Ahmed
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Aravindhan Ganesan
- ArGan's Lab, School of Pharmacy, University of Waterloo, Kitchener, ON, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada. .,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada.
| |
Collapse
|
5
|
Ge Y, Wych DC, Samways ML, Wall ME, Essex JW, Mobley DL. Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques. J Chem Theory Comput 2022; 18:1359-1381. [PMID: 35148093 PMCID: PMC9241631 DOI: 10.1021/acs.jctc.1c00590] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Water often plays a key role in protein structure, molecular recognition, and mediating protein-ligand interactions. Thus, free energy calculations must adequately sample water motions, which often proves challenging in typical MD simulation time scales. Thus, the accuracy of methods relying on MD simulations ends up limited by slow water sampling. Particularly, as a ligand is removed or modified, bulk water may not have time to fill or rearrange in the binding site. In this work, we focus on several molecular dynamics (MD) simulation-based methods attempting to help rehydrate buried water sites: BLUES, using nonequilibrium candidate Monte Carlo (NCMC); grand, using grand canonical Monte Carlo (GCMC); and normal MD. We assess the accuracy and efficiency of these methods in rehydrating target water sites. We selected a range of systems with varying numbers of waters in the binding site, as well as those where water occupancy is coupled to the identity or binding mode of the ligand. We analyzed the rehydration of buried water sites in binding pockets using both clustering of trajectories and direct analysis of electron density maps. Our results suggest both BLUES and grand enhance water sampling relative to normal MD and grand is more robust than BLUES, but also that water sampling remains a major challenge for all of the methods tested. The lessons we learned for these methods and systems are discussed.
Collapse
Affiliation(s)
- Yunhui Ge
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - David C Wych
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Marley L Samways
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Michael E Wall
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
- Department of Chemistry, University of California, Irvine, California 92697, United States
| |
Collapse
|
6
|
Pantsar T, Kaiser PD, Kudolo M, Forster M, Rothbauer U, Laufer SA. Decisive role of water and protein dynamics in residence time of p38α MAP kinase inhibitors. Nat Commun 2022; 13:569. [PMID: 35091547 PMCID: PMC8799644 DOI: 10.1038/s41467-022-28164-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 01/06/2022] [Indexed: 12/31/2022] Open
Abstract
Target residence time plays a crucial role in the pharmacological activity of small molecule inhibitors. Little is known, however, about the underlying causes of inhibitor residence time at the molecular level, which complicates drug optimization processes. Here, we employ all-atom molecular dynamics simulations (~400 μs in total) to gain insight into the binding modes of two structurally similar p38α MAPK inhibitors (type I and type I½) with short and long residence times that otherwise show nearly identical inhibitory activities in the low nanomolar IC50 range. Our results highlight the importance of protein conformational stability and solvent exposure, buried surface area of the ligand and binding site resolvation energy for residence time. These findings are further confirmed by simulations with a structurally diverse short residence time inhibitor SB203580. In summary, our data provide guidance in compound design when aiming for inhibitors with improved target residence time. The molecular determinants of the residence time of a small molecule inhibitor at its target protein are not well understood. Here, Pantsar et al. show that the target protein’s conformational stability and solvent exposure are key factors governing the target residence time of kinase inhibitors.
Collapse
Affiliation(s)
- Tatu Pantsar
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1, 70210, Kuopio, Finland
| | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Mark Kudolo
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
| | - Michael Forster
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, 72076, Tuebingen, Germany
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany. .,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, 72076, Tuebingen, Germany. .,Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany.
| |
Collapse
|
7
|
Hamdy R, Fayed B, Mostafa A, Shama NMA, Mahmoud SH, Mehta CH, Nayak Y, M. Soliman SS. Iterated Virtual Screening-Assisted Antiviral and Enzyme Inhibition Assays Reveal the Discovery of Novel Promising Anti-SARS-CoV-2 with Dual Activity. Int J Mol Sci 2021; 22:9057. [PMID: 34445763 PMCID: PMC8396542 DOI: 10.3390/ijms22169057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 02/06/2023] Open
Abstract
Unfortunately, COVID-19 is still a threat to humankind and has a dramatic impact on human health, social life, the world economy, and food security. With the limited number of suggested therapies under clinical trials, the discovery of novel therapeutic agents is essential. Here, a previously identified anti-SARS-CoV-2 compound named Compound 13 (1,2,5-Oxadiazole-3-carboximidic acid, 4,4'-(methylenediimino) bis,bis[[(2-hydroxyphenyl)methylene]hydrazide) was subjected to an iterated virtual screening against SARS-CoV-2 Mpro using a combination of Ligand Designer and PathFinder. PathFinder, a computational reaction enumeration tool, was used for the rapid generation of enumerated structures via default reaction library. Ligand designer was employed for the computerized lead optimization and selection of the best structural modification that resulted in a favorable ligand-protein complex. The obtained compounds that showed the best binding to Mpro were re-screened against TMPRSS2, leading to the identification of 20 shared compounds. The compounds were further visually inspected, which resulted in the identification of five shared compounds M1-5 with dual binding affinity. In vitro evaluation and enzyme inhibition assay indicated that M3, an analogue of Compound 13 afforded by replacing the phenolic moiety with pyridinyl, possesses an improved antiviral activity and safety. M3 displayed in vitro antiviral activity with IC50 0.016 µM and Mpro inhibition activity with IC50 0.013 µM, 7-fold more potent than the parent Compound 13 and potent than the antivirals drugs that are currently under clinical trials. Moreover, M3 showed potent activity against human TMPRSS2 and furin enzymes with IC50 0.05, and 0.08 µM, respectively. Molecular docking, WaterMap analysis, molecular dynamics simulation, and R-group analysis confirmed the superiority of the binding fit to M3 with the target enzymes. WaterMap analysis calculated the thermodynamic properties of the hydration site in the binding pocket that significantly affects the biological activity. Loading M3 on zinc oxide nanoparticles (ZnO NPs) increased the antiviral activity of the compound 1.5-fold, while maintaining a higher safety profile. In conclusion, lead optimized discovery following an iterated virtual screening in association with molecular docking and biological evaluation revealed a novel compound named M3 with promising dual activity against SARS-CoV-2. The compound deserves further investigation for potential clinical-based studies.
Collapse
Affiliation(s)
- Rania Hamdy
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.H.); (B.F.)
- Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Bahgat Fayed
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.H.); (B.F.)
- Chemistry of Natural and Microbial Product Department, National Research Centre, Cairo 12622, Egypt
| | - Ahmed Mostafa
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.M.); (N.M.A.S.); (S.H.M.)
| | - Noura M. Abo Shama
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.M.); (N.M.A.S.); (S.H.M.)
| | - Sara Hussein Mahmoud
- Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.M.); (N.M.A.S.); (S.H.M.)
| | - Chetan Hasmukh Mehta
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, India; (C.H.M.); (Y.N.)
| | - Yogendra Nayak
- Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, India; (C.H.M.); (Y.N.)
| | - Sameh S. M. Soliman
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.H.); (B.F.)
- College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| |
Collapse
|
8
|
Andreev S, Pantsar T, Tesch R, Kahlke N, El-Gokha A, Ansideri F, Grätz L, Romasco J, Sita G, Geibel C, Lämmerhofer M, Tarozzi A, Knapp S, Laufer SA, Koch P. Addressing a Trapped High-Energy Water: Design and Synthesis of Highly Potent Pyrimidoindole-Based Glycogen Synthase Kinase-3β Inhibitors. J Med Chem 2021; 65:1283-1301. [PMID: 34213342 DOI: 10.1021/acs.jmedchem.0c02146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In small molecule binding, water is not a passive bystander but rather takes an active role in the binding site, which may be decisive for the potency of the inhibitor. Here, by addressing a high-energy water, we improved the IC50 value of our co-crystallized glycogen synthase kinase-3β (GSK-3β) inhibitor by nearly two orders of magnitude. Surprisingly, our results demonstrate that this high-energy water was not displaced by our potent inhibitor (S)-3-(3-((7-ethynyl-9H-pyrimido[4,5-b]indol-4-yl)(methyl)amino)piperidin-1-yl)propanenitrile ((S)-15, IC50 value of 6 nM). Instead, only a subtle shift in the location of this water molecule resulted in a dramatic decrease in the energy of this high-energy hydration site, as shown by the WaterMap analysis combined with microsecond timescale molecular dynamics simulations. (S)-15 demonstrated both a favorable kinome selectivity profile and target engagement in a cellular environment and reduced GSK-3 autophosphorylation in neuronal SH-SY5Y cells. Overall, our findings highlight that even a slight adjustment in the location of a high-energy water can be decisive for ligand binding.
Collapse
Affiliation(s)
- Stanislav Andreev
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Tatu Pantsar
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Roberta Tesch
- Institute for Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Niclas Kahlke
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Ahmed El-Gokha
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Chemistry Department, Faculty of Science, Menoufia University, Gamal Abdel-Nasser Street, 32511 Shebin El-Kom, Egypt
| | - Francesco Ansideri
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Lukas Grätz
- Department of Pharmaceutical/Medicinal Chemistry II, Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Jenny Romasco
- Department for Life Quality Studies, Alma Mater Studiorum, University of Bologna, Corso D'Augusto 237, 47921 Rimini, Italy
| | - Giulia Sita
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Christian Geibel
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical (Bio-)Analysis, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical (Bio-)Analysis, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Andrea Tarozzi
- Department for Life Quality Studies, Alma Mater Studiorum, University of Bologna, Corso D'Augusto 237, 47921 Rimini, Italy
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
| | - Stefan A Laufer
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Tübingen Center for Academic Drug Discovery (TüCAD2), Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Pierre Koch
- Institute of Pharmaceutical Sciences, Department of Medicinal and Pharmaceutical Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany.,Department of Pharmaceutical/Medicinal Chemistry II, Institute of Pharmacy, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| |
Collapse
|
9
|
Bergazin TD, Ben-Shalom IY, Lim NM, Gill SC, Gilson MK, Mobley DL. Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo. J Comput Aided Mol Des 2021; 35:167-177. [PMID: 32968887 PMCID: PMC7904576 DOI: 10.1007/s10822-020-00344-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/16/2020] [Indexed: 11/26/2022]
Abstract
Water molecules can be found interacting with the surface and within cavities in proteins. However, water exchange between bulk and buried hydration sites can be slow compared to simulation timescales, thus leading to the inefficient sampling of the locations of water. This can pose problems for free energy calculations for computer-aided drug design. Here, we apply a hybrid method that combines nonequilibrium candidate Monte Carlo (NCMC) simulations and molecular dynamics (MD) to enhance sampling of water in specific areas of a system, such as the binding site of a protein. Our approach uses NCMC to gradually remove interactions between a selected water molecule and its environment, then translates the water to a new region, before turning the interactions back on. This approach of gradual removal of interactions, followed by a move and then reintroduction of interactions, allows the environment to relax in response to the proposed water translation, improving acceptance of moves and thereby accelerating water exchange and sampling. We validate this approach on several test systems including the ligand-bound MUP-1 and HSP90 proteins with buried crystallographic waters removed. We show that our BLUES (NCMC/MD) method enhances water sampling relative to normal MD when applied to these systems. Thus, this approach provides a strategy to improve water sampling in molecular simulations which may be useful in practical applications in drug discovery and biomolecular design.
Collapse
Affiliation(s)
| | - Ido Y Ben-Shalom
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Nathan M Lim
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Sam C Gill
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA.
- Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
| |
Collapse
|
10
|
Hüfner-Wulsdorf T, Klebe G. Advancing GIST-Based Solvent Functionals through Multiobjective Optimization of Solvent Enthalpy and Entropy Scoring Terms. J Chem Inf Model 2020; 60:6654-6665. [DOI: 10.1021/acs.jcim.0c01133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Tobias Hüfner-Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| |
Collapse
|
11
|
Wan H, Aravamuthan V, Pearlstein RA. Probing the Dynamic Structure-Function and Structure-Free Energy Relationships of the Coronavirus Main Protease with Biodynamics Theory. ACS Pharmacol Transl Sci 2020; 3:1111-1143. [PMID: 33330838 PMCID: PMC7671103 DOI: 10.1021/acsptsci.0c00089] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Indexed: 02/01/2023]
Abstract
![]()
The
SARS-CoV-2 main protease (Mpro) is of major interest
as an antiviral drug target. Structure-based virtual screening efforts,
fueled by a growing list of apo and inhibitor-bound SARS-CoV/CoV-2
Mpro crystal structures, are underway in many laboratories.
However, little is known about the dynamic enzyme mechanism, which
is needed to inform both assay development and structure-based inhibitor
design. Here, we apply biodynamics theory to characterize the structural
dynamics of substrate-induced Mpro activation under nonequilibrium conditions. The catalytic cycle
is governed by concerted dynamic structural
rearrangements of domain 3 and the m-shaped loop (residues 132–147)
on which Cys145 (comprising the thiolate nucleophile and half of the
oxyanion hole) and Gly143 (comprising the second half of the oxyanion
hole) reside. In particular, we observed the following: (1) Domain
3 undergoes dynamic rigid-body rotation about the domain 2–3
linker, alternately visiting two primary conformational states (denoted
as M1pro ↔
M2pro); (2)
The Gly143-containing crest of the m-shaped loop undergoes up and
down translations caused by conformational changes within the rising
stem of the loop (Lys137–Asn142) in response to domain 3 rotation
and dimerization (denoted as M1/downpro ↔ 2·M2/uppro) (noting that the Cys145-containing
crest is fixed in the up position). We propose that substrates associate
to the M1/downpro state, which promotes the M2/downpro state, dimerization (denoted as 2·M2/uppro–substrate),
and catalysis. Here, we explore the state transitions of Mpro under nonequilibrium conditions, the mechanisms by which they are
powered, and the implications thereof for efficacious inhibition under in vivo conditions.
Collapse
Affiliation(s)
- Hongbin Wan
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Vibhas Aravamuthan
- Vibhas Aravamuthan - NIBR Informatics, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Robert A Pearlstein
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
12
|
Wan H, Selvaggio G, Pearlstein RA. Toward in vivo-relevant hERG safety assessment and mitigation strategies based on relationships between non-equilibrium blocker binding, three-dimensional channel-blocker interactions, dynamic occupancy, dynamic exposure, and cellular arrhythmia. PLoS One 2020; 15:e0234946. [PMID: 33147278 PMCID: PMC7641409 DOI: 10.1371/journal.pone.0234946] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/16/2020] [Indexed: 12/26/2022] Open
Abstract
The human ether-a-go-go-related voltage-gated cardiac ion channel (commonly known as hERG) conducts the rapid outward repolarizing potassium current in cardiomyocytes (IKr). Inadvertent blockade of this channel by drug-like molecules represents a key challenge in pharmaceutical R&D due to frequent overlap between the structure-activity relationships of hERG and many primary targets. Building on our previous work, together with recent cryo-EM structures of hERG, we set about to better understand the energetic and structural basis of promiscuous blocker-hERG binding in the context of Biodynamics theory. We propose a two-step blocker binding process consisting of: The initial capture step: diffusion of a single fully solvated blocker copy into a large cavity lined by the intra-cellular cyclic nucleotide binding homology domain (CNBHD). Occupation of this cavity is a necessary but insufficient condition for ion current disruption.The IKr disruption step: translocation of the captured blocker along the channel axis, such that: The head group, consisting of a quasi-rod-shaped moiety, projects into the open pore, accompanied by partial de-solvation of the binding interface.One tail moiety packs along a kink between the S6 helix and proximal C-linker helix adjacent to the intra-cellular entrance of the pore, likewise accompanied by mutual de-solvation of the binding interface (noting that the association barrier is comprised largely of the total head + tail group de-solvation cost).Blockers containing a highly planar moiety that projects into a putative constriction zone within the closed channel become trapped upon closing, as do blockers terminating prior to this region.A single captured blocker copy may conceivably associate and dissociate to/from the pore many times before exiting the CNBHD cavity. Lastly, we highlight possible flaws in the current hERG safety index (SI), and propose an alternate in vivo-relevant strategy factoring in: Benefit/risk.The predicted arrhythmogenic fractional hERG occupancy (based on action potential (AP) simulations of the undiseased human ventricular cardiomyocyte).Alteration of the safety threshold due to underlying disease.Risk of exposure escalation toward the predicted arrhythmic limit due to patient-to-patient pharmacokinetic (PK) variability, drug-drug interactions, overdose, and use for off-label indications in which the hERG safety parameters may differ from their on-label counterparts.
Collapse
Affiliation(s)
- Hongbin Wan
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Gianluca Selvaggio
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Robert A. Pearlstein
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| |
Collapse
|
13
|
Pearlstein RA, Wan H, Aravamuthan V. Toward in vivo relevant drug design. Drug Discov Today 2020; 26:637-650. [PMID: 33132106 DOI: 10.1016/j.drudis.2020.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/16/2020] [Accepted: 10/15/2020] [Indexed: 11/28/2022]
Abstract
Current early and preclinical drug discovery are rooted in decades-old empirical principles describing structure-free energy and structure-function relationships under equilibrium conditions that frequently break down under in vivo conditions. Improved prediction of efficacy and toxicity depends on a paradigm shift to in vivo-relevant principles describing the true nonequilibrium/nonlinear dynamic (NLD) nature of cellular systems. Here, we outline a holistic, in vivo-relevant first principles theory ('Biodynamics'), in which cellular function/dysfunction, and pharmaco-/toxicodynamic effects are considered as emergent behaviors of multimolecular systems powered by covalent and noncovalent free energy sources. The reduction to practice of Biodynamics theory consists of in silico simulations performed at the atomistic and molecular systems levels, versus empirical models fit to in vitro data under the classical paradigm.
Collapse
Affiliation(s)
- Robert A Pearlstein
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Hongbin Wan
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Vibhas Aravamuthan
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| |
Collapse
|
14
|
Li Y, Gao Y, Holloway MK, Wang R. Prediction of the Favorable Hydration Sites in a Protein Binding Pocket and Its Application to Scoring Function Formulation. J Chem Inf Model 2020; 60:4359-4375. [DOI: 10.1021/acs.jcim.9b00619] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yan Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People’s Republic of China
| | - Yingduo Gao
- Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
- Merck Research Laboratories, 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | | | - Renxiao Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, People’s Republic of China
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
- Shanxi Key Laboratory of Innovative Drugs for the Treatment of Serious Diseases Basing on Chronic Inflammation, College of Traditional Chinese Medicines, Shanxi University of Chinese Medicine, Taiyuan, Shanxi 030619, People’s Republic of China
| |
Collapse
|
15
|
IJzerman AP, Guo D. Drug-Target Association Kinetics in Drug Discovery. Trends Biochem Sci 2019; 44:861-871. [PMID: 31101454 DOI: 10.1016/j.tibs.2019.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 03/28/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
Abstract
The important role of ligand-receptor binding kinetics in drug design and discovery is increasingly recognized by the drug research community. Over the past decade, accumulating evidence has shown that optimizing the ligand's dissociation rate constant can lead to desirable duration of in vivo target occupancy and, hence, improved pharmacodynamic properties. However, the association rate constant as a pharmacological principle remains less investigated, whereas it can play an equally important role in the selection of drug candidates. This review provides a compilation and discussion of otherwise scarce and dispersed information on this topic, bringing to light the importance of drug-target association in kinetics-directed drug design and discovery.
Collapse
Affiliation(s)
- Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300, RA, Leiden, The Netherlands
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, 221004, Jiangsu, China.
| |
Collapse
|
16
|
Magarkar A, Schnapp G, Apel AK, Seeliger D, Tautermann CS. Enhancing Drug Residence Time by Shielding of Intra-Protein Hydrogen Bonds: A Case Study on CCR2 Antagonists. ACS Med Chem Lett 2019; 10:324-328. [PMID: 30891134 DOI: 10.1021/acsmedchemlett.8b00590] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/07/2019] [Indexed: 12/15/2022] Open
Abstract
The target residence time (RT) for a given ligand is one of the important parameters that have to be optimized during drug design. It is well established that shielding the receptor-ligand hydrogen bond (H-bond) interactions from water has been one of the factors in increasing ligand RT. Building on this foundation, here we report that shielding an intra-protein H-bond, which confers rigidity to the binding pocket and which is not directly involved in drug-receptor interactions, can strongly influence RT for CCR2 antagonists. Based on our recently solved CCR2 structure with MK-0812 and molecular dynamics (MD) simulations, we show that the RT for this and structurally related ligands is directly dependent on the shielding of the Tyr120-Glu291 H-bond from the water. If solvated this H-bond is often broken, making the binding pocket flexible and leading to shorter RT.
Collapse
Affiliation(s)
- Aniket Magarkar
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
| | - Gisela Schnapp
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
| | - Anna-Katharina Apel
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
| | - Daniel Seeliger
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
| | - Christofer S. Tautermann
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Strasse 65, D-88397 Biberach a.d. Riss, Germany
| |
Collapse
|
17
|
Selvaggio G, Pearlstein RA. Biodynamics: A novel quasi-first principles theory on the fundamental mechanisms of cellular function/dysfunction and the pharmacological modulation thereof. PLoS One 2018; 13:e0202376. [PMID: 30383749 PMCID: PMC6211658 DOI: 10.1371/journal.pone.0202376] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/24/2018] [Indexed: 11/30/2022] Open
Abstract
Cellular function depends on heterogeneous dynamic intra-, inter-, and supramolecular structure-function relationships. However, the specific mechanisms by which cellular function is transduced from molecular systems, and by which cellular dysfunction arises from molecular dysfunction are poorly understood. We proposed previously that cellular function manifests as a molecular form of analog computing, in which specific time-dependent state transition fluxes within sets of molecular species ("molecular differential equations" (MDEs)) are sped and slowed in response to specific perturbations (inputs). In this work, we offer a theoretical treatment of the molecular mechanisms underlying cellular analog computing (which we refer to as "biodynamics"), focusing primarily on non-equilibrium (dynamic) intermolecular state transitions that serve as the principal means by which MDE systems are solved (the molecular equivalent of mathematical "integration"). Under these conditions, bound state occupancy is governed by kon and koff, together with the rates of binding partner buildup and decay. Achieving constant fractional occupancy over time depends on: 1) equivalence between kon and the rate of binding site buildup); 2) equivalence between koff and the rate of binding site decay; and 3) free ligand concentration relative to koff/kon (n · Kd, where n is the fold increase in binding partner concentration needed to achieve a given fractional occupancy). Failure to satisfy these conditions results in fractional occupancy well below that corresponding to n · Kd. The implications of biodynamics for cellular function/dysfunction and drug discovery are discussed.
Collapse
Affiliation(s)
- Gianluca Selvaggio
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, United States of America
| | - Robert Alan Pearlstein
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA, United States of America
| |
Collapse
|
18
|
Pantsar T, Poso A. Binding Affinity via Docking: Fact and Fiction. Molecules 2018; 23:molecules23081899. [PMID: 30061498 PMCID: PMC6222344 DOI: 10.3390/molecules23081899] [Citation(s) in RCA: 238] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/22/2018] [Accepted: 07/26/2018] [Indexed: 01/03/2023] Open
Abstract
In 1982, Kuntz et al. published an article with the title “A Geometric Approach to Macromolecule-Ligand Interactions”, where they described a method “to explore geometrically feasible alignment of ligands and receptors of known structure”. Since then, small molecule docking has been employed as a fast way to estimate the binding pose of a given compound within a specific target protein and also to predict binding affinity. Remarkably, the first docking method suggested by Kuntz and colleagues aimed to predict binding poses but very little was specified about binding affinity. This raises the question as to whether docking is the right tool to estimate binding affinity. The short answer is no, and this has been concluded in several comprehensive analyses. However, in this opinion paper we discuss several critical aspects that need to be reconsidered before a reliable binding affinity prediction through docking is realistic. These are not the only issues that need to be considered, but they are perhaps the most critical ones. We also consider that in spite of the huge efforts to enhance scoring functions, the accuracy of binding affinity predictions is perhaps only as good as it was 10–20 years ago. There are several underlying reasons for this poor performance and these are analyzed. In particular, we focus on the role of the solvent (water), the poor description of H-bonding and the lack of the systems’ true dynamics. We hope to provide readers with potential insights and tools to overcome the challenging issues related to binding affinity prediction via docking.
Collapse
Affiliation(s)
- Tatu Pantsar
- School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland.
| | - Antti Poso
- School of Pharmacy, University of Eastern Finland, P.O. BOX 1627, 70211 Kuopio, Finland.
- Department of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Strasse 14, 72076 Tübingen, Germany.
| |
Collapse
|
19
|
Kunstmann S, Gohlke U, Broeker NK, Roske Y, Heinemann U, Santer M, Barbirz S. Solvent Networks Tune Thermodynamics of Oligosaccharide Complex Formation in an Extended Protein Binding Site. J Am Chem Soc 2018; 140:10447-10455. [DOI: 10.1021/jacs.8b03719] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sonja Kunstmann
- Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Ulrich Gohlke
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Nina K. Broeker
- Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Yvette Roske
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Institut für Chemie und Biochemie, Freie Universität, Takustr. 6, 14195 Berlin, Germany
| | - Mark Santer
- Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Stefanie Barbirz
- Physikalische Biochemie, Universität Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| |
Collapse
|
20
|
You W, Chang CEA. Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors. J Chem Inf Model 2018; 58:968-981. [PMID: 29620886 PMCID: PMC5975198 DOI: 10.1021/acs.jcim.7b00640] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding the governing factors of fast or slow inhibitor binding/unbinding assists in developing drugs with preferred kinetic properties. For inhibitors with the same binding affinity targeting different binding sites of the same protein, the kinetic behavior can profoundly differ. In this study, we investigated unbinding kinetics and mechanisms of fast (type-I) and slow (type-II/III) binders of p38α mitogen-activated protein kinase, where the crystal structures showed that type-I and type-II/III inhibitors bind to pockets with different conformations of the Asp-Phe-Gly (DFG) motif. The work used methods that combine conventional molecular dynamics (MD), accelerated molecular dynamics (AMD) simulations, and the newly developed pathway search guided by internal motions (PSIM) method to find dissociation pathways. The study focuses on revealing key interactions and molecular rearrangements that hinder ligand dissociation by using umbrella sampling and post-MD processing to examine changes in free energy during ligand unbinding. As anticipated, the initial dissociation steps all require breaking interactions that appeared in crystal structures of the bound complexes. Interestingly, for type-I inhibitors such as SB2, p38α keeps barrier-free conformational fluctuation in the ligand-bound complex and during ligand dissociation. In contrast, with a type-II/III inhibitor such as BIRB796, with the rearrangements of p38α in its bound state, ligand unbinding features energetically unfavorable protein-ligand concerted movement. Our results also show that the type-II/III inhibitors preferred dissociation pathways through the allosteric channel, which is consistent with an existing publication. The study suggests that the level of required protein rearrangement is one major determining factor of drug binding kinetics in p38α systems, providing useful information for development of inhibitors.
Collapse
Affiliation(s)
- Wanli You
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Chia-en A. Chang
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| |
Collapse
|
21
|
Cuzzolin A, Deganutti G, Salmaso V, Sturlese M, Moro S. AquaMMapS: An Alternative Tool to Monitor the Role of Water Molecules During Protein-Ligand Association. ChemMedChem 2018; 13:522-531. [DOI: 10.1002/cmdc.201700564] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/21/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Alberto Cuzzolin
- Molecular Modeling Section, MMS, Department of Pharmaceutical and Pharmacological Sciences; University of Padova; via Marzolo 5 35131 Padova Italy
| | - Giuseppe Deganutti
- Molecular Modeling Section, MMS, Department of Pharmaceutical and Pharmacological Sciences; University of Padova; via Marzolo 5 35131 Padova Italy
| | - Veronica Salmaso
- Molecular Modeling Section, MMS, Department of Pharmaceutical and Pharmacological Sciences; University of Padova; via Marzolo 5 35131 Padova Italy
| | - Mattia Sturlese
- Molecular Modeling Section, MMS, Department of Pharmaceutical and Pharmacological Sciences; University of Padova; via Marzolo 5 35131 Padova Italy
| | - Stefano Moro
- Molecular Modeling Section, MMS, Department of Pharmaceutical and Pharmacological Sciences; University of Padova; via Marzolo 5 35131 Padova Italy
| |
Collapse
|
22
|
Masuda Y, Yoshida T, Yamaotsu N, Hirono S. Linear Discriminant Analysis for the <i>in Silico</i> Discovery of Mechanism-Based Reversible Covalent Inhibitors of a Serine Protease: Application of Hydration Thermodynamics Analysis and Semi-empirical Molecular Orbital Calculation. Chem Pharm Bull (Tokyo) 2018; 66:399-409. [DOI: 10.1248/cpb.c17-00854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yosuke Masuda
- School of Pharmaceutical Sciences, Kitasato University
| | | | | | | |
Collapse
|
23
|
Xia L, de Vries H, Yang X, Lenselink EB, Kyrizaki A, Barth F, Louvel J, Dreyer MK, van der Es D, IJzerman AP, Heitman LH. Kinetics of human cannabinoid 1 (CB1) receptor antagonists: Structure-kinetics relationships (SKR) and implications for insurmountable antagonism. Biochem Pharmacol 2017; 151:166-179. [PMID: 29102677 DOI: 10.1016/j.bcp.2017.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/31/2017] [Indexed: 10/18/2022]
Abstract
While equilibrium binding affinities and in vitro functional antagonism of CB1 receptor antagonists have been studied in detail, little is known on the kinetics of their receptor interaction. In this study, we therefore conducted kinetic assays for nine 1-(4,5-diarylthiophene-2-carbonyl)-4-phenylpiperidine-4-carboxamide derivatives and included the CB1 antagonist rimonabant as a comparison. For this we newly developed a dual-point competition association assay with [3H]CP55940 as the radioligand. This assay yielded Kinetic Rate Index (KRI) values from which structure-kinetics relationships (SKR) of hCB1 receptor antagonists could be established. The fast dissociating antagonist 6 had a similar receptor residence time (RT) as rimonabant, i.e. 19 and 14 min, respectively, while the slowest dissociating antagonist (9) had a very long RT of 2222 min, i.e. pseudo-irreversible dissociation kinetics. In functional assays, 9 displayed insurmountable antagonism, while the effects of the shortest RT antagonist 6 and rimonabant were surmountable. Taken together, this study shows that hCB1 receptor antagonists can have very divergent RTs, which are not correlated to their equilibrium affinities. Furthermore, their RTs appear to define their mode of functional antagonism, i.e. surmountable vs. insurmountable. Finally, based on the recently resolved hCB1 receptor crystal structure, we propose that the differences in RT can be explained by a different binding mode of antagonist 9 from short RT antagonists that is able to displace unfavorable water molecules. Taken together, these findings are of importance for future design and evaluation of potent and safe hCB1 receptor antagonists.
Collapse
Affiliation(s)
- Lizi Xia
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Henk de Vries
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Xue Yang
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Eelke B Lenselink
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Athina Kyrizaki
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Francis Barth
- Sanofi-Aventis Research and Development, 371, Rue du Professeur Blayac, 34184 Montpellier Cedex 04, France
| | - Julien Louvel
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Matthias K Dreyer
- Sanofi-Aventis Deutschland GmbH R&D, Integrated Drug Discovery, Industriepark Hoechst, 65926 Frankfurt, Germany
| | - Daan van der Es
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, The Netherlands.
| |
Collapse
|
24
|
Levy RM, Cui D, Zhang BW, Matubayasi N. Relationship between Solvation Thermodynamics from IST and DFT Perspectives. J Phys Chem B 2017; 121:3825-3841. [PMID: 28186751 DOI: 10.1021/acs.jpcb.6b12889] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Inhomogeneous solvation theory (IST) and classical density functional theory (DFT) each provide a framework for relating distribution functions of solutions to their thermodynamic properties. As reviewed in this work, both IST and DFT can be formulated in a way that use two "end point" simulations, one of the pure solvent and the other of the solution, to determine the solute chemical potential and other thermodynamic properties of the solution and of subvolumes in regions local to the solute containing hydrating waters. In contrast to IST, where expressions for the excess energy and entropy of solution are the object of analysis, in the DFT end point formulation of the problem, the solute-solvent potential of mean force (PMF) plays a central role. The indirect part of the PMF corresponds to the lowest order (1-body) truncation of the IST expression. Because the PMF is a free energy function, powerful numerical methods can be used to estimate it. We show that the DFT expressions for the solute excess chemical potential can be written in a form which is local, involving integrals only over regions proximate to the solute. The DFT end point route to estimating solvation free energies provides an alternative path to that of IST for analyzing solvation effects on molecular recognition and conformational changes in solution, which can lead to new insights. In order to illustrate the kind of information that is contained in the solute-solvent PMF, we have carried out simulations of β-cyclodextrin in water. This solute is a well studied "host" molecule to which "guest" molecules bind; host-guest systems serve as models for molecular recognition. We illustrate the range of values the direct and indirect parts of the solute-solvent PMF can have as a water molecule is brought to the interface of β-cyclodextrin from the bulk; we discuss the "competition" between these two terms, and the role it plays in molecular recognition.
Collapse
Affiliation(s)
- Ronald M Levy
- Center for Biophysics and Computational Biology, Department of Chemistry, and Institute for Computational Molecular Science, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Di Cui
- Center for Biophysics and Computational Biology, Department of Chemistry, and Institute for Computational Molecular Science, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Bin W Zhang
- Center for Biophysics and Computational Biology, Department of Chemistry, and Institute for Computational Molecular Science, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan and Elements Strategy Initiative for Catalysts and Batteries, Kyoto University , Katsura, Kyoto 615-8520, Japan
| |
Collapse
|
25
|
Huang YMM, Raymundo MAV, Chen W, Chang CEA. Mechanism of the Association Pathways for a Pair of Fast and Slow Binding Ligands of HIV-1 Protease. Biochemistry 2017; 56:1311-1323. [PMID: 28060481 DOI: 10.1021/acs.biochem.6b01112] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Equilibrium constants, together with kinetic rate constants of binding, are key factors in the efficacy and safety of drug compounds, informing drug design. However, the association pathways of protein-ligand binding, which contribute to their kinetic behaviors, are little understood. In this work, we used unbiased all-atom molecular dynamics (MD) simulations with an explicit solvent model to study the association processes of protein-ligand binding. Using the HIV protease (HIVp)-xk263 and HIVp-ritonavir protein-ligand systems as cases, we observed that ligand association is a multistep process involving diffusion, localization, and conformational rearrangements of the protein, ligand, and water molecules. Moreover, these two ligands preferred different routes of binding, which reflect two well-known binding mechanisms: induced-fit and conformation selection models. Our study shows that xk263 has a stronger capacity for desolvating surrounding water molecules, thereby inducing a semiopen conformation of the HIVp flaps (induced-fit model). In contrast, the slow dehydration characteristic of ritonavir allows for gradual association with the binding pocket of HIVp when the protein's flap conformation is fully open (conformation selection model). By studying the mechanism of ligand association and understanding the role of solvent molecules during the binding event, we can obtain a different perspective on the mechanism of macromolecule recognition, providing insights into drug discovery.
Collapse
Affiliation(s)
- Yu-Ming M Huang
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States
| | - Mark Anthony V Raymundo
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States
| | - Wei Chen
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States.,ChemConsulting LLC , Frederick, Maryland 21704, United States
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside , Riverside, California 92521, United States
| |
Collapse
|
26
|
Cramer J, Krimmer SG, Fridh V, Wulsdorf T, Karlsson R, Heine A, Klebe G. Elucidating the Origin of Long Residence Time Binding for Inhibitors of the Metalloprotease Thermolysin. ACS Chem Biol 2017; 12:225-233. [PMID: 27959500 DOI: 10.1021/acschembio.6b00979] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Kinetic parameters of protein-ligand interactions are progressively acknowledged as valuable information for rational drug discovery. However, a targeted optimization of binding kinetics is not easy to achieve, and further systematic studies are necessary to increase the understanding about molecular mechanisms involved. We determined association and dissociation rate constants for 17 inhibitors of the metalloprotease thermolysin by surface plasmon resonance spectroscopy and correlated kinetic data with high-resolution crystal structures in complex with the protein. From the structure-kinetics relationship, we conclude that the strength of interaction with Asn112 correlates with the rate-limiting step of dissociation. This residue is located at the beginning of a β-strand motif that lines the binding cleft and is commonly believed to align a substrate for catalysis. A reduced mobility of the Asn112 side chain owing to an enhanced engagement in charge-assisted hydrogen bonds prevents the conformational adjustment associated with ligand release and transformation of the enzyme to its open state. This hypothesis is supported by kinetic data of ZFPLA, a known pseudopeptidic inhibitor of thermolysin, which blocks the conformational transition of Asn112. Interference with this retrograde induced-fit mechanism results in variation of the residence time of thermolysin inhibitors by a factor of 74 000. The high conservation of this structural motif within the M4 and M13 metalloprotease families underpins the importance of this feature and has significant implications for drug discovery.
Collapse
Affiliation(s)
- Jonathan Cramer
- Institute
of Pharmaceutical Chemistry, University of Marburg, Marbacher
Weg 6, 35032 Marburg, Germany
| | - Stefan G. Krimmer
- Institute
of Pharmaceutical Chemistry, University of Marburg, Marbacher
Weg 6, 35032 Marburg, Germany
| | - Veronica Fridh
- GE Healthcare Bio-Sciences AB, SE-751 84 Uppsala, Sweden
| | - Tobias Wulsdorf
- Institute
of Pharmaceutical Chemistry, University of Marburg, Marbacher
Weg 6, 35032 Marburg, Germany
| | | | - Andreas Heine
- Institute
of Pharmaceutical Chemistry, University of Marburg, Marbacher
Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institute
of Pharmaceutical Chemistry, University of Marburg, Marbacher
Weg 6, 35032 Marburg, Germany
| |
Collapse
|
27
|
Masuda Y, Yamaotsu N, Hirono S. Gibbs Free Energy of Hydrolytic Water Molecule in Acyl-Enzyme Intermediates of a Serine Protease: A Potential Application for Computer-Aided Discovery of Mechanism-Based Reversible Covalent Inhibitors. Chem Pharm Bull (Tokyo) 2017; 65:889-892. [DOI: 10.1248/cpb.c17-00425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yosuke Masuda
- School of Pharmaceutical Sciences, Kitasato University
| | | | | |
Collapse
|
28
|
AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking. Molecules 2016; 21:molecules21111604. [PMID: 27886114 PMCID: PMC6274120 DOI: 10.3390/molecules21111604] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/15/2016] [Accepted: 11/16/2016] [Indexed: 11/27/2022] Open
Abstract
Water plays a significant role in the binding process between protein and ligand. However, the thermodynamics of water molecules are often underestimated, or even ignored, in protein-ligand docking. Usually, the free energies of active-site water molecules are substantially different from those of waters in the bulk region. The binding of a ligand to a protein causes a displacement of these waters from an active site to bulk, and this displacement process substantially contributes to the free energy change of protein-ligand binding. The free energy of active-site water molecules can be calculated by grid inhomogeneous solvation theory (GIST), using molecular dynamics (MD) and the trajectory of a target protein and water molecules. Here, we show a case study of the combination of GIST and a docking program and discuss the effectiveness of the displacing gain of unfavorable water in protein-ligand docking. We combined the GIST-based desolvation function with the scoring function of AutoDock4, which is called AutoDock-GIST. The proposed scoring function was assessed employing 51 ligands of coagulation factor Xa (FXa), and results showed that both scoring accuracy and docking success rate were improved. We also evaluated virtual screening performance of AutoDock-GIST using FXa ligands in the directory of useful decoys-enhanced (DUD-E), thus finding that the displacing gain of unfavorable water is effective for a successful docking campaign.
Collapse
|
29
|
Pearlstein RA, Dickson CJ, Hornak V. Contributions of the membrane dipole potential to the function of voltage-gated cation channels and modulation by small molecule potentiators. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1859:177-194. [PMID: 27836643 DOI: 10.1016/j.bbamem.2016.11.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 10/28/2016] [Accepted: 11/06/2016] [Indexed: 01/27/2023]
Abstract
The membrane dipole potential (Ψd) constitutes one of three electrical potentials generated by cell membranes. Ψd arises from the unfavorable parallel alignment of phospholipid and water dipoles, and varies in magnitude both longitudinally and laterally across the bilayer according to membrane composition and phospholipid packing density. In this work, we propose that dynamic counter-balancing between Ψd and the transmembrane potential (ΔΨm) governs the conformational state transitions of voltage-gated ion channels. Ψd consists of 1) static outer, and dynamic inner leaflet components (Ψd(extra) and Ψd(intra), respectively); and 2) a transmembrane component (ΔΨd(inner-outer)), ariing from differences in intra- and extracellular leaflet composition. Ψd(intra), which transitions between high and low energy states (Ψd(intra, high) and Ψd(intra, low)) as a function of channel conformation, is transduced by the pore domain. ΔΨd(inner-outer) is transduced by the voltage-sensing (VS) domain in summation with ΔΨm. Potentiation of voltage-gated ion channels is of interest for the treatment of cardiac, neuronal, and other disorders arising from inherited/acquired ion channel dysfunction. Potentiators are widely believed to alter the rates and voltage-dependencies of channel gating transitions by binding to pockets in the membrane-facing and other regions of ion channel targets. Here, we propose that potentiators alter Ψd(intra) and/or Ψd(extra), thereby increasing or decreasing the energy barriers governing channel gating transitions. We used quantum mechanical and molecular dynamics (MD) simulations to predict the overall Ψd-modulating effects of a series of published positive hERG potentiators partitioned into model DOPC bilayers. Our findings suggest a strong correlation between the magnitude of Ψd-lowering and positive hERG potentiation across the series.
Collapse
Affiliation(s)
- Robert A Pearlstein
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, MA 02139, USA.
| | - Callum J Dickson
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, MA 02139, USA
| | - Viktor Hornak
- Global Discovery Chemistry, Computer-Aided Drug Discovery, Novartis Institutes for BioMedical Research, 181 Mass Ave., Cambridge, MA 02139, USA
| |
Collapse
|
30
|
Bodnarchuk MS. Water, water, everywhere… It's time to stop and think. Drug Discov Today 2016; 21:1139-46. [DOI: 10.1016/j.drudis.2016.05.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/15/2016] [Accepted: 05/13/2016] [Indexed: 12/11/2022]
|
31
|
Ramsey S, Nguyen C, Salomon-Ferrer R, Walker RC, Gilson MK, Kurtzman T. Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. J Comput Chem 2016; 37:2029-37. [PMID: 27317094 DOI: 10.1002/jcc.24417] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/19/2016] [Accepted: 05/17/2016] [Indexed: 02/06/2023]
Abstract
The expulsion of water from surfaces upon molecular recognition and nonspecific association makes a major contribution to the free energy changes of these processes. In order to facilitate the characterization of water structure and thermodynamics on surfaces, we have incorporated Grid Inhomogeneous Solvation Theory (GIST) into the CPPTRAJ toolset of AmberTools. GIST is a grid-based implementation of Inhomogeneous Fluid Solvation Theory, which analyzes the output from molecular dynamics simulations to map out solvation thermodynamic and structural properties on a high-resolution, three-dimensional grid. The CPPTRAJ implementation, called GIST-cpptraj, has a simple, easy-to-use command line interface, and is open source and freely distributed. We have also developed a set of open-source tools, called GISTPP, which facilitate the analysis of GIST output grids. Tutorials for both GIST-cpptraj and GISTPP can be found at ambermd.org. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Steven Ramsey
- Department of Chemistry, Lehman College, 205 W Bedford Pk Blvd, Bronx, New York, 10468.,Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York, 10016
| | - Crystal Nguyen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093-0736
| | - Romelia Salomon-Ferrer
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, California, 92093-0505
| | - Ross C Walker
- San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, California, 92093-0505.,Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093-0505
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093-0736
| | - Tom Kurtzman
- Department of Chemistry, Lehman College, 205 W Bedford Pk Blvd, Bronx, New York, 10468.,Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York, 10016.,Ph. D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York, 10016
| |
Collapse
|
32
|
Dickson CJ, Hornak V, Velez-Vega C, McKay DJJ, Reilly J, Sandham DA, Shaw D, Fairhurst RA, Charlton SJ, Sykes DA, Pearlstein RA, Duca JS. Uncoupling the Structure-Activity Relationships of β2 Adrenergic Receptor Ligands from Membrane Binding. J Med Chem 2016; 59:5780-9. [PMID: 27239696 DOI: 10.1021/acs.jmedchem.6b00358] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Ligand binding to membrane proteins may be significantly influenced by the interaction of ligands with the membrane. In particular, the microscopic ligand concentration within the membrane surface solvation layer may exceed that in bulk solvent, resulting in overestimation of the intrinsic protein-ligand binding contribution to the apparent/measured affinity. Using published binding data for a set of small molecules with the β2 adrenergic receptor, we demonstrate that deconvolution of membrane and protein binding contributions allows for improved structure-activity relationship analysis and structure-based drug design. Molecular dynamics simulations of ligand bound membrane protein complexes were used to validate binding poses, allowing analysis of key interactions and binding site solvation to develop structure-activity relationships of β2 ligand binding. The resulting relationships are consistent with intrinsic binding affinity (corrected for membrane interaction). The successful structure-based design of ligands targeting membrane proteins may require an assessment of membrane affinity to uncouple protein binding from membrane interactions.
Collapse
Affiliation(s)
- Callum J Dickson
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Camilo Velez-Vega
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Daniel J J McKay
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - John Reilly
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - David A Sandham
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Duncan Shaw
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Robin A Fairhurst
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Pharma AG , Werk Klybeck, Postfach, CH-4002 Basel, Switzerland
| | - Steven J Charlton
- Cell Signalling Research Group, School of Life Sciences, University of Nottingham, Queen's Medical Centre , Nottingham NG7 2UH, U.K
| | - David A Sykes
- Cell Signalling Research Group, School of Life Sciences, University of Nottingham, Queen's Medical Centre , Nottingham NG7 2UH, U.K
| | - Robert A Pearlstein
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Jose S Duca
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
33
|
Robinson D, Bertrand T, Carry JC, Halley F, Karlsson A, Mathieu M, Minoux H, Perrin MA, Robert B, Schio L, Sherman W. Differential Water Thermodynamics Determine PI3K-Beta/Delta Selectivity for Solvent-Exposed Ligand Modifications. J Chem Inf Model 2016; 56:886-94. [DOI: 10.1021/acs.jcim.5b00641] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Robinson
- Schrodinger, 120 W 45th St, New York, New York 10036, United States
| | | | | | | | | | | | | | | | | | | | - Woody Sherman
- Schrodinger, 120 W 45th St, New York, New York 10036, United States
| |
Collapse
|
34
|
Murphy RB, Repasky MP, Greenwood JR, Tubert-Brohman I, Jerome S, Annabhimoju R, Boyles NA, Schmitz CD, Abel R, Farid R, Friesner RA. WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand–Receptor Docking. J Med Chem 2016; 59:4364-84. [DOI: 10.1021/acs.jmedchem.6b00131] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Robert B. Murphy
- Schrödinger, Inc., 101 SW Main Street, Portland Oregon 97204, United States
| | - Matthew P. Repasky
- Schrödinger, Inc., 101 SW Main Street, Portland Oregon 97204, United States
| | - Jeremy R. Greenwood
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Ivan Tubert-Brohman
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Steven Jerome
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | | | - Nicholas A. Boyles
- Schrödinger, Inc., 101 SW Main Street, Portland Oregon 97204, United States
| | | | - Robert Abel
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Ramy Farid
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Richard A. Friesner
- Department of
Chemistry, Columbia University, New York, 3000 Broadway,
MC 3110, New York 10036, United States
| |
Collapse
|
35
|
Kürten C, Syrén PO. Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes. J Vis Exp 2016:e53168. [PMID: 26862836 PMCID: PMC4781653 DOI: 10.3791/53168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Enzyme catalysis evolved in an aqueous environment. The influence of solvent dynamics on catalysis is, however, currently poorly understood and usually neglected. The study of water dynamics in enzymes and the associated thermodynamical consequences is highly complex and has involved computer simulations, nuclear magnetic resonance (NMR) experiments, and calorimetry. Water tunnels that connect the active site with the surrounding solvent are key to solvent displacement and dynamics. The protocol herein allows for the engineering of these motifs for water transport, which affects specificity, activity and thermodynamics. By providing a biophysical framework founded on theory and experiments, the method presented herein can be used by researchers without previous expertise in computer modeling or biophysical chemistry. The method will advance our understanding of enzyme catalysis on the molecular level by measuring the enthalpic and entropic changes associated with catalysis by enzyme variants with obstructed water tunnels. The protocol can be used for the study of membrane-bound enzymes and other complex systems. This will enhance our understanding of the importance of solvent reorganization in catalysis as well as provide new catalytic strategies in protein design and engineering.
Collapse
Affiliation(s)
- Charlotte Kürten
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology
| | - Per-Olof Syrén
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology;
| |
Collapse
|
36
|
Biggin PC, Aldeghi M, Bodkin MJ, Heifetz A. Beyond Membrane Protein Structure: Drug Discovery, Dynamics and Difficulties. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:161-181. [PMID: 27553242 DOI: 10.1007/978-3-319-35072-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Most of the previous content of this book has focused on obtaining the structures of membrane proteins. In this chapter we explore how those structures can be further used in two key ways. The first is their use in structure based drug design (SBDD) and the second is how they can be used to extend our understanding of their functional activity via the use of molecular dynamics. Both aspects now heavily rely on computations. This area is vast, and alas, too large to consider in depth in a single book chapter. Thus where appropriate we have referred the reader to recent reviews for deeper assessment of the field. We discuss progress via the use of examples from two main drug target areas; G-protein coupled receptors (GPCRs) and ion channels. We end with a discussion of some of the main challenges in the area.
Collapse
Affiliation(s)
- Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Matteo Aldeghi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Michael J Bodkin
- Evotec Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Alexander Heifetz
- Evotec Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| |
Collapse
|
37
|
Wolf RM. Extracting ligands from receptors by reversed targeted molecular dynamics. J Comput Aided Mol Des 2015; 29:1025-34. [PMID: 26243273 DOI: 10.1007/s10822-015-9863-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/28/2015] [Indexed: 11/26/2022]
Abstract
Short targeted MD trajectories are used to expel ligands from binding sites. The expulsion is governed by a linear increase of the target RMSD value, growing from zero to an arbitrary chosen final RMSD that forces the ligand to a selected distance outside of the receptor. The RMSD lag (i.e., the difference between the imposed and the actual RMSD) can be used to follow barriers encountered by the ligand during its way out of the receptor. The force constant used for the targeted MD can transform the RMSD lag into a strain energy. Integration of the (time-dependent) strain energy over time yields a value with the dimensions of "action" (i.e, energy multiplied by time) and can serve as a measure for the overall effort required to extract the ligand from its binding site. Possibilities to compare (numerically and graphically) the randomly detected exit pathways are discussed. As an example, the method is tested on the exit of bisphenol A from the human estrogen-related receptor [Formula: see text] and of GW0072 from the peroxysome proliferator activated receptor.
Collapse
Affiliation(s)
- Romain M Wolf
- Novartis Institutes for Biomedical Research, NIBR, Novartis Pharma AG, Basel, Switzerland.
| |
Collapse
|
38
|
Velez-Vega C, McKay DJJ, Kurtzman T, Aravamuthan V, Pearlstein RA, Duca JS. Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen-Hydrogen Correlations. J Chem Theory Comput 2015; 11:5090-102. [PMID: 26574307 DOI: 10.1021/acs.jctc.5b00439] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A statistical-mechanical framework for estimation of solvation entropies and enthalpies is proposed, which is based on the analysis of water as a mixture of correlated water oxygens and water hydrogens. Entropic contributions of increasing order are cast in terms of a Mutual Information Expansion that is evaluated to pairwise interactions. In turn, the enthalpy is computed directly from a distance-based hydrogen bonding energy algorithm. The resulting expressions are employed for grid-based analyses of Molecular Dynamics simulations. In this first assessment of the methodology, we obtained global estimates of the excess entropy and enthalpy of water that are in good agreement with experiment and examined the method's ability to enable detailed elucidation of solvation thermodynamic structures, which can provide valuable knowledge toward molecular design.
Collapse
Affiliation(s)
- Camilo Velez-Vega
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Daniel J J McKay
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Tom Kurtzman
- Department of Chemistry, Lehman College, The City University of New York , 250 Bedford Park Boulevard West, Bronx, New York 10468, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York , New York, New York 10016, United States
| | - Vibhas Aravamuthan
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Robert A Pearlstein
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | - José S Duca
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
39
|
Bayden AS, Moustakas DT, Joseph-McCarthy D, Lamb ML. Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP. J Chem Inf Model 2015; 55:1552-65. [DOI: 10.1021/ci500746d] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Alexander S. Bayden
- Oncology and Infection Innovative Medicines Units, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Demetri T. Moustakas
- Oncology and Infection Innovative Medicines Units, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Diane Joseph-McCarthy
- Oncology and Infection Innovative Medicines Units, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Michelle L. Lamb
- Oncology and Infection Innovative Medicines Units, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| |
Collapse
|
40
|
Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
41
|
Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 424] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
Collapse
Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
| | | | | |
Collapse
|
42
|
Velez-Vega C, McKay DJJ, Aravamuthan V, Pearlstein R, Duca JS. Time-averaged distributions of solute and solvent motions: exploring proton wires of GFP and PfM2DH. J Chem Inf Model 2014; 54:3344-61. [PMID: 25405925 DOI: 10.1021/ci500571h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proton translocation pathways of selected variants of the green fluorescent protein (GFP) and Pseudomonas fluorescens mannitol 2-dehydrogenase (PfM2DH) were investigated via an explicit solvent molecular dynamics-based analysis protocol that allows for direct quantitative relationship between a crystal structure and its time-averaged solute-solvent structure obtained from simulation. Our study of GFP is in good agreement with previous research suggesting that the proton released from the chromophore upon photoexcitation can diffuse through an extended internal hydrogen bonding network that allows for the proton to exit to bulk or be recaptured by the anionic chromophore. Conversely for PfM2DH, we identified the most probable ionization states of key residues along the proton escape channel from the catalytic site to bulk solvent, wherein the solute and high-density solvent crystal structures of binary and ternary complexes were properly reproduced. Furthermore, we proposed a plausible mechanism for this proton translocation process that is consistent with the state-dependent structural shifts observed in our analysis. The time-averaged structures generated from our analyses facilitate validation of MD simulation results and provide a comprehensive profile of the dynamic all-occupancy solvation network within and around a flexible solute, from which detailed hydrogen-bonding networks can be inferred. In this way, potential drawbacks arising from the elucidation of these networks by examination of static crystal structures or via alternate rigid-protein solvation analysis procedures can be overcome. Complementary studies aimed at the effective use of our methodology for alternate implementations (e.g., ligand design) are currently underway.
Collapse
Affiliation(s)
- Camilo Velez-Vega
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research , 100 Technology Square, Cambridge, Massachusetts 02139, United States
| | | | | | | | | |
Collapse
|
43
|
Mondal J, Friesner RA, Berne BJ. Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase. J Chem Theory Comput 2014; 10:5696-5705. [PMID: 25516727 PMCID: PMC4263462 DOI: 10.1021/ct500584n] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Indexed: 12/29/2022]
Abstract
![]()
Computer
simulations are used to determine the free energy landscape
for the binding of the anticancer drug Dasatinib to its src kinase
receptor and show that before settling into a free energy basin the
ligand must surmount a free energy barrier. An analysis based on using
both the ligand-pocket separation and the pocket-water occupancy as
reaction coordinates shows that the free energy barrier is a result
of the free energy cost for almost complete desolvation of the binding
pocket. The simulations further show that the barrier is not a result
of the reorganization free energy of the binding pocket. Although
a continuum solvent model gives the location of free energy minima,
it is not able to reproduce the intermediate free energy barrier.
Finally, it is shown that a kinetic model for the on rate constant
in which the ligand diffuses up to a doorway state and then surmounts
the desolvation free energy barrier is consistent with published microsecond
time-scale simulations of the ligand binding kinetics for this system
[Shaw, D. E. et al. J. Am.
Chem. Soc.2011, 133, 9181−918321545110].
Collapse
Affiliation(s)
- Jagannath Mondal
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
| | - Richard A Friesner
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
| | - B J Berne
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
| |
Collapse
|
44
|
Alvarez-Garcia D, Barril X. Molecular Simulations with Solvent Competition Quantify Water Displaceability and Provide Accurate Interaction Maps of Protein Binding Sites. J Med Chem 2014; 57:8530-9. [DOI: 10.1021/jm5010418] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Daniel Alvarez-Garcia
- Departament
de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Gran Via de les Corts Catalanes,
585, 08007 Barcelona, Spain
| | - Xavier Barril
- Departament
de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Gran Via de les Corts Catalanes,
585, 08007 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| |
Collapse
|
45
|
Kříž Z, Adam J, Mrázková J, Zotos P, Chatzipavlou T, Wimmerová M, Koča J. Engineering the Pseudomonas aeruginosa II lectin: designing mutants with changed affinity and specificity. J Comput Aided Mol Des 2014; 28:951-60. [DOI: 10.1007/s10822-014-9774-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 07/02/2014] [Indexed: 12/20/2022]
|
46
|
Mason JS, Bortolato A, Weiss DR, Deflorian F, Tehan B, Marshall FH. High end GPCR design: crafted ligand design and druggability analysis using protein structure, lipophilic hotspots and explicit water networks. In Silico Pharmacol 2013. [PMCID: PMC4796210 DOI: 10.1186/2193-9616-1-23] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Purpose G Protein-Coupled Receptors (GPCRs) are a large family of therapeutically important proteins and as diverse X-ray structures become available it is increasingly possible to leverage structural information for rational drug design. We present herein approaches that use explicit water networks combined with energetic surveys of the binding site (GRID), providing an enhanced druggability and ligand design approach, with structural understanding of ligand binding, including a ‘magic’ methyl and binding site mutations, and a fast new approach to generate and score waters. Methods The GRID program was used to identify lipophilic and hydrogen bonding hotspots. Explicit full water networks were generated and scored for (pseudo)apo structures and ligand-protein complexes using a new approach, WaterFLAP (Molecular Discovery), together with WaterMap (Schrödinger) for (pseudo)apo structures. A scoring function (MetaScore) was developed using a fast computational protocol based on several short adiabatic biased MD simulations followed by multiple short well-tempered metadynamics runs. Results Analysis of diverse ligands binding to the adenosine A2A receptor together with new structures for the δ/κ/μ opioid and CCR5 receptors confirmed the key role of lipophilic hotspots in driving ligand binding and thus design; the displacement of ‘unhappy’ waters generally found in these regions provides a key binding energy component. Complete explicit water networks could be robustly generated for protein-ligand complexes using a WaterFLAP based approach. They provide a structural understanding of structure-activity relationships such as a ‘magic methyl’ effect and with the metadynamics approach a useful estimation of the binding energy changes resulting from active site mutations. Conclusions The promise of full structure-based drug design (SBDD) for GPCRs is now possible using a combination of advanced experimental and computational data. The conformational thermostabilisation of StaR® proteins provide the ability to easily generate biophysical screening data (binding including fragments, kinetics) and to get crystal structures with both potent and weak ligands. Explicit water networks for apo and ligand-complex structures are a critical ‘third dimension’ for SBDD and are key for understanding ligand binding energies and kinetics. GRID lipophilic hotspots are found to be key drivers for binding. In this context ‘high end’ GPCR ligand design is now enabled. Electronic supplementary material The online version of this article (doi:10.1186/2193-9616-1-23) contains supplementary material, which is available to authorized users.
Collapse
|
47
|
Bortolato A, Tehan BG, Bodnarchuk MS, Essex JW, Mason JS. Water Network Perturbation in Ligand Binding: Adenosine A2A Antagonists as a Case Study. J Chem Inf Model 2013; 53:1700-13. [DOI: 10.1021/ci4001458] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Bortolato
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
| | - Ben G. Tehan
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
| | - Michael S. Bodnarchuk
- School of
Chemistry, University of Southampton, Highfield,
Southampton,
Hampshire, SO17 1BJ, U.K
| | - Jonathan W. Essex
- School of
Chemistry, University of Southampton, Highfield,
Southampton,
Hampshire, SO17 1BJ, U.K
| | - Jonathan S. Mason
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts,
AL7 3AX, U.K
| |
Collapse
|