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Guareschi R, Lukac I, Gilbert IH, Zuccotto F. SophosQM: Accurate Binding Affinity Prediction in Compound Optimization. ACS Omega 2023; 8:15083-15098. [PMID: 37151542 PMCID: PMC10157843 DOI: 10.1021/acsomega.2c08132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/07/2023] [Indexed: 05/09/2023]
Abstract
The optimization of compounds' binding affinity for a biological target is a crucial aspect of the drug development process. Being able to accurately predict binding energies in advance of synthesizing compounds would have a massive impact on the speed of the drug discovery process. The ideal binding affinity prediction method should combine accuracy, reliability, and speed. In this paper, we present SophosQM, a quantum mechanics (QM)-based approach, which can accurately predict the binding affinities of compounds to proteins. The binding affinity predictive models generated by SophosQM are based on the fragment molecular orbital (FMO) method to estimate the enthalpic component of the binding free energy, and a macroscopic descriptor, clog P, is used as an approximation of the entropic component. The affinity prediction is performed using multilinear regression, fitting the experimental values against the FMO-computed enthalpic term and clog P. The quality of the prediction can be assessed in terms of the correlation coefficient between experimental and predicted values. In this work, the method's reliability and accuracy are exemplified by applying SophosQM to 70 compounds binding to six different targets of pharmaceutical relevance. Overall, the results show a very satisfactory performance with a global correlation coefficient in the order of 0.9. Our predictions also show a satisfactory performance compared to data based on free energy perturbation. Finally, SophosQM can also be applied in high-throughput mode by using semiempirical QM methods to evaluate large portions of chemical space, while retaining a good level of accuracy, but decreasing the computing time to just a few seconds per compound.
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Korn P, Classen A, Murthy S, Guareschi R, Maksimainen MM, Lippok BE, Galera‐Prat A, Sowa ST, Voigt C, Rossetti G, Lehtiö L, Bolm C, Lüscher B. Evaluation of 3- and 4-Phenoxybenzamides as Selective Inhibitors of the Mono-ADP-Ribosyltransferase PARP10. ChemistryOpen 2021; 10:939-948. [PMID: 34145784 PMCID: PMC8485830 DOI: 10.1002/open.202100087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/30/2021] [Indexed: 02/03/2023] Open
Abstract
Intracellular ADP-ribosyltransferases catalyze mono- and poly-ADP-ribosylation and affect a broad range of biological processes. The mono-ADP-ribosyltransferase PARP10 is involved in signaling and DNA repair. Previous studies identified OUL35 as a selective, cell permeable inhibitor of PARP10. We have further explored the chemical space of OUL35 by synthesizing and investigating structurally related analogs. Key synthetic steps were metal-catalyzed cross-couplings and functional group modifications. We identified 4-(4-cyanophenoxy)benzamide and 3-(4-carbamoylphenoxy)benzamide as PARP10 inhibitors with distinct selectivities. Both compounds were cell permeable and interfered with PARP10 toxicity. Moreover, both revealed some inhibition of PARP2 but not PARP1, unlike clinically used PARP inhibitors, which typically inhibit both enzymes. Using crystallography and molecular modeling the binding of the compounds to different ADP-ribosyltransferases was explored regarding selectivity. Together, these studies define additional compounds that interfere with PARP10 function and thus expand our repertoire of inhibitors to further optimize selectivity and potency.
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Affiliation(s)
- Patricia Korn
- Institute of Biochemistry and Molecular BiologyMedical FacultyRWTH Aachen UniversityPauwelsstrasse 3052074AachenGermany
| | - Arno Classen
- Institute of Organic ChemistryRWTH Aachen UniversityLandoltweg 152056AachenGermany
| | - Sudarshan Murthy
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuloUniversity of OuluPentti Kaiteran katu 190014OuluFinland
| | - Riccardo Guareschi
- Institute for Advanced Simulation (IAS-5)/Institute of Neuroscience and Medicine (INM-9)Jülich Supercomputing Centre (JSC)Forschungszentrum JülichWilhelm-Johnen-Strasse52425JülichGermany
| | - Mirko M. Maksimainen
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuloUniversity of OuluPentti Kaiteran katu 190014OuluFinland
| | - Barbara E. Lippok
- Institute of Biochemistry and Molecular BiologyMedical FacultyRWTH Aachen UniversityPauwelsstrasse 3052074AachenGermany
| | - Albert Galera‐Prat
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuloUniversity of OuluPentti Kaiteran katu 190014OuluFinland
| | - Sven T. Sowa
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuloUniversity of OuluPentti Kaiteran katu 190014OuluFinland
| | - Catharina Voigt
- Institute of Biochemistry and Molecular BiologyMedical FacultyRWTH Aachen UniversityPauwelsstrasse 3052074AachenGermany
| | - Giulia Rossetti
- Institute for Advanced Simulation (IAS-5)/Institute of Neuroscience and Medicine (INM-9)Jülich Supercomputing Centre (JSC)Forschungszentrum JülichWilhelm-Johnen-Strasse52425JülichGermany
- Juelich Supercomputing Center (JSC)Forschungszentrum JülichWilhelm-Johnen-Strasse52425JülichGermany
- Department of Oncology, Hematology and Stem Cell TransplantationMedical FacultyRWTH Aachen UniversityPauwelsstrasse 3052074AachenGermany
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuloUniversity of OuluPentti Kaiteran katu 190014OuluFinland
| | - Carsten Bolm
- Institute of Organic ChemistryRWTH Aachen UniversityLandoltweg 152056AachenGermany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular BiologyMedical FacultyRWTH Aachen UniversityPauwelsstrasse 3052074AachenGermany
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Korn P, Classen A, Murthy S, Guareschi R, Maksimainen MM, Lippok BE, Galera‐Prat A, Sowa ST, Voigt C, Rossetti G, Lehtiö L, Bolm C, Lüscher B. Cover Feature: Evaluation of 3‐ and 4‐Phenoxybenzamides as Selective Inhibitors of the Mono‐ADP‐Ribosyltransferase PARP10 (ChemistryOpen 10/2021). Chemistry 2021. [DOI: 10.1002/open.202100215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Patricia Korn
- Institute of Biochemistry and Molecular Biology Medical Faculty RWTH Aachen University Pauwelsstrasse 30 52074 Aachen Germany
| | - Arno Classen
- Institute of Organic Chemistry RWTH Aachen University Landoltweg 1 52056 Aachen Germany
| | - Sudarshan Murthy
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulo University of Oulu Pentti Kaiteran katu 1 90014 Oulu Finland
| | - Riccardo Guareschi
- Institute for Advanced Simulation (IAS-5)/Institute of Neuroscience and Medicine (INM-9) Jülich Supercomputing Centre (JSC) Forschungszentrum Jülich Wilhelm-Johnen-Strasse 52425 Jülich Germany
| | - Mirko M. Maksimainen
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulo University of Oulu Pentti Kaiteran katu 1 90014 Oulu Finland
| | - Barbara E. Lippok
- Institute of Biochemistry and Molecular Biology Medical Faculty RWTH Aachen University Pauwelsstrasse 30 52074 Aachen Germany
| | - Albert Galera‐Prat
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulo University of Oulu Pentti Kaiteran katu 1 90014 Oulu Finland
| | - Sven T. Sowa
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulo University of Oulu Pentti Kaiteran katu 1 90014 Oulu Finland
| | - Catharina Voigt
- Institute of Biochemistry and Molecular Biology Medical Faculty RWTH Aachen University Pauwelsstrasse 30 52074 Aachen Germany
| | - Giulia Rossetti
- Institute for Advanced Simulation (IAS-5)/Institute of Neuroscience and Medicine (INM-9) Jülich Supercomputing Centre (JSC) Forschungszentrum Jülich Wilhelm-Johnen-Strasse 52425 Jülich Germany
- Juelich Supercomputing Center (JSC) Forschungszentrum Jülich Wilhelm-Johnen-Strasse 52425 Jülich Germany
- Department of Oncology, Hematology and Stem Cell Transplantation Medical Faculty RWTH Aachen University Pauwelsstrasse 30 52074 Aachen Germany
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulo University of Oulu Pentti Kaiteran katu 1 90014 Oulu Finland
| | - Carsten Bolm
- Institute of Organic Chemistry RWTH Aachen University Landoltweg 1 52056 Aachen Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology Medical Faculty RWTH Aachen University Pauwelsstrasse 30 52074 Aachen Germany
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Zeng J, Guareschi R, Damre M, Cao R, Kless A, Neumaier B, Bauer A, Giorgetti A, Carloni P, Rossetti G. Structural Prediction of the Dimeric Form of the Mammalian Translocator Membrane Protein TSPO: A Key Target for Brain Diagnostics. Int J Mol Sci 2018; 19:E2588. [PMID: 30200318 PMCID: PMC6165245 DOI: 10.3390/ijms19092588] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 08/21/2018] [Accepted: 08/28/2018] [Indexed: 11/17/2022] Open
Abstract
Positron emission tomography (PET) radioligands targeting the human translocator membrane protein (TSPO) are broadly used for the investigations of neuroinflammatory conditions associated with neurological disorders. Structural information on the mammalian protein homodimers-the suggested functional state of the protein-is limited to a solid-state nuclear magnetic resonance (NMR) study and to a model based on the previously-deposited solution NMR structure of the monomeric mouse protein. Computational studies performed here suggest that the NMR-solved structure in the presence of detergents is not prone to dimer formation and is furthermore unstable in its native membrane environment. We, therefore, propose a new model of the functionally-relevant dimeric form of the mouse protein, based on a prokaryotic homologue. The model, fully consistent with solid-state NMR data, is very different from the previous predictions. Hence, it provides, for the first time, structural insights into this pharmaceutically-important target which are fully consistent with experimental data.
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Affiliation(s)
- Juan Zeng
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, 518055 Shenzhen, China.
| | - Riccardo Guareschi
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
| | - Mangesh Damre
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
- Neurobiology, International School for Advanced Studies (SISSA), 34136 Trieste, Italy.
| | - Ruyin Cao
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
| | - Achim Kless
- Grünenthal Innovation, Translational Science & Intelligence, Grünenthal GmbH, 52078 Aachen, Germany.
| | - Bernd Neumaier
- Institute for Neuroscience and Medicine (INM)-5, Forschungszentrum Jülich, 52428 Jülich, Germany.
| | - Andreas Bauer
- Institute for Neuroscience and Medicine (INM)-2, Forschungszentrum Jülich, 52428 Jülich, Germany.
| | - Alejandro Giorgetti
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
| | - Paolo Carloni
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
- RWTH Aachen University, Department of Physics, 52078 Aachen, Germany.
| | - Giulia Rossetti
- Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.
- Jülich Supercomputing Center (JSC), Forschungszentrum Jülich, 52428 Jülich, Germany.
- University Hospital Aachen, RWTH Aachen University, 52078 Aachen, Germany.
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Guareschi R, Valsson O, Curutchet C, Mennucci B, Filippi C. Electrostatic versus Resonance Interactions in Photoreceptor Proteins: The Case of Rhodopsin. J Phys Chem Lett 2016; 7:4547-4553. [PMID: 27786481 DOI: 10.1021/acs.jpclett.6b02043] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Light sensing in photoreceptor proteins is subtly modulated by the multiple interactions between the chromophoric unit and its binding pocket. Many theoretical and experimental studies have tried to uncover the fundamental origin of these interactions but reached contradictory conclusions as to whether electrostatics, polarization, or intrinsically quantum effects prevail. Here, we select rhodopsin as a prototypical photoreceptor system to reveal the molecular mechanism underlying these interactions and regulating the spectral tuning. Combining a multireference perturbation method and density functional theory with a classical but atomistic and polarizable embedding scheme, we show that accounting for electrostatics only leads to a qualitatively wrong picture, while a responsive environment can successfully capture both the classical and quantum dominant effects. Several residues are found to tune the excitation by both differentially stabilizing ground and excited states and through nonclassical "inductive resonance" interactions. The results obtained with such a quantum-in-classical model are validated against both experimental data and fully quantum calculations.
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Affiliation(s)
- Riccardo Guareschi
- MESA+ Institute for Nanotechnology, University of Twente , P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Omar Valsson
- Department of Chemistry and Applied Bioscience, ETH Zurich and Facoltà di Informatica, Instituto di Scienze Computazionali, Università della Svizzera italiana , Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Carles Curutchet
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , Av. Joan XXIII, s/n 08028 Barcelona, Spain
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa , Via Giuseppe Moruzzi 13, 56124 Pisa, Italy
| | - Claudia Filippi
- MESA+ Institute for Nanotechnology, University of Twente , P.O. Box 217, 7500 AE Enschede, The Netherlands
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Guareschi R, Zulfikri H, Daday C, Floris FM, Amovilli C, Mennucci B, Filippi C. Introducing QMC/MMpol: Quantum Monte Carlo in Polarizable Force Fields for Excited States. J Chem Theory Comput 2016; 12:1674-83. [DOI: 10.1021/acs.jctc.6b00044] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Riccardo Guareschi
- MESA+
Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Habiburrahman Zulfikri
- MESA+
Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Csaba Daday
- MESA+
Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Franca Maria Floris
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe
Moruzzi 13, 56124 Pisa, Italy
| | - Claudio Amovilli
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe
Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe
Moruzzi 13, 56124 Pisa, Italy
| | - Claudia Filippi
- MESA+
Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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Guareschi R, Floris FM, Amovilli C, Filippi C. Solvent Effects on Excited-State Structures: A Quantum Monte Carlo and Density Functional Study. J Chem Theory Comput 2014; 10:5528-37. [DOI: 10.1021/ct500723s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Riccardo Guareschi
- MESA+
Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Franca Maria Floris
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe
Moruzzi 3, 56124 Pisa, Italy
| | - Claudio Amovilli
- Dipartimento
di Chimica e Chimica Industriale, Università di Pisa, Via Giuseppe
Moruzzi 3, 56124 Pisa, Italy
| | - Claudia Filippi
- MESA+
Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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Guareschi R, Filippi C. Ground- and Excited-State Geometry Optimization of Small Organic Molecules with Quantum Monte Carlo. J Chem Theory Comput 2013; 9:5513-25. [DOI: 10.1021/ct400876y] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Riccardo Guareschi
- MESA+ Institute for Nanotechnology, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - Claudia Filippi
- MESA+ Institute for Nanotechnology, University of Twente,
P.O. Box 217, 7500 AE Enschede, The Netherlands
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