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Hanessian S. My 50-Plus Years of Academic Research Collaborations with Industry. A Retrospective. J Org Chem 2024; 89:9147-9186. [PMID: 38865159 DOI: 10.1021/acs.joc.4c00652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
A retrospective is presented highlighting the synthesis of selected "first-in-kind" natural products, their synthetic analogues, structure elucidations, and rationally designed bioactive synthetic compounds that were accomplished because of collaborations with past and present pharmaceutical and agrochemical companies. Medicinal chemistry projects involving structure-based design exploiting cocrystal structures of small molecules with biologically relevant enzymes, receptors, and bacterial ribosomes with synthetic small molecules leading to marketed products, clinical candidates, and novel drug prototypes were realized in collaboration. Personal reflections, historical insights, behind the scenes stories from various long-term projects are shared in this retrospective article.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, P.O. Box 6128, Succ. Centre-ville, Montréal, Québec, Canada H3C 3J7
- Department of Pharmaceutical Sciences, University of California, Irvine, California 91266, United States
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2
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Perrone S, Messa F, Troisi L, Salomone A. N-, O- and S-Heterocycles Synthesis in Deep Eutectic Solvents. Molecules 2023; 28:molecules28083459. [PMID: 37110694 PMCID: PMC10142562 DOI: 10.3390/molecules28083459] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/09/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The synthesis of heterocycles is a fundamental area of organic chemistry that offers enormous potential for the discovery of new products with important applications in our daily life such as pharmaceuticals, agrochemicals, flavors, dyes, and, more generally, engineered materials with innovative properties. As heterocyclic compounds find application across multiple industries and are prepared in very large quantities, the development of sustainable approaches for their synthesis has become a crucial objective for contemporary green chemistry committed to reducing the environmental impact of chemical processes. In this context, the present review focuses on the recent methodologies aimed at preparing N-, O- and S-heterocyclic compounds in Deep Eutectic Solvents, a new class of ionic solvents that are non-volatile, non-toxic, easy to prepare, easy to recycle, and can be obtained from renewable sources. Emphasis has been placed on those processes that prioritize the recycling of catalyst and solvent, as they offer the dual benefit of promoting synthetic efficiency while demonstrating environmental responsibility.
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Affiliation(s)
- Serena Perrone
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Prov.le Lecce-Monteroni, I-73100 Lecce, Italy
| | - Francesco Messa
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Prov.le Lecce-Monteroni, I-73100 Lecce, Italy
| | - Luigino Troisi
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, Prov.le Lecce-Monteroni, I-73100 Lecce, Italy
| | - Antonio Salomone
- Dipartimento di Chimica, Consorzio C.I.N.M.P.I.S., Università degli Studi di Bari "Aldo Moro", Via E. Orabona 4, I-70125 Bari, Italy
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3
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Meixner M, Zachmann M, Metzler S, Scheerer J, Zacharias M, Antes I. Dynamic Docking of Macrocycles in Bound and Unbound Protein Structures with DynaDock. J Chem Inf Model 2022; 62:3426-3441. [PMID: 35796228 DOI: 10.1021/acs.jcim.2c00436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Macrocycles are interesting molecules with unique features due to their conformationally constrained yet flexible ring structure. This characteristic poses a difficult challenge for computational modeling studies since they rely on accurate structural descriptions. In particular, molecular docking calculations suffer from the lack of ring flexibility during pose generation, which is often compensated by using pregenerated ligand conformer ensembles. Moreover, receptor structures are mainly treated rigidly, which limits the use of many docking tools. In this study, we optimized our previous molecular dynamics-based sampling and docking pipeline specifically designed for the accurate prediction of macrocyclic compounds. We developed a dihedral classification procedure for in-depth conformational analysis of the macrocyclic rings and extracted structural ensembles that were subsequently docked in both bound and unbound protein structures employing a fully flexible approach. Our results suggest that including a ring conformer close to the bound state in the starting ensemble increases the chance of successful docking. The bioactive conformations of a diverse set of ligands could be predicted with high and decent accuracy in bound and unbound protein structures, respectively, due to the incorporation of full molecular flexibility in our approach. The remaining unsuccessful docking calculations were mainly caused by large flexible substituents that bind to surface-exposed binding sites, rather than the macrocyclic ring per se and could be further improved by explicit molecular dynamics simulations of the docked complex.
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Affiliation(s)
- Maximilian Meixner
- TUM School of Life Sciences, Technical University Munich, Am Staudengarten 2, Freising 85354, Germany
| | - Martin Zachmann
- TUM School of Life Sciences, Technical University Munich, Am Staudengarten 2, Freising 85354, Germany
| | - Sebastian Metzler
- TUM School of Life Sciences, Technical University Munich, Am Staudengarten 2, Freising 85354, Germany
| | - Jonathan Scheerer
- TUM School of Life Sciences, Technical University Munich, Am Staudengarten 2, Freising 85354, Germany
| | - Martin Zacharias
- Center of Functional Protein Assemblies, Technical University Munich, Ernst-Otto-Fischer-Straße 8, Garching bei München 85748, Germany
| | - Iris Antes
- TUM School of Life Sciences, Technical University Munich, Am Staudengarten 2, Freising 85354, Germany
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4
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Zivanovic S, Colizzi F, Moreno D, Hospital A, Soliva R, Orozco M. Exploring the Conformational Landscape of Bioactive Small Molecules. J Chem Theory Comput 2020; 16:6575-6585. [DOI: 10.1021/acs.jctc.0c00304] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Sanja Zivanovic
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Francesco Colizzi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - David Moreno
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Robert Soliva
- Nostrum Biodiscovery, Nexus II Building, 08034 Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Baldiri Reixac, 10, 08028 Barcelona, Spain
- Departament de Bioquímica i Biomedicina, Facultat de Biologia, Universitat de Barcelona, E08028 Barcelona, Spain
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5
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Van Lam van T, Ivanova T, Hardes K, Heindl MR, Morty RE, Böttcher-Friebertshäuser E, Lindberg I, Than ME, Dahms SO, Steinmetzer T. Design, Synthesis, and Characterization of Macrocyclic Inhibitors of the Proprotein Convertase Furin. ChemMedChem 2019; 14:673-685. [PMID: 30680958 DOI: 10.1002/cmdc.201800807] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/18/2019] [Indexed: 12/20/2022]
Abstract
The activation of viral glycoproteins by the host protease furin is an essential step in the replication of numerous pathogenic viruses. Thus, effective inhibitors of furin could serve as broad-spectrum antiviral drugs. A crystal structure of an inhibitory hexapeptide derivative in complex with furin served as template for the rational design of various types of new cyclic inhibitors. Most of the prepared derivatives are relatively potent furin inhibitors with inhibition constants in the low nanomolar or even sub-nanomolar range. For seven derivatives the crystal structures in complex with furin could be determined. In three complexes, electron density was found for the entire inhibitor. In the other cases the structures could be determined only for the P6/P5-P1 segments, which directly interact with furin. The cyclic derivatives together with two non-cyclic reference compounds were tested as inhibitors of the proteolytic activation and replication of respiratory syncytial virus in cells. Significant antiviral activity was found for both linear reference inhibitors, whereas a negligible efficacy was determined for the cyclic derivatives.
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Affiliation(s)
- Thuy Van Lam van
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032, Marburg, Germany
| | - Teodora Ivanova
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032, Marburg, Germany
| | - Kornelia Hardes
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032, Marburg, Germany
| | - Miriam Ruth Heindl
- Institute of Virology, Philipps University, Hans-Meerwein-Str. 2, 35043, Marburg, Germany
| | - Rory E Morty
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | | | - Iris Lindberg
- Department of Anatomy and Neurobiology, University of Maryland Medical School, Baltimore, MD, 21201, USA
| | - Manuel E Than
- Protein Crystallography Group, Leibniz Institute on Aging-Fritz Lipmann Institute, Beutenbergstr. 11, 07745, Jena, Germany
| | - Sven O Dahms
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, 35032, Marburg, Germany
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Al-Horani RA, Afosah DK. Recent advances in the discovery and development of factor XI/XIa inhibitors. Med Res Rev 2018; 38:1974-2023. [PMID: 29727017 PMCID: PMC6173998 DOI: 10.1002/med.21503] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 03/09/2018] [Accepted: 04/04/2018] [Indexed: 12/12/2022]
Abstract
Factor XIa (FXIa) is a serine protease homodimer that belongs to the intrinsic coagulation pathway. FXIa primarily catalyzes factor IX activation to factor IXa, which subsequently activates factor X to factor Xa in the common coagulation pathway. Growing evidence suggests that FXIa plays an important role in thrombosis with a relatively limited contribution to hemostasis. Therefore, inhibitors targeting factor XI (FXI)/FXIa system have emerged as a paradigm-shifting strategy so as to develop a new generation of anticoagulants to effectively prevent and/or treat thromboembolic diseases without the life-threatening risk of internal bleeding. Several inhibitors of FXI/FXIa proteins have been discovered or designed over the last decade including polypeptides, active site peptidomimetic inhibitors, allosteric inhibitors, antibodies, and aptamers. Antisense oligonucleotides (ASOs), which ultimately reduce the hepatic biosynthesis of FXI, have also been introduced. A phase II study, which included patients undergoing elective primary unilateral total knee arthroplasty, revealed that a specific FXI ASO effectively protects patients against venous thrombosis with a relatively limited risk of bleeding. Initial findings have also demonstrated the potential of FXI/FXIa inhibitors in sepsis, listeriosis, and arterial hypertension. This review highlights various chemical, biochemical, and pharmacological aspects of FXI/FXIa inhibitors with the goal of advancing their development toward clinical use.
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Affiliation(s)
- Rami A. Al-Horani
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, Louisiana 70125
| | - Daniel K. Afosah
- Department of Medicinal Chemistry and Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219
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7
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Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 332] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
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Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
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8
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Perrone S, Capua M, Messa F, Salomone A, Troisi L. Green synthesis of 2-pyrazinones in deep eutectic solvents: From α-chloro oximes to peptidomimetic scaffolds. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Corte JR, Fang T, Osuna H, Pinto DJP, Rossi KA, Myers JE, Sheriff S, Lou Z, Zheng JJ, Harper TW, Bozarth JM, Wu Y, Luettgen JM, Seiffert DA, Decicco CP, Wexler RR, Quan ML. Structure-Based Design of Macrocyclic Factor XIa Inhibitors: Discovery of the Macrocyclic Amide Linker. J Med Chem 2017; 60:1060-1075. [DOI: 10.1021/acs.jmedchem.6b01460] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- James R. Corte
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Tianan Fang
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Honey Osuna
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Donald J. P. Pinto
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Karen A. Rossi
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Joseph E. Myers
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Steven Sheriff
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Zhen Lou
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Joanna J. Zheng
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Timothy W. Harper
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Jeffrey M. Bozarth
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Yiming Wu
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Joseph M. Luettgen
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Dietmar A. Seiffert
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Carl P. Decicco
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Ruth R. Wexler
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
| | - Mimi L. Quan
- Research and Development, Bristol-Myers Squibb Company, P.O. Box
5400, Princeton, New Jersey 08543, United States
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10
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Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy. Sci Rep 2016; 6:31488. [PMID: 27507430 PMCID: PMC4979035 DOI: 10.1038/srep31488] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 07/19/2016] [Indexed: 01/17/2023] Open
Abstract
Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derived polarized protein-specific charge (PPC). The PPC includes the electronic polarization effect of the thrombin-ligand complex, which is absent in the standard force field. A detailed analysis and comparison of the results of the MD simulation with experimental data provided strong evidence that intra-protein, protein-ligand hydrogen bonds and the root-mean-square deviation of backbone atoms were significantly stabilized through electronic polarization. Specifically, two critical hydrogen bonds between thrombin and the ligand were broken at approximately 190 ns when AMBER force field was used and the number of intra-protein backbone hydrogen bonds was higher under PPC than under AMBER. The thrombin-ligand binding energy was computed using the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method, and the results were consistent with the experimental value obtained using PPC. Because hydrogen bonds were unstable, it was failed to predict the binding affinity under the AMBER force field. Furthermore, the results of the present study revealed that differences in the binding free energy between AMBER and PPC almost comes from the electrostatic interaction. Thus, this study provides evidence that protein polarization is critical to accurately describe protein-ligand binding.
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11
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Knight JL, Krilov G, Borrelli KW, Williams J, Gunn JR, Clowes A, Cheng L, Friesner RA, Abel R. Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods. J Chem Theory Comput 2015; 10:3207-20. [PMID: 26588291 DOI: 10.1021/ct500189s] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Accurate and efficient affinity calculations are critical to enhancing the contribution of in silico modeling during the lead optimization phase of a drug discovery campaign. Here, we present a large-scale study of the efficacy of data fusion strategies to leverage results from end-point MM/GBSA calculations in multiple receptors to identify potent inhibitors among an ensemble of congeneric ligands. The retrospective analysis of 13 congeneric ligand series curated from publicly available data across seven biological targets demonstrates that in 90% of the individual receptor structures MM/GBSA scores successfully identify subsets of inhibitors that are more potent than a random selection, and data fusion strategies that combine MM/GBSA scores from each of the receptors significantly increase the robustness of the predictions. Among nine different data fusion metrics based on consensus scores or receptor rankings, the SumZScore (i.e., converting MM/GBSA scores into standardized Z-Scores within a receptor and computing the sum of the Z-Scores for a given ligand across the ensemble of receptors) is found to be a robust and physically meaningful metric for combining results across multiple receptors. Perhaps most surprisingly, even with relatively low to modest overall correlations between SumZScore and experimental binding affinities, SumZScore tends to reliably prioritize subsets of inhibitors that are at least as potent as those that are prioritized from a "best" single receptor identified from known compounds within the congeneric series.
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Affiliation(s)
- Jennifer L Knight
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Goran Krilov
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Kenneth W Borrelli
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Joshua Williams
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - John R Gunn
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Alec Clowes
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Luciano Cheng
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Richard A Friesner
- Columbia University , Department of Chemistry, 3000 Broadway, MC 3110, New York, New York 10027, United States
| | - Robert Abel
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
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12
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Hussain A, Yousuf SK, Mukherjee D. Importance and synthesis of benzannulated medium-sized and macrocyclic rings (BMRs). RSC Adv 2014. [DOI: 10.1039/c4ra07434c] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Cyclic molecular frameworks, especially the benzannulated medium-sized and macrocyclic ring (BMR) systems, constitute an integral component of a large number of biologically significant natural or synthetic molecules.
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Affiliation(s)
- Altaf Hussain
- Acedemy of Scientific and Innovative Research (AcSIR)
- New Delhi, India
- Indian Institute of Integrative Medicine (CSIR-IIIM)
- , India
| | - S. K. Yousuf
- Indian Institute of Integrative Medicine (CSIR-IIIM)
- , India
| | - Debaraj Mukherjee
- Acedemy of Scientific and Innovative Research (AcSIR)
- New Delhi, India
- Indian Institute of Integrative Medicine (CSIR-IIIM)
- , India
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13
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Marsault E, Peterson ML. Macrocycles Are Great Cycles: Applications, Opportunities, and Challenges of Synthetic Macrocycles in Drug Discovery. J Med Chem 2011; 54:1961-2004. [DOI: 10.1021/jm1012374] [Citation(s) in RCA: 591] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Eric Marsault
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke Québec, J1H5N4, Canada
| | - Mark L. Peterson
- Tranzyme Pharma Inc., 3001 12e Avenue Nord, Sherbrooke, Québec, J1H5N4, Canada
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14
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Hanessian S, Larsson A, Fex T, Knecht W, Blomberg N. Design and synthesis of macrocyclic indoles targeting blood coagulation cascade Factor XIa. Bioorg Med Chem Lett 2010; 20:6925-8. [DOI: 10.1016/j.bmcl.2010.09.141] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 09/27/2010] [Accepted: 09/28/2010] [Indexed: 11/27/2022]
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15
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Jing YQ, Han KL. Quantum mechanical effect in protein–ligand interaction. Expert Opin Drug Discov 2009; 5:33-49. [DOI: 10.1517/17460440903440127] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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16
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Marsault E, Hoveyda HR, Gagnon R, Peterson ML, Vézina M, Saint-Louis C, Landry A, Pinault JF, Ouellet L, Beauchemin S, Beaubien S, Mathieu A, Benakli K, Wang Z, Brassard M, Lonergan D, Bilodeau F, Ramaseshan M, Fortin N, Lan R, Li S, Galaud F, Plourde V, Champagne M, Doucet A, Bhérer P, Gauthier M, Olsen G, Villeneuve G, Bhat S, Foucher L, Fortin D, Peng X, Bernard S, Drouin A, Déziel R, Berthiaume G, Dory YL, Fraser GL, Deslongchamps P. Efficient parallel synthesis of macrocyclic peptidomimetics. Bioorg Med Chem Lett 2008; 18:4731-5. [PMID: 18640834 DOI: 10.1016/j.bmcl.2008.06.085] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 06/25/2008] [Accepted: 06/25/2008] [Indexed: 10/21/2022]
Abstract
A new method for solid phase parallel synthesis of chemically and conformationally diverse macrocyclic peptidomimetics is reported. A key feature of the method is access to broad chemical and conformational diversity. Synthesis and mechanistic studies on the macrocyclization step are reported.
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Affiliation(s)
- Eric Marsault
- Tranzyme Pharma Inc. 3001, 12e av. Nord, Sherbrooke, Que., Canada J1H5N4.
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17
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Wu EL, Mei Y, Han K, Zhang JZH. Quantum and molecular dynamics study for binding of macrocyclic inhibitors to human alpha-thrombin. Biophys J 2007; 92:4244-53. [PMID: 17384076 PMCID: PMC1877793 DOI: 10.1529/biophysj.106.099150] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2006] [Accepted: 02/12/2007] [Indexed: 11/18/2022] Open
Abstract
Molecular dynamics simulations followed by quantum mechanical calculation and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) analysis have been carried out to study binding of proline- and pyrazinone-based macrocyclic inhibitors (L86 and T76) to human alpha-thrombin. Detailed binding interaction energies between these inhibitors and individual protein fragments are calculated using DFT method based on a new quantum mechanical approach for computing protein-ligand interaction energy. The analysis of detailed interaction energies provides insight on the protein-ligand binding mechanism. Study shows that T76 and L86 bind to thrombin in a very similar "inhibition mode" except that T76 has relatively weaker binding interaction with Glu(217). The analysis from quantum calculation of binding interaction is consistent with the MM-PBSA calculation of binding free energy, and the calculated free energies for L86/T76-thrombin binding agree well with the experimental data.
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Affiliation(s)
- Emilia L Wu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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Larhed M, Wannberg J, Hallberg A. Controlled Microwave Heating as an Enabling Technology: Expedient Synthesis of Protease Inhibitors in Perspective. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/qsar.200620028] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Kinoshita T, Kitatani T, Warizaya M, Tada T. Structure of the complex of porcine pancreatic elastase with a trimacrocyclic peptide inhibitor FR901451. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:808-11. [PMID: 16511165 PMCID: PMC1978120 DOI: 10.1107/s1744309105026047] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Accepted: 08/16/2005] [Indexed: 11/10/2022]
Abstract
Porcine pancreatic elastase (PPE) resembles the attractive drug target leukocyte elastase, which has the ability to degrade connective tissue in the body. The crystal structure of PPE complexed with a novel trimacrocyclic peptide inhibitor, FR901451, was solved at 1.9 A resolution. The inhibitor occupied the subsites S3 through S3' of PPE and induced conformational changes in the side chains of Arg64 and Arg226, which are located at the edges of the substrate-binding cleft. Structural comparison of five PPE-inhibitor complexes, including the FR901451 complex and non-ligated PPE, reveals that the residues forming the S2, S1, S1' and S2' subsites in the cleft are rigid, but the two arginine residues playing a part in the S3 and S3' subsites are flexible. Structural comparison of PPE with human leukocyte elastase (HLE) implies that the inhibitor binds to HLE in a similar manner to the FR901451-PPE complex. This structural insight may help in the design of potent elastase inhibitors.
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Affiliation(s)
- Takayoshi Kinoshita
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Gakuen-cho 1-1, Sakai, Osaka 599-8531, Japan
| | - Tomoya Kitatani
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Gakuen-cho 1-1, Sakai, Osaka 599-8531, Japan
| | - Masaichi Warizaya
- Lead Generation Research Laboratory, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan
| | - Toshiji Tada
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Gakuen-cho 1-1, Sakai, Osaka 599-8531, Japan
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Azzam R, De Borggraeve WM, Compernolle F, Hoornaert GJ. Expanding the substitution pattern of 2(1H)-pyrazinones via Suzuki and Heck reactions. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.02.056] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Miles SM, Leatherbarrow RJ, Marsden SP, Coates WJ. Synthesis and bio-assay of RCM-derived Bowman–Birk inhibitor analogues. Org Biomol Chem 2004; 2:281-3. [PMID: 14747852 DOI: 10.1039/b312908j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bowman-Birk inhibitor analogues containing 2, 3 and 4-carbon analogues of the natural disulfide were synthesised via solid phase microwave-assisted RCM and found to have K(i) values against chymotrypsin in the low to sub-micromolar range, the best replacement for the disulfide arising from the linkage by RCM of two l-homoallylglycine residues.
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Affiliation(s)
- Steven M Miles
- Department of Chemistry, Imperial College London, South Kensington Campus, London, UKSW7 2AZ
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