1
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Papadourakis M, Sinenka H, Matricon P, Hénin J, Brannigan G, Pérez-Benito L, Pande V, van Vlijmen H, de Graaf C, Deflorian F, Tresadern G, Cecchini M, Cournia Z. Alchemical Free Energy Calculations on Membrane-Associated Proteins. J Chem Theory Comput 2023; 19:7437-7458. [PMID: 37902715 PMCID: PMC11017255 DOI: 10.1021/acs.jctc.3c00365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Indexed: 10/31/2023]
Abstract
Membrane proteins have diverse functions within cells and are well-established drug targets. The advances in membrane protein structural biology have revealed drug and lipid binding sites on membrane proteins, while computational methods such as molecular simulations can resolve the thermodynamic basis of these interactions. Particularly, alchemical free energy calculations have shown promise in the calculation of reliable and reproducible binding free energies of protein-ligand and protein-lipid complexes in membrane-associated systems. In this review, we present an overview of representative alchemical free energy studies on G-protein-coupled receptors, ion channels, transporters as well as protein-lipid interactions, with emphasis on best practices and critical aspects of running these simulations. Additionally, we analyze challenges and successes when running alchemical free energy calculations on membrane-associated proteins. Finally, we highlight the value of alchemical free energy calculations calculations in drug discovery and their applicability in the pharmaceutical industry.
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Affiliation(s)
- Michail Papadourakis
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Hryhory Sinenka
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
| | - Pierre Matricon
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Jérôme Hénin
- Laboratoire
de Biochimie Théorique UPR 9080, CNRS and Université Paris Cité, 75005 Paris, France
| | - Grace Brannigan
- Center
for Computational and Integrative Biology, Rutgers University−Camden, Camden, New Jersey 08103, United States of America
- Department
of Physics, Rutgers University−Camden, Camden, New Jersey 08102, United States
of America
| | - Laura Pérez-Benito
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Vineet Pande
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Herman van Vlijmen
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Chris de Graaf
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Francesca Deflorian
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Gary Tresadern
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Marco Cecchini
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
| | - Zoe Cournia
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
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2
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Baumann H, Dybeck E, McClendon CL, Pickard FC, Gapsys V, Pérez-Benito L, Hahn DF, Tresadern G, Mathiowetz AM, Mobley DL. Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach. J Chem Theory Comput 2023; 19:5058-5076. [PMID: 37487138 PMCID: PMC10413862 DOI: 10.1021/acs.jctc.3c00282] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Indexed: 07/26/2023]
Abstract
Binding free energy calculations predict the potency of compounds to protein binding sites in a physically rigorous manner and see broad application in prioritizing the synthesis of novel drug candidates. Relative binding free energy (RBFE) calculations have emerged as an industry-standard approach to achieve highly accurate rank-order predictions of the potency of related compounds; however, this approach requires that the ligands share a common scaffold and a common binding mode, restricting the methods' domain of applicability. This is a critical limitation since complex modifications to the ligands, especially core hopping, are very common in drug design. Absolute binding free energy (ABFE) calculations are an alternate method that can be used for ligands that are not congeneric. However, ABFE suffers from a known problem of long convergence times due to the need to sample additional degrees of freedom within each system, such as sampling rearrangements necessary to open and close the binding site. Here, we report on an alternative method for RBFE, called Separated Topologies (SepTop), which overcomes the issues in both of the aforementioned methods by enabling large scaffold changes between ligands with a convergence time comparable to traditional RBFE. Instead of only mutating atoms that vary between two ligands, this approach performs two absolute free energy calculations at the same time in opposite directions, one for each ligand. Defining the two ligands independently allows the comparison of the binding of diverse ligands without the artificial constraints of identical poses or a suitable atom-atom mapping. This approach also avoids the need to sample the unbound state of the protein, making it more efficient than absolute binding free energy calculations. Here, we introduce an implementation of SepTop. We developed a general and efficient protocol for running SepTop, and we demonstrated the method on four diverse, pharmaceutically relevant systems. We report the performance of the method, as well as our practical insights into the strengths, weaknesses, and challenges of applying this method in an industrial drug design setting. We find that the accuracy of the approach is sufficiently high to rank order ligands with an accuracy comparable to traditional RBFE calculations while maintaining the additional flexibility of SepTop.
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Affiliation(s)
- Hannah
M. Baumann
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697, United States
| | - Eric Dybeck
- Pfizer
Worldwide Research, Development, and Medical, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Christopher L. McClendon
- Pfizer
Worldwide Research, Development, and Medical, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Frank C. Pickard
- Pfizer
Worldwide Research, Development, and Medical, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Vytautas Gapsys
- Computational
Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Laura Pérez-Benito
- Computational
Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - David F. Hahn
- Computational
Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Gary Tresadern
- Computational
Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Alan M. Mathiowetz
- Pfizer
Worldwide Research, Development, and Medical, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - David L. Mobley
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697, United States
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697, United States
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3
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Pérez-Benito L, Llinas del Torrent C, Pardo L, Tresadern G. The computational modeling of allosteric modulation of metabotropic glutamate receptors. From Structure to Clinical Development: Allosteric Modulation of G Protein-Coupled Receptors 2020; 88:1-33. [DOI: 10.1016/bs.apha.2020.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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4
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Jiménez-Luna J, Pérez-Benito L, Martínez-Rosell G, Sciabola S, Torella R, Tresadern G, De Fabritiis G. DeltaDelta neural networks for lead optimization of small molecule potency. Chem Sci 2019; 10:10911-10918. [PMID: 32190246 PMCID: PMC7066671 DOI: 10.1039/c9sc04606b] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/15/2019] [Indexed: 12/29/2022] Open
Abstract
The capability to rank different potential drug molecules against a protein target for potency has always been a fundamental challenge in computational chemistry due to its importance in drug design. While several simulation-based methodologies exist, they are hard to use prospectively and thus predicting potency in lead optimization campaigns remains an open challenge. Here we present the first machine learning approach specifically tailored for ranking congeneric series based on deep 3D-convolutional neural networks. Furthermore we prove its effectiveness by blindly testing it on datasets provided by Janssen, Pfizer and Biogen totalling over 3246 ligands and 13 targets as well as several well-known openly available sets, representing one the largest evaluations ever performed. We also performed online learning simulations of lead optimization using the approach in a predictive manner obtaining significant advantage over experimental choice. We believe that the evaluation performed in this study is strong evidence of the usefulness of a modern deep learning model in lead optimization pipelines against more expensive simulation-based alternatives.
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Affiliation(s)
- José Jiménez-Luna
- Computational Science Laboratory , Parc de Recerca Biomèdica de Barcelona , Universitat Pompeu Fabra , C Dr Aiguader 88 , Barcelona , 08003 , Spain .
| | - Laura Pérez-Benito
- Laboratori de Medicina Computacional , Unitat de Bioestadística , Facultat de Medicina , Universitat Autònoma de Barcelona , Spain
- Janssen Research and Development , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | | | - Simone Sciabola
- Biogen Chemistry and Molecular Therapeutics , 115 Broadway Street , Cambridge , MA 02142 , USA
| | - Rubben Torella
- Pfizer I&I , 610 Main Street , Cambridge , MA 02139 , USA
| | - Gary Tresadern
- Janssen Research and Development , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - Gianni De Fabritiis
- Computational Science Laboratory , Parc de Recerca Biomèdica de Barcelona , Universitat Pompeu Fabra , C Dr Aiguader 88 , Barcelona , 08003 , Spain .
- Acellera , Carrer del Dr Trueta, 183 , 08005 Barcelona , Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) , Passeig Lluis Companys 23 , 08010 Barcelona , Spain
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5
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Gapsys V, Pérez-Benito L, Aldeghi M, Seeliger D, van Vlijmen H, Tresadern G, de Groot BL. Large scale relative protein ligand binding affinities using non-equilibrium alchemy. Chem Sci 2019; 11:1140-1152. [PMID: 34084371 PMCID: PMC8145179 DOI: 10.1039/c9sc03754c] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/01/2019] [Indexed: 12/14/2022] Open
Abstract
Ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-physical (alchemical) thermodynamic cycles have shown great promise for structure-based drug design. However, their broad uptake and impact is held back by the notoriously complex setup of the calculations. Only a few tools other than the free energy perturbation approach by Schrödinger Inc. (referred to as FEP+) currently enable end-to-end application. Here, we present for the first time an approach based on the open-source software pmx that allows to easily set up and run alchemical calculations for diverse sets of small molecules using the GROMACS MD engine. The method relies on theoretically rigorous non-equilibrium thermodynamic integration (TI) foundations, and its flexibility allows calculations with multiple force fields. In this study, results from the Amber and Charmm force fields were combined to yield a consensus outcome performing on par with the commercial FEP+ approach. A large dataset of 482 perturbations from 13 different protein-ligand datasets led to an average unsigned error (AUE) of 3.64 ± 0.14 kJ mol-1, equivalent to Schrödinger's FEP+ AUE of 3.66 ± 0.14 kJ mol-1. For the first time, a setup is presented for overall high precision and high accuracy relative protein-ligand alchemical free energy calculations based on open-source software.
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Affiliation(s)
- Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry D-37077 Göttingen Germany
| | - Laura Pérez-Benito
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. Turnhoutseweg 30 B-2340 Beerse Belgium
| | - Matteo Aldeghi
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry D-37077 Göttingen Germany
| | - Daniel Seeliger
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG Birkendorfer Strasse 65 D-88397 Biberach a.d. Riss Germany
| | - Herman van Vlijmen
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. Turnhoutseweg 30 B-2340 Beerse Belgium
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. Turnhoutseweg 30 B-2340 Beerse Belgium
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry D-37077 Göttingen Germany
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6
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Pérez-Benito L, Henry A, Matsoukas MT, Lopez L, Pulido D, Royo M, Cordomí A, Tresadern G, Pardo L. The size matters? A computational tool to design bivalent ligands. Bioinformatics 2019; 34:3857-3863. [PMID: 29850769 PMCID: PMC6223368 DOI: 10.1093/bioinformatics/bty422] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 05/23/2018] [Indexed: 12/15/2022] Open
Abstract
Motivation Bivalent ligands are increasingly important such as for targeting G protein-coupled receptor (GPCR) dimers or proteolysis targeting chimeras (PROTACs). They contain two pharmacophoric units that simultaneously bind in their corresponding binding sites, connected with a spacer chain. Here, we report a molecular modelling tool that links the pharmacophore units via the shortest pathway along the receptors van der Waals surface and then scores the solutions providing prioritization for the design of new bivalent ligands. Results Bivalent ligands of known dimers of GPCRs, PROTACs and a model bivalent antibody/antigen system were analysed. The tool could rapidly assess the preferred linker length for the different systems and recapitulated the best reported results. In the case of GPCR dimers the results suggest that in some cases these ligands might bind to a secondary binding site at the extracellular entrance (vestibule or allosteric site) instead of the orthosteric binding site. Availability and implementation Freely accessible from the Molecular Operating Environment svl exchange server (https://svl.chemcomp.com/). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Laura Pérez-Benito
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Andrew Henry
- Chemical Computing Group, St John's Innovation Centre Cowley Road, Cambridge, UK
| | - Minos-Timotheos Matsoukas
- Department of Pharmacy, University Campus, University of Patras, School of Health Sciences, Rion, Patras, Greece
| | - Laura Lopez
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Daniel Pulido
- Combinatorial Chemistry Unit, Barcelona Science Park, Barcelona, Spain.,Centro de Investigación Biomédica en Red-Bioingeniería Biomateriales y Nanomedicina (CIBER-BBN), Spain
| | - Miriam Royo
- Combinatorial Chemistry Unit, Barcelona Science Park, Barcelona, Spain.,Centro de Investigación Biomédica en Red-Bioingeniería Biomateriales y Nanomedicina (CIBER-BBN), Spain
| | - Arnau Cordomí
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | | | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
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7
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Llinas Del Torrent C, Pérez-Benito L, Tresadern G. Computational Drug Design Applied to the Study of Metabotropic Glutamate Receptors. Molecules 2019; 24:molecules24061098. [PMID: 30897742 PMCID: PMC6470756 DOI: 10.3390/molecules24061098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 11/16/2022] Open
Abstract
Metabotropic glutamate (mGlu) receptors are a family of eight GPCRs that are attractive drug discovery targets to modulate glutamate action and response. Here we review the application of computational methods to the study of this family of receptors. X-ray structures of the extracellular and 7-transmembrane domains have played an important role to enable structure-based modeling approaches, whilst we also discuss the successful application of ligand-based methods. We summarize the literature and highlight the areas where modeling and experiment have delivered important understanding for mGlu receptor drug discovery. Finally, we offer suggestions of future areas of opportunity for computational work.
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Affiliation(s)
- Claudia Llinas Del Torrent
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina, Universitat Autónoma de Barcelona, 08193 Bellaterra, Spain.
| | - Laura Pérez-Benito
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium.
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium.
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8
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Cid JM, Lavreysen H, Tresadern G, Pérez-Benito L, Tovar F, Fontana A, Trabanco AA. Computationally Guided Identification of Allosteric Agonists of the Metabotropic Glutamate 7 Receptor. ACS Chem Neurosci 2019; 10:1043-1054. [PMID: 30216043 DOI: 10.1021/acschemneuro.8b00331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The metabotropic glutamate 7 (mGlu7) receptor belongs to the group III of mGlu receptors. Since the mGlu7 receptor can control excitatory neurotransmission in the hippocampus and cortex, modulation of the receptor may have therapeutic benefit in several CNS diseases. However, mGlu7 remains relatively unexplored among the eight known mGlu receptors partly because of the limited availability of tool compounds to interrogate its potential therapeutic utility. Here we report the discovery of a new class of mGlu7 allosteric agonists. Hits originating from virtual screening were followed up with further analogue searching and screening, leading to a novel series of mGlu7 allosteric agonists. Guided by docking into a structural model of the mGlu7 receptor the initial hit 5 was successfully optimized to analogues with comparable potencies and more attractive drug-like attributes than AMN082.
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Affiliation(s)
- Jose María Cid
- Janssen Research and Development, Calle Jarama 75A, Toledo 45007, Spain
| | - Hilde Lavreysen
- Janssen Research and Development, Turnhoutseweg 30, 2440 Beerse, Belgium
| | - Gary Tresadern
- Janssen Research and Development, Turnhoutseweg 30, 2440 Beerse, Belgium
| | - Laura Pérez-Benito
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina, Universitat Autonoma de Barcelona, Bellaterra 08193, Spain
| | - Fulgencio Tovar
- Villapharma Research
S.L., Parque Tecnológico de Fuente Álamo. Ctra. El Estrecho-Lobosillo, Km. 2.5- Av. Azul, 30320 Fuente Álamo de Murcia, Murcia, Spain
| | - Alberto Fontana
- Janssen Research and Development, Calle Jarama 75A, Toledo 45007, Spain
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9
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Llinas Del Torrent C, Casajuana-Martin N, Pardo L, Tresadern G, Pérez-Benito L. Mechanisms Underlying Allosteric Molecular Switches of Metabotropic Glutamate Receptor 5. J Chem Inf Model 2019; 59:2456-2466. [PMID: 30811196 DOI: 10.1021/acs.jcim.8b00924] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The metabotropic glutamate 5 (mGlu5) receptor is a class C G protein-coupled receptor (GPCR) that is implicated in several CNS disorders making it a popular drug discovery target. Years of research have revealed allosteric mGlu5 ligands showing an unexpected complete switch in functional activity despite only small changes in their chemical structure, resulting in positive allosteric modulators (PAM) or negative allosteric modulators (NAM) for the same scaffold. Up to now, the origins of this effect are not understood, causing difficulties in a drug discovery context. In this work, experimental data was gathered and analyzed alongside docking and Molecular Dynamics (MD) calculations for three sets of PAM and NAM pairs. The results consistently show the role of specific interactions formed between ligand substituents and amino acid side chains that block or promote local movements associated with receptor activation. The work provides an explanation for how such small structural changes lead to remarkable differences in functional activity. While this work can greatly help drug discovery programs avoid these switches, it also provides valuable insight into the mechanisms of class C GPCR allosteric activation. Furthermore, the approach shows the value of applying MD to understand functional activity in drug design programs, even for such close structural analogues.
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Affiliation(s)
- Claudia Llinas Del Torrent
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina , Universitat Autonoma de Barcelona , 08193 Bellaterra , Spain
| | - Nil Casajuana-Martin
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina , Universitat Autonoma de Barcelona , 08193 Bellaterra , Spain
| | - Leonardo Pardo
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina , Universitat Autonoma de Barcelona , 08193 Bellaterra , Spain
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development , Janssen Pharmaceutica N. V. , Turnhoutseweg 30 , B-2340 Beerse , Belgium
| | - Laura Pérez-Benito
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina , Universitat Autonoma de Barcelona , 08193 Bellaterra , Spain.,Computational Chemistry, Janssen Research & Development , Janssen Pharmaceutica N. V. , Turnhoutseweg 30 , B-2340 Beerse , Belgium
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10
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Pérez-Benito L, Casajuana-Martin N, Jiménez-Rosés M, van Vlijmen H, Tresadern G. Predicting Activity Cliffs with Free-Energy Perturbation. J Chem Theory Comput 2019; 15:1884-1895. [DOI: 10.1021/acs.jctc.8b01290] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Laura Pérez-Benito
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, Beerse B-2340, Belgium
| | - Nil Casajuana-Martin
- Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autonoma de Barcelona, Bellaterra 08193, Spain
| | - Mireia Jiménez-Rosés
- Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autonoma de Barcelona, Bellaterra 08193, Spain
| | - Herman van Vlijmen
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, Beerse B-2340, Belgium
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, Beerse B-2340, Belgium
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11
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Pulido D, Casadó-Anguera V, Pérez-Benito L, Moreno E, Cordomí A, López L, Cortés A, Ferré S, Pardo L, Casadó V, Royo M. Design of a True Bivalent Ligand with Picomolar Binding Affinity for a G Protein-Coupled Receptor Homodimer. J Med Chem 2018; 61:9335-9346. [PMID: 30257092 DOI: 10.1021/acs.jmedchem.8b01249] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bivalent ligands have emerged as chemical tools to study G protein-coupled receptor dimers. Using a combination of computational, chemical, and biochemical tools, here we describe the design of bivalent ligand 13 with high affinity ( KDB1 = 21 pM) for the dopamine D2 receptor (D2R) homodimer. Bivalent ligand 13 enhances the binding affinity relative to monovalent compound 15 by 37-fold, indicating simultaneous binding at both protomers. Using synthetic peptides with amino acid sequences of transmembrane (TM) domains of D2R, we provide evidence that TM6 forms the interface of the homodimer. Notably, the disturber peptide TAT-TM6 decreased the binding of bivalent ligand 13 by 52-fold and had no effect on monovalent compound 15, confirming the D2R homodimer through TM6 ex vivo. In conclusion, by using a versatile multivalent chemical platform, we have developed a precise strategy to generate a true bivalent ligand that simultaneously targets both orthosteric sites of the D2R homodimer.
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Affiliation(s)
- Daniel Pulido
- Biomaterials and Nanomedicine , Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Barcelona Science Park , 08028 Barcelona , Spain.,Combinatorial Chemistry Unit , Barcelona Science Park , 08028 Barcelona , Spain
| | - Verònica Casadó-Anguera
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology , University of Barcelona , 08028 Barcelona , Spain.,Biomedical Research Networking Center in Neurodegenerative Diseases (CIBERNED) , 08028 Barcelona , Spain.,Institute of Biomedicine , University of Barcelona (IBUB) , 08028 Barcelona , Spain
| | - Laura Pérez-Benito
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine , Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain
| | - Estefanía Moreno
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology , University of Barcelona , 08028 Barcelona , Spain.,Biomedical Research Networking Center in Neurodegenerative Diseases (CIBERNED) , 08028 Barcelona , Spain.,Institute of Biomedicine , University of Barcelona (IBUB) , 08028 Barcelona , Spain
| | - Arnau Cordomí
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine , Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain
| | - Laura López
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine , Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain
| | - Antoni Cortés
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology , University of Barcelona , 08028 Barcelona , Spain.,Biomedical Research Networking Center in Neurodegenerative Diseases (CIBERNED) , 08028 Barcelona , Spain.,Institute of Biomedicine , University of Barcelona (IBUB) , 08028 Barcelona , Spain
| | - Sergi Ferré
- Integrative Neurobiology Section, National Institute on Drug Abuse, Intramural Research Program , National Institutes of Health , Baltimore , Maryland 21224 , United States
| | - Leonardo Pardo
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine , Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain
| | - Vicent Casadó
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology , University of Barcelona , 08028 Barcelona , Spain.,Biomedical Research Networking Center in Neurodegenerative Diseases (CIBERNED) , 08028 Barcelona , Spain.,Institute of Biomedicine , University of Barcelona (IBUB) , 08028 Barcelona , Spain
| | - Miriam Royo
- Biomaterials and Nanomedicine , Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Barcelona Science Park , 08028 Barcelona , Spain.,Combinatorial Chemistry Unit , Barcelona Science Park , 08028 Barcelona , Spain
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12
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Doornbos MLJ, Wang X, Vermond SC, Peeters L, Pérez-Benito L, Trabanco AA, Lavreysen H, Cid JM, Heitman LH, Tresadern G, IJzerman AP. Covalent Allosteric Probe for the Metabotropic Glutamate Receptor 2: Design, Synthesis, and Pharmacological Characterization. J Med Chem 2018; 62:223-233. [PMID: 29494768 PMCID: PMC6331142 DOI: 10.1021/acs.jmedchem.8b00051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Covalent labeling
of G protein-coupled receptors (GPCRs) by small
molecules is a powerful approach to understand binding modes, mechanism
of action, pharmacology, and even facilitate structure elucidation.
We report the first covalent positive allosteric modulator (PAM) for
a class C GPCR, the mGlu2 receptor. Three putatively covalent
mGlu2 PAMs were designed and synthesized. Pharmacological
characterization identified 2 to bind the receptor covalently.
Computational modeling combined with receptor mutagenesis revealed
T7917.29×30 as the likely position of covalent interaction.
We show how this covalent ligand can be used to characterize the PAM
binding mode and that it is a valuable tool compound in studying receptor
function and binding kinetics. Our findings advance the understanding
of the mGlu2 PAM interaction and suggest that 2 is a valuable probe for further structural and chemical biology
approaches.
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Affiliation(s)
- Maarten L J Doornbos
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR) , Leiden University , P.O. Box 9502, 2300RA Leiden , The Netherlands
| | - Xuesong Wang
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR) , Leiden University , P.O. Box 9502, 2300RA Leiden , The Netherlands
| | - Sophie C Vermond
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR) , Leiden University , P.O. Box 9502, 2300RA Leiden , The Netherlands
| | - Luc Peeters
- Janssen Research and Development , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - Laura Pérez-Benito
- Janssen Research and Development , Calle Jarama 75A , 45007 Toledo , Spain.,Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina , Universitat Autonoma de Barcelona , 08193 Bellaterra , Spain
| | - Andrés A Trabanco
- Janssen Research and Development , Calle Jarama 75A , 45007 Toledo , Spain
| | - Hilde Lavreysen
- Janssen Research and Development , Turnhoutseweg 30 , 2340 Beerse , Belgium
| | - José María Cid
- Janssen Research and Development , Calle Jarama 75A , 45007 Toledo , Spain
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR) , Leiden University , P.O. Box 9502, 2300RA Leiden , The Netherlands
| | - Gary Tresadern
- Janssen Research and Development , Calle Jarama 75A , 45007 Toledo , Spain
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR) , Leiden University , P.O. Box 9502, 2300RA Leiden , The Netherlands
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13
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Navarro G, Cordomí A, Brugarolas M, Moreno E, Aguinaga D, Pérez-Benito L, Ferre S, Cortés A, Casadó V, Mallol J, Canela EI, Lluís C, Pardo L, McCormick PJ, Franco R. Cross-communication between G i and G s in a G-protein-coupled receptor heterotetramer guided by a receptor C-terminal domain. BMC Biol 2018; 16:24. [PMID: 29486745 PMCID: PMC6389107 DOI: 10.1186/s12915-018-0491-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/22/2018] [Indexed: 12/02/2022] Open
Abstract
Background G-protein-coupled receptor (GPCR) heteromeric complexes have distinct properties from homomeric GPCRs, giving rise to new receptor functionalities. Adenosine receptors (A1R or A2AR) can form A1R-A2AR heteromers (A1-A2AHet), and their activation leads to canonical G-protein-dependent (adenylate cyclase mediated) and -independent (β-arrestin mediated) signaling. Adenosine has different affinities for A1R and A2AR, allowing the heteromeric receptor to detect its concentration by integrating the downstream Gi- and Gs-dependent signals. cAMP accumulation and β-arrestin recruitment assays have shown that, within the complex, activation of A2AR impedes signaling via A1R. Results We examined the mechanism by which A1-A2AHet integrates Gi- and Gs-dependent signals. A1R blockade by A2AR in the A1-A2AHet is not observed in the absence of A2AR activation by agonists, in the absence of the C-terminal domain of A2AR, or in the presence of synthetic peptides that disrupt the heteromer interface of A1-A2AHet, indicating that signaling mediated by A1R and A2AR is controlled by both Gi and Gs proteins. Conclusions We identified a new mechanism of signal transduction that implies a cross-communication between Gi and Gs proteins guided by the C-terminal tail of the A2AR. This mechanism provides the molecular basis for the operation of the A1-A2AHet as an adenosine concentration-sensing device that modulates the signals originating at both A1R and A2AR. Electronic supplementary material The online version of this article (10.1186/s12915-018-0491-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gemma Navarro
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Arnau Cordomí
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Marc Brugarolas
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Estefanía Moreno
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - David Aguinaga
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Laura Pérez-Benito
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Sergi Ferre
- Integrative Neurobiology Section, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Antoni Cortés
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Vicent Casadó
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Josefa Mallol
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Enric I Canela
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Carme Lluís
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Peter J McCormick
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain. .,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain. .,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain. .,School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, UK.
| | - Rafael Franco
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain. .,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain. .,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain.
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14
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Tresadern G, Trabanco AA, Pérez-Benito L, Overington JP, van Vlijmen HWT, van Westen GJP. Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling. J Chem Inf Model 2017; 57:2976-2985. [PMID: 29172488 PMCID: PMC5755953 DOI: 10.1021/acs.jcim.7b00338] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Indexed: 01/07/2023]
Abstract
Proteochemometric modeling (PCM) is a computational approach that can be considered an extension of quantitative structure-activity relationship (QSAR) modeling, where a single model incorporates information for a family of targets and all the associated ligands instead of modeling activity versus one target. This is especially useful for situations where bioactivity data exists for similar proteins but is scarce for the protein of interest. Here we demonstrate the application of PCM to identify allosteric modulators of metabotropic glutamate (mGlu) receptors. Given our long-running interest in modulating mGlu receptor function we compiled a matrix of compound-target bioactivity data. Some members of the mGlu family are well explored both internally and in the public domain, while there are much fewer examples of ligands for other targets such as the mGlu7 receptor. Using a PCM approach mGlu7 receptor hits were found. In comparison to conventional single target modeling the identified hits were more diverse, had a better confirmation rate, and provide starting points for further exploration. We conclude that the robust structure-activity relationship from well explored target family members translated to better quality hits for PCM compared to virtual screening (VS) based on a single target.
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Affiliation(s)
- Gary Tresadern
- Computational
Chemistry and Neuroscience Medicinal Chemistry, Janssen
Research & Development, Janssen-Cilag
S.A., Jarama 75A, 45007 Toledo, Spain
| | - Andres A. Trabanco
- Computational
Chemistry and Neuroscience Medicinal Chemistry, Janssen
Research & Development, Janssen-Cilag
S.A., Jarama 75A, 45007 Toledo, Spain
| | - Laura Pérez-Benito
- Computational
Chemistry and Neuroscience Medicinal Chemistry, Janssen
Research & Development, Janssen-Cilag
S.A., Jarama 75A, 45007 Toledo, Spain
| | - John P. Overington
- ChEMBL Group, EMBL-EBI,
Wellcome Trust Genome Campus, CB10 1SD Hinxton, United Kingdom
| | - Herman W. T. van Vlijmen
- Computational
Chemistry, Janssen Research & Development, Turnhoutseweg 30, B-2340 Beerse, Belgium
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15
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Keränen H, Pérez-Benito L, Ciordia M, Delgado F, Steinbrecher TB, Oehlrich D, van Vlijmen HWT, Trabanco AA, Tresadern G. Acylguanidine Beta Secretase 1 Inhibitors: A Combined Experimental and Free Energy Perturbation Study. J Chem Theory Comput 2017; 13:1439-1453. [PMID: 28103438 DOI: 10.1021/acs.jctc.6b01141] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A series of acylguanidine beta secretase 1 (BACE1) inhibitors with modified scaffold and P3 pocket substituent was synthesized and studied with free energy perturbation (FEP) calculations. The resulting molecules showed potencies in enzymatic BACE1 inhibition assays up to 1 nM. The correlation between the predicted activity from the FEP calculations and the experimental activity was good for the P3 pocket substituents. The average mean unsigned error (MUE) between prediction and experiment was 0.68 ± 0.17 kcal/mol for the default 5 ns lambda window simulation time improving to 0.35 ± 0.13 kcal/mol for 40 ns. FEP calculations for the P2' pocket substituents on the same acylguanidine scaffold also showed good agreement with experiment and the results remained stable with repeated simulations and increased simulation time. It proved more difficult to use FEP calculations to study the scaffold modification from increasing 5 to 6 and 7 membered-rings. Although prediction and experiment were in agreement for short 2 ns simulations, as the simulation time increased the results diverged. This was improved by the use of a newly developed "Core Hopping FEP+" approach, which also showed improved stability in repeat calculations. The origins of these differences along with the value of repeat and longer simulation times are discussed. This work provides a further example of the use of FEP as a computational tool for molecular design.
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Affiliation(s)
- Henrik Keränen
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. , Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Laura Pérez-Benito
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina, Universitat Autonoma de Barcelona , 08193, Bellaterra, Spain.,Computational Chemistry, Janssen Research and Development, Janssen-Cilag , c/ Jarama 75A, 45007, Toledo, Spain
| | - Myriam Ciordia
- Neuroscience Medicinal Chemistry, Janssen Research and Development, Janssen-Cilag , c/ Jarama 75A, 45007, Toledo, Spain
| | - Francisca Delgado
- Neuroscience Medicinal Chemistry, Janssen Research and Development, Janssen-Cilag , c/ Jarama 75A, 45007, Toledo, Spain
| | | | - Daniel Oehlrich
- Neuroscience Medicinal Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. , Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Herman W T van Vlijmen
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V. , Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Andrés A Trabanco
- Neuroscience Medicinal Chemistry, Janssen Research and Development, Janssen-Cilag , c/ Jarama 75A, 45007, Toledo, Spain
| | - Gary Tresadern
- Computational Chemistry, Janssen Research and Development, Janssen-Cilag , c/ Jarama 75A, 45007, Toledo, Spain
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16
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Cid JM, Tresadern G, Vega JA, de Lucas AI, Del Cerro A, Matesanz E, Linares ML, García A, Iturrino L, Pérez-Benito L, Macdonald GJ, Oehlrich D, Lavreysen H, Peeters L, Ceusters M, Ahnaou A, Drinkenburg W, Mackie C, Somers M, Trabanco AA. Discovery of 8-Trifluoromethyl-3-cyclopropylmethyl-7-[(4-(2,4-difluorophenyl)-1-piperazinyl)methyl]-1,2,4-triazolo[4,3-a]pyridine (JNJ-46356479), a Selective and Orally Bioavailable mGlu2 Receptor Positive Allosteric Modulator (PAM). J Med Chem 2016; 59:8495-507. [PMID: 27579727 DOI: 10.1021/acs.jmedchem.6b00913] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Positive allosteric modulators of the metabotropic glutamate 2 receptor have generated great interest in the past decade. There is mounting evidence of their potential as therapeutic agents in the treatment of multiple central nervous system disorders. We have previously reported substantial efforts leading to potent and selective mGlu2 PAMs. However, finding compounds with the optimal combination of in vitro potency and good druglike properties has remained elusive, in part because of the hydrophobic nature of the allosteric binding site. Herein, we report on the lead optimization process to overcome the poor solubility inherent to the advanced lead 6. Initial prototypes already showed significant improvements in solubility while retaining good functional activity but displayed new liabilities associated with metabolism and hERG inhibition. Subsequent subtle modifications efficiently addressed those issues leading to the identification of compound 27 (JNJ-46356479). This new lead represents a more balanced profile that offers a significant improvement on the druglike attributes compared to previously reported leads.
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Affiliation(s)
- Jose María Cid
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Gary Tresadern
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Juan Antonio Vega
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Ana Isabel de Lucas
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Alcira Del Cerro
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Encarnación Matesanz
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - María Lourdes Linares
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Aránzazu García
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Laura Iturrino
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Laura Pérez-Benito
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina, Universitat Autonoma de Barcelona , Bellaterra 08193, Spain
| | - Gregor J Macdonald
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | - Daniel Oehlrich
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | - Hilde Lavreysen
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | - Luc Peeters
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | - Marc Ceusters
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | - Abdellah Ahnaou
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | | | - Claire Mackie
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | - Marijke Somers
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | - Andrés A Trabanco
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
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17
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Ciordia M, Pérez-Benito L, Delgado F, Trabanco AA, Tresadern G. Application of Free Energy Perturbation for the Design of BACE1 Inhibitors. J Chem Inf Model 2016; 56:1856-71. [PMID: 27500414 DOI: 10.1021/acs.jcim.6b00220] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Novel spiroaminodihydropyrroles probing for optimized interactions at the P3 pocket of β-secretase 1 (BACE1) were designed with the use of free energy perturbation (FEP) calculations. The resulting molecules showed pIC50 potencies in enzymatic BACE1 inhibition assays ranging from approximately 5 to 7. Good correlation was observed between the predicted activity from the FEP calculations and experimental activity. Simulations run with a default 5 ns approach delivered a mean unsigned error (MUE) between prediction and experiment of 0.58 and 0.91 kcal/mol for retrospective and prospective applications, respectively. With longer simulations of 10 and 20 ns, the MUE was in both cases 0.57 kcal/mol for the retrospective application, and 0.69 and 0.59 kcal/mol for the prospective application. Other considerations that impact the quality of the calculations are discussed. This work provides an example of the value of FEP as a computational tool for drug discovery.
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Affiliation(s)
- Myriam Ciordia
- Janssen Research and Development , c/Jarama 75A, 45007 Toledo, Spain.,Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad CEU San Pablo , Urbanización Montepríncipe Ctra., Boadilla del Monte Km 5.3, 28668 Madrid, Spain
| | - Laura Pérez-Benito
- Janssen Research and Development , c/Jarama 75A, 45007 Toledo, Spain.,Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina, Universitat Autonoma de Barcelona , 08193 Bellaterra, Spain
| | - Francisca Delgado
- Janssen Research and Development , c/Jarama 75A, 45007 Toledo, Spain
| | - Andrés A Trabanco
- Janssen Research and Development , c/Jarama 75A, 45007 Toledo, Spain
| | - Gary Tresadern
- Janssen Research and Development , c/Jarama 75A, 45007 Toledo, Spain
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18
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Doornbos MLJ, Pérez-Benito L, Tresadern G, Mulder-Krieger T, Biesmans I, Trabanco AA, Cid JM, Lavreysen H, IJzerman AP, Heitman LH. Molecular mechanism of positive allosteric modulation of the metabotropic glutamate receptor 2 by JNJ-46281222. Br J Pharmacol 2016; 173:588-600. [PMID: 26589404 DOI: 10.1111/bph.13390] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 11/09/2015] [Accepted: 11/10/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND AND PURPOSE Allosteric modulation of the mGlu2 receptor is a potential strategy for treatment of various neurological and psychiatric disorders. Here, we describe the in vitro characterization of the mGlu2 positive allosteric modulator (PAM) JNJ-46281222 and its radiolabelled counterpart [(3) H]-JNJ-46281222. Using this novel tool, we also describe the allosteric effect of orthosteric glutamate binding and the presence of a bound G protein on PAM binding and use computational approaches to further investigate the binding mode. EXPERIMENTAL APPROACH We have used radioligand binding studies, functional assays, site-directed mutagenesis, homology modelling and molecular dynamics to study the binding of JNJ-46281222. KEY RESULTS JNJ-46281222 is an mGlu2 -selective, highly potent PAM with nanomolar affinity (KD = 1.7 nM). Binding of [(3) H]-JNJ-46281222 was increased by the presence of glutamate and greatly reduced by the presence of GTP, indicating the preference for a G protein bound state of the receptor for PAM binding. Its allosteric binding site was visualized and analysed by a computational docking and molecular dynamics study. The simulations revealed amino acid movements in regions expected to be important for activation. The binding mode was supported by [(3) H]-JNJ-46281222 binding experiments on mutant receptors. CONCLUSION AND IMPLICATIONS Our results obtained with JNJ-46281222 in unlabelled and tritiated form further contribute to our understanding of mGlu2 allosteric modulation. The computational simulations and mutagenesis provide a plausible binding mode with indications of how the ligand permits allosteric activation. This study is therefore of interest for mGlu2 and class C receptor drug discovery.
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Affiliation(s)
- Maarten L J Doornbos
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Laura Pérez-Benito
- Janssen Research and Development, Toledo, Spain.,Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina, Universitat Autonoma de Barcelona, Bellaterra, Spain
| | | | - Thea Mulder-Krieger
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | | | | | | | | | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
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19
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Mateu N, Ciordia M, Delgado O, Sánchez-Roselló M, Trabanco AA, Van Gool M, Tresadern G, Pérez-Benito L, Fustero S. A Versatile Approach to CF 3-Containing 2-Pyrrolidones by Tandem Michael Addition-Cyclization: Exemplification in the Synthesis of Amidine Class BACE1 Inhibitors. Chemistry 2015. [DOI: 10.1002/chem.201502483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Mateu N, Ciordia M, Delgado O, Sánchez-Roselló M, Trabanco AA, Van Gool M, Tresadern G, Pérez-Benito L, Fustero S. Cover Picture: A Versatile Approach to CF 3-Containing 2-Pyrrolidones by Tandem Michael Addition-Cyclization: Exemplification in the Synthesis of Amidine Class BACE1 Inhibitors (Chem. Eur. J. 33/2015). Chemistry 2015. [DOI: 10.1002/chem.201590147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Mateu N, Ciordia M, Delgado O, Sánchez-Roselló M, Trabanco AA, Van Gool M, Tresadern G, Pérez-Benito L, Fustero S. A Versatile Approach to CF3-Containing 2-Pyrrolidones by Tandem Michael Addition-Cyclization: Exemplification in the Synthesis of Amidine Class BACE1 Inhibitors. Chemistry 2015; 21:11719-26. [DOI: 10.1002/chem.201501662] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Indexed: 12/19/2022]
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Masià-Balagué M, Izquierdo I, Garrido G, Cordomí A, Pérez-Benito L, Miller NLG, Schlaepfer DD, Gigoux V, Aragay AM. Gastrin-stimulated Gα13 Activation of Rgnef Protein (ArhGEF28) in DLD-1 Colon Carcinoma Cells. J Biol Chem 2015; 290:15197-209. [PMID: 25922072 PMCID: PMC4463461 DOI: 10.1074/jbc.m114.628164] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 04/27/2015] [Indexed: 12/15/2022] Open
Abstract
The guanine nucleotide exchange factor Rgnef (also known as ArhGEF28 or p190RhoGEF) promotes colon carcinoma cell motility and tumor progression via interaction with focal adhesion kinase (FAK). Mechanisms of Rgnef activation downstream of integrin or G protein-coupled receptors remain undefined. In the absence of a recognized G protein signaling homology domain in Rgnef, no proximal linkage to G proteins was known. Utilizing multiple methods, we have identified Rgnef as a new effector for Gα13 downstream of gastrin and the type 2 cholecystokinin receptor. In DLD-1 colon carcinoma cells depleted of Gα13, gastrin-induced FAK Tyr(P)-397 and paxillin Tyr(P)-31 phosphorylation were reduced. RhoA GTP binding and promoter activity were increased by Rgnef in combination with active Gα13. Rgnef co-immunoprecipitated with activated Gα13Q226L but not Gα12Q229L. The Rgnef C-terminal (CT, 1279-1582) region was sufficient for co-immunoprecipitation, and Rgnef-CT exogenous expression prevented Gα13-stimulated SRE activity. A domain at the C terminus of the protein close to the FAK binding domain is necessary to bind to Gα13. Point mutations of Rgnef-CT residues disrupt association with active Gα13 but not Gαq. These results show that Rgnef functions as an effector of Gα13 signaling and that this linkage may mediate FAK activation in DLD-1 colon carcinoma cells.
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Affiliation(s)
- Miriam Masià-Balagué
- From the Molecular Biology Institute of Barcelona, Spanish National Research Council (CSIC), 08028 Barcelona, Spain
| | - Ismael Izquierdo
- From the Molecular Biology Institute of Barcelona, Spanish National Research Council (CSIC), 08028 Barcelona, Spain
| | - Georgina Garrido
- From the Molecular Biology Institute of Barcelona, Spanish National Research Council (CSIC), 08028 Barcelona, Spain
| | - Arnau Cordomí
- the Departament de Pediatria, Unitat de Bioestadística, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Laura Pérez-Benito
- the Departament de Pediatria, Unitat de Bioestadística, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Nichol L G Miller
- the Université Paul Sabatier Réceptologie et Ciblage Thérapeutique en Cancérologie, INSERM, Toulouse, France, and
| | - David D Schlaepfer
- the Université Paul Sabatier Réceptologie et Ciblage Thérapeutique en Cancérologie, INSERM, Toulouse, France, and
| | - Véronique Gigoux
- the Moores Cancer Center, University of California at San Diego, La Jolla, California 92093
| | - Anna M Aragay
- From the Molecular Biology Institute of Barcelona, Spanish National Research Council (CSIC), 08028 Barcelona, Spain,
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Affiliation(s)
- S Peláez-Dominguez
- Department of Internal Medicine, Hospital General Básico de la Axarquía, Velez-Malaga, Spain
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Martín-Rico P, Martínez-Rubio C, Pérez-Benito L, Sanz-Moreno J. [Subacute bacterial endocarditis caused by Cardiobacterium hominis]. Enferm Infecc Microbiol Clin 1990; 8:186. [PMID: 2094394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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