1
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Martino SD, Petri GL, De Rosa M. Hepatitis C: The Story of a Long Journey through First, Second, and Third Generation NS3/4A Peptidomimetic Inhibitors. What Did We Learn? J Med Chem 2024; 67:885-921. [PMID: 38179950 DOI: 10.1021/acs.jmedchem.3c01971] [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: 01/06/2024]
Abstract
Hepatitis C viral (HCV) infection is the leading cause of liver failure and still represents a global health burden. Over the past decade, great advancements made HCV curable, and sustained viral remission significantly improved to more than 98%. Historical treatment with pegylated interferon alpha and ribavirin has been displaced by combinations of direct-acting antivirals. These regimens include drugs targeting different stages of the HCV life cycle. However, the emergence of viral resistance remains a big concern. The design of peptidomimetic inhibitors (PIs) able to fit and fill the conserved substrate envelope region within the active site helped avoid contact with the vulnerable sites of the most common resistance-associated substitutions Arg155, Ala156, and Asp168. Herein, we give an overview of HCV NS3 PIs discovered during the past decade, and we deeply discuss the rationale behind the structural optimization efforts essential to achieve pangenotypic activity.
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Affiliation(s)
- Simona Di Martino
- Drug Discovery Unit, Medicinal Chemistry Group, Ri.MED Foundation, Palermo 90133, Italy
| | - Giovanna Li Petri
- Drug Discovery Unit, Medicinal Chemistry Group, Ri.MED Foundation, Palermo 90133, Italy
| | - Maria De Rosa
- Drug Discovery Unit, Medicinal Chemistry Group, Ri.MED Foundation, Palermo 90133, Italy
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2
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Janin YL. On the origins of SARS-CoV-2 main protease inhibitors. RSC Med Chem 2024; 15:81-118. [PMID: 38283212 PMCID: PMC10809347 DOI: 10.1039/d3md00493g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024] Open
Abstract
In order to address the world-wide health challenge caused by the COVID-19 pandemic, the 3CL protease/SARS-CoV-2 main protease (SARS-CoV-2-Mpro) coded by its nsp5 gene became one of the biochemical targets for the design of antiviral drugs. In less than 3 years of research, 4 inhibitors of SARS-CoV-2-Mpro have actually been authorized for COVID-19 treatment (nirmatrelvir, ensitrelvir, leritrelvir and simnotrelvir) and more such as EDP-235, FB-2001 and STI-1558/Olgotrelvir or five undisclosed compounds (CDI-988, ASC11, ALG-097558, QLS1128 and H-10517) are undergoing clinical trials. This review is an attempt to picture this quite unprecedented medicinal chemistry feat and provide insights on how these cysteine protease inhibitors were discovered. Since many series of covalent SARS-CoV-2-Mpro inhibitors owe some of their origins to previous work on other proteases, we first provided a description of various inhibitors of cysteine-bearing human caspase-1 or cathepsin K, as well as inhibitors of serine proteases such as human dipeptidyl peptidase-4 or the hepatitis C protein complex NS3/4A. This is then followed by a description of the results of the approaches adopted (repurposing, structure-based and high throughput screening) to discover coronavirus main protease inhibitors.
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Affiliation(s)
- Yves L Janin
- Structure et Instabilité des Génomes (StrInG), Muséum National d'Histoire Naturelle, INSERM, CNRS, Alliance Sorbonne Université 75005 Paris France
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3
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Garbini M, Brunetti A, Pedrazzani R, Monari M, Marcaccio M, Bertuzzi G, Bandini M. Reductive cyclodimerization of chalcones: exploring the "self-adaptability" of galvanostatic electrosynthesis. Chem Commun (Camb) 2024; 60:404-407. [PMID: 38084060 DOI: 10.1039/d3cc04920e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The "self-adaptability" of galvanostatic electrolysis was shown to assist a multistage unprecedented chemo- and diastereoselective electrochemically promoted cyclodimerization of chalcones. The process, all involving the reductive events, delivered densely functionalized cyclopentanes featuring five contiguous stereocenters (25 examples, yields of up to 95%, dr values up to >20 : 1). Dedicated and combined experimental as well as electrochemical investigation revealed the key role of a dynamic kinetic resolution of the aldol intermediate for the reaction mechanism.
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Affiliation(s)
- Mauro Garbini
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via P. Gobetti 85, 40129, Bologna, Italy.
| | - Andrea Brunetti
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via P. Gobetti 85, 40129, Bologna, Italy.
- Center for Chemical Catalysis - C3, Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via P. Gobetti 85, 40129, Bologna, Italy
| | - Riccardo Pedrazzani
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via P. Gobetti 85, 40129, Bologna, Italy.
- Center for Chemical Catalysis - C3, Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via P. Gobetti 85, 40129, Bologna, Italy
| | - Magda Monari
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via P. Gobetti 85, 40129, Bologna, Italy.
- Center for Chemical Catalysis - C3, Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via P. Gobetti 85, 40129, Bologna, Italy
| | - Massimo Marcaccio
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via P. Gobetti 85, 40129, Bologna, Italy.
- Center for Chemical Catalysis - C3, Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via P. Gobetti 85, 40129, Bologna, Italy
| | - Giulio Bertuzzi
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via P. Gobetti 85, 40129, Bologna, Italy.
- Center for Chemical Catalysis - C3, Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via P. Gobetti 85, 40129, Bologna, Italy
| | - Marco Bandini
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via P. Gobetti 85, 40129, Bologna, Italy.
- Center for Chemical Catalysis - C3, Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via P. Gobetti 85, 40129, Bologna, Italy
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4
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Choi K. The Structure-property Relationships of Clinically Approved Protease Inhibitors. Curr Med Chem 2024; 31:1441-1463. [PMID: 37031455 DOI: 10.2174/0929867330666230409232655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/17/2023] [Accepted: 02/24/2023] [Indexed: 04/11/2023]
Abstract
BACKGROUND Proteases play important roles in the regulation of many physiological processes, and protease inhibitors have become one of the important drug classes. Especially because the development of protease inhibitors often starts from a substrate- based peptidomimetic strategy, many of the initial lead compounds suffer from pharmacokinetic liabilities. OBJECTIVE To reduce drug attrition rates, drug metabolism and pharmacokinetics studies are fully integrated into modern drug discovery research, and the structure-property relationship illustrates how the modification of the chemical structure influences the pharmacokinetic and toxicological properties of drug compounds. Understanding the structure- property relationships of clinically approved protease inhibitor drugs and their analogues could provide useful information on the lead-to-candidate optimization strategies. METHODS About 70 inhibitors against human or pathogenic viral proteases have been approved until the end of 2021. In this review, 17 inhibitors are chosen for the structure- property relationship analysis because detailed pharmacological and/or physicochemical data have been disclosed in the medicinal chemistry literature for these inhibitors and their close analogues. RESULTS The compiled data are analyzed primarily focusing on the pharmacokinetic or toxicological deficiencies found in lead compounds and the structural modification strategies used to generate candidate compounds. CONCLUSION The structure-property relationships hereby summarized how the overall druglike properties could be successfully improved by modifying the structure of protease inhibitors. These specific examples are expected to serve as useful references and guidance for developing new protease inhibitor drugs in the future.
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Affiliation(s)
- Kihang Choi
- Department of Chemistry, Korea University, Seoul, 02841, Korea (ROK)
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5
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Danelius E, Bu G, Wieske LHE, Gonen T. MicroED as a Powerful Tool for Structure Determination of Macrocyclic Drug Compounds Directly from Their Powder Formulations. ACS Chem Biol 2023; 18:2582-2589. [PMID: 37944119 PMCID: PMC10728894 DOI: 10.1021/acschembio.3c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Macrocycles are important drug leads with many advantages including the ability to target flat and featureless binding sites as well as to act as molecular chameleons and thereby reach intracellular targets. However, due to their complex structures and inherent flexibility, macrocycles are difficult to study structurally, and there are limited structural data available. Herein, we use the cryo-EM method MicroED to determine the novel atomic structures of several macrocycles that have previously resisted structural determination. We show that structures of similar complexity can now be obtained rapidly from nanograms of material and that different conformations of flexible compounds can be derived from the same experiment. These results will have an impact on contemporary drug discovery as well as natural product exploration.
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Affiliation(s)
- Emma Danelius
- Howard
Hughes Medical Institute, University of
California Los Angeles, Los Angeles, California 90095, United States
- Department
of Biological Chemistry, University of California
Los Angeles, 615 Charles E.Young Drive South, Los Angeles, California 90095, United States
| | - Guanhong Bu
- Department
of Biological Chemistry, University of California
Los Angeles, 615 Charles E.Young Drive South, Los Angeles, California 90095, United States
| | - Lianne H. E. Wieske
- Department
of Chemistry − BMC, Uppsala University, Husargatan 3, 75237 Uppsala, Sweden
| | - Tamir Gonen
- Howard
Hughes Medical Institute, University of
California Los Angeles, Los Angeles, California 90095, United States
- Department
of Biological Chemistry, University of California
Los Angeles, 615 Charles E.Young Drive South, Los Angeles, California 90095, United States
- Department
of Physiology, University of California
Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
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6
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Xun SS, Wang H, Yu CB, Lu SM, Zhou YG. Diarylborinic Acid-Catalyzed Ring Opening of cis-4-Hydroxymethyl-1,2-Cyclopentene Oxides: Synthesis of 1,2,4-Trisubstituted Cyclopentanes. Org Lett 2023; 25:7540-7544. [PMID: 37812068 DOI: 10.1021/acs.orglett.3c02886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
A diarylborinic acid-catalyzed ring opening of cis-4-hydroxymethyl-1,2-cyclopentene oxides was developed with N-nucleophiles including anilines, benzotriazole, and alkylamines, as well as S-nucleophiles, affording 1,2,4-trisubstituted cyclopentane compounds containing a quaternary carbon center. The mechanism study indicated that the "half-cage" structure formed by the epoxide substrate and the catalyst prevents the nucleophiles from attacking the inner side of the "half-cage", resulting in the desired ring-opening product.
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Affiliation(s)
- Shan-Shan Xun
- School of Chemistry and Material Science, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Han Wang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, People's Republic of China
| | - Chang-Bin Yu
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, People's Republic of China
| | - Sheng-Mei Lu
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, People's Republic of China
| | - Yong-Gui Zhou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, Liaoning 116023, People's Republic of China
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7
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Urmi UL, Attard S, Vijay AK, Willcox MDP, Kumar N, Islam S, Kuppusamy R. Antiviral Activity of Anthranilamide Peptidomimetics against Herpes Simplex Virus 1 and a Coronavirus. Antibiotics (Basel) 2023; 12:1436. [PMID: 37760732 PMCID: PMC10525570 DOI: 10.3390/antibiotics12091436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
The development of potent antiviral agents is of utmost importance to combat the global burden of viral infections. Traditional antiviral drug development involves targeting specific viral proteins, which may lead to the emergence of resistant strains. To explore alternative strategies, we investigated the antiviral potential of antimicrobial peptidomimetic compounds. In this study, we evaluated the antiviral potential of 17 short anthranilamide-based peptidomimetic compounds against two viruses: Murine hepatitis virus 1 (MHV-1) which is a surrogate of human coronaviruses and herpes simplex virus 1 (HSV-1). The half-maximal inhibitory concentration (IC50) values of these compounds were determined in vitro to assess their potency as antiviral agents. Compounds 11 and 14 displayed the most potent inhibitory effects with IC50 values of 2.38 μM, and 6.3 μM against MHV-1 while compounds 9 and 14 showed IC50 values of 14.8 μM and 13 μM against HSV-1. Multiple antiviral assessments and microscopic images obtained through transmission electron microscopy (TEM) collectively demonstrated that these compounds exert a direct influence on the viral envelope. Based on this outcome, it can be concluded that peptidomimetic compounds could offer a new approach for the development of potent antiviral agents.
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Affiliation(s)
- Umme Laila Urmi
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; (A.K.V.); (S.I.); (R.K.)
| | - Samuel Attard
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia; (S.A.); (N.K.)
| | - Ajay Kumar Vijay
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; (A.K.V.); (S.I.); (R.K.)
| | - Mark D. P. Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; (A.K.V.); (S.I.); (R.K.)
| | - Naresh Kumar
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia; (S.A.); (N.K.)
| | - Salequl Islam
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; (A.K.V.); (S.I.); (R.K.)
- Department of Microbiology, Jahangirnagar University, Savar 1342, Bangladesh
| | - Rajesh Kuppusamy
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia; (A.K.V.); (S.I.); (R.K.)
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia; (S.A.); (N.K.)
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8
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Chen YJ, Wu LT, Li TA, Pu MQ, Sun XL, Bao H, Wan WM. Ketyl Radical Anion Mediated Radical Polymerization and Anionic Ring-Opening Polymerization to Give Polymers with Low Molecular Weight Distribution. Angew Chem Int Ed Engl 2023; 62:e202304033. [PMID: 37263979 DOI: 10.1002/anie.202304033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/03/2023]
Abstract
The development of novel polymerization capable of yielding polymers with low molecular weight distribution (Đ) is essential and significant in polymer chemistry, where monofunctional initiator contains only one initiation site in these polymerizations generally. Here, ketyl radical anion species is introduced to develop a novel Ketyl Mediated Polymerization (KMP), which enables radical polymerization at carbon radical site and anionic ring-opening polymerization at oxygen anion site, respectively. Meanwhile, polymerization and corresponding organic synthesis generally couldn't be performed simultaneously in one pot. Through KMP, organic synthesis and polymerization are achieved in one pot, where small molecules (cyclopentane derivates) and polymers with low Đ are successfully prepared under mild condition simultaneously. At the initiation step, both organic synthesis and polymerization are initiated by single electron transfer reaction with ketyl radical anion formation. Cyclopentane derivates are synthesized through 3-3 coupling reaction and cyclization. Polystyrene and polycaprolactone with low Đ and a full monomer conversion are prepared by KMP via radical polymerization and anionic ring-opening polymerization, respectively. This work therefore enables both organic synthesis and two different polymerizations from same initiation system, which saves time, labour, resource and energy and expands the reaction mode and method libraries of organic chemistry and polymer chemistry.
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Affiliation(s)
- Yu-Jiao Chen
- College of Environment and Resources, Engineering Research Center of Polymer Green Recycling of Ministry of Education, Fujian Key Laboratory of Pollution Control & Resource Reuse, Fujian Normal University, Fuzhou, 350007, P. R. China
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, State Key Laboratory of Structural Chemistry, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, P. R. China
| | - Liang-Tao Wu
- College of Environment and Resources, Engineering Research Center of Polymer Green Recycling of Ministry of Education, Fujian Key Laboratory of Pollution Control & Resource Reuse, Fujian Normal University, Fuzhou, 350007, P. R. China
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, State Key Laboratory of Structural Chemistry, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, P. R. China
| | - Tai-An Li
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, State Key Laboratory of Structural Chemistry, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, P. R. China
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, P. R. China
| | - Meng-Qin Pu
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, State Key Laboratory of Structural Chemistry, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, P. R. China
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, P. R. China
| | - Xiao-Li Sun
- College of Environment and Resources, Engineering Research Center of Polymer Green Recycling of Ministry of Education, Fujian Key Laboratory of Pollution Control & Resource Reuse, Fujian Normal University, Fuzhou, 350007, P. R. China
| | - Hongli Bao
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, State Key Laboratory of Structural Chemistry, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, P. R. China
| | - Wen-Ming Wan
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, State Key Laboratory of Structural Chemistry, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, P. R. China
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9
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Danelius E, Bu G, Wieske H, Gonen T. MicroED as a powerful tool for structure determination of macrocyclic drug compounds directly from their powder formulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551405. [PMID: 37577574 PMCID: PMC10418104 DOI: 10.1101/2023.07.31.551405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Macrocycles are important drug leads with many advantages including the ability to target flat and featureless binding sites as well as act as molecular chameleons and thereby reach intracellular targets. However, due to their complex structures and inherent flexibility, macrocycles are difficult to study structurally and there are limited structural data available. Herein, we use the cryo-EM method MicroED to determine the novel atomic structures of several macrocycles which have previously resisted structural determination. We show that structures of similar complexity can now be obtained rapidly from nanograms of material, and that different conformations of flexible compounds can be derived from the same experiment. These results will have impact on contemporary drug discovery as well as natural product exploration.
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Affiliation(s)
- E Danelius
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
| | - G Bu
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
| | - H Wieske
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, 75237 Uppsala, Sweden
| | - T Gonen
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
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10
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Ding D, Xu S, da Silva-Júnior EF, Liu X, Zhan P. Medicinal chemistry insights into antiviral peptidomimetics. Drug Discov Today 2023; 28:103468. [PMID: 36528280 DOI: 10.1016/j.drudis.2022.103468] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
The (re)emergence of multidrug-resistant viruses and the emergence of new viruses highlight the urgent and ongoing need for new antiviral agents. The use of peptidomimetics as therapeutic drugs has often been associated with advantages, such as enhanced binding affinity, improved metabolic stability, and good bioavailability profiles. The development of novel antivirals is currently driven by strategies of converting peptides into peptidomimetic derivatives. In this review, we outline different structural modification design strategies for developing novel peptidomimetics as antivirals, involving N- or C-cap terminal structure modifications, pseudopeptides, amino acid modifications, inverse-peptides, cyclization, and molecular hybridization. We also present successful recent examples of peptidomimetic designs.
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Affiliation(s)
- Dang Ding
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Shujing Xu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | | | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.
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11
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Wieske LHE, Atilaw Y, Poongavanam V, Erdélyi M, Kihlberg J. Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds. Chemistry 2023; 29:e202202798. [PMID: 36286339 PMCID: PMC10107787 DOI: 10.1002/chem.202202798] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 12/15/2022]
Abstract
The ability to adjust conformations in response to the polarity of the environment, i.e. molecular chameleonicity, is considered to be important for conferring both high aqueous solubility and high cell permeability to drugs in chemical space beyond Lipinski's rule of 5. We determined the conformational ensembles populated by the antiviral drugs asunaprevir, simeprevir, atazanavir and daclatasvir in polar (DMSO-d6 ) and non-polar (chloroform) environments with NMR spectroscopy. Daclatasvir was fairly rigid, whereas the first three showed large flexibility in both environments, that translated into major differences in solvent accessible 3D polar surface area within each conformational ensemble. No significant differences in size and polar surface area were observed between the DMSO-d6 and chloroform ensembles of these three drugs. We propose that such flexible compounds are characterized as "partial molecular chameleons" and hypothesize that their ability to adopt conformations with low polar surface area contributes to their membrane permeability and oral absorption.
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Affiliation(s)
- Lianne H E Wieske
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | | | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
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12
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Ren J, Vaid TM, Lee H, Ojeda I, Johnson ME. Evaluation of interactions between the hepatitis C virus NS3/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations. J Comput Aided Mol Des 2023; 37:53-65. [PMID: 36427108 PMCID: PMC9839505 DOI: 10.1007/s10822-022-00490-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/17/2022] [Indexed: 11/26/2022]
Abstract
The Hepatitis C Virus (HCV) NS3/4A is an attractive target for the treatment of Hepatitis C infection. Herein, we present an investigation of HCV NS3/4A inhibitors based on a sulfonamidobenzamide scaffold. Inhibitor interactions with HCV NS3/4A were explored by molecular docking, molecular dynamics simulations, and MM/PBSA binding free energy calculations. All of the inhibitors adopt similar molecular docking poses in the catalytic site of the protease that are stabilized by hydrogen bond interactions with G137 and the catalytic S139, which are known to be important for potency and binding stability. The quantitative assessments of binding free energies from MM/PBSA correlate well with the experimental results, with a high coefficient of determination, R2 of 0.92. Binding free energy decomposition analyses elucidate the different contributions of Q41, F43, H57, R109, K136, G137, S138, S139, A156, M485, and Q526 in binding different inhibitors. The importance of these sidechain contributions was further confirmed by computational alanine scanning mutagenesis. In addition, the sidechains of K136 and S139 show crucial but distinct contributions to inhibitor binding with HCV NS3/4A. The structural basis of the potency has been elucidated, demonstrating the importance of the R155 sidechain conformation. This extensive exploration of binding energies and interactions between these compounds and HCV NS3/4A at the atomic level should benefit future antiviral drug design.
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Affiliation(s)
- Jinhong Ren
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
- BeiGene (Beijing) Co., Ltd, No. 30 Science Park Road, Zhong-Guan-Cun Life Sciences Park, Changping District, Beijing, 102206, People's Republic of China
| | - Tasneem M Vaid
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
| | - Hyun Lee
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
- Biophysics Core at Research Resource Center, University of Illinois at Chicago, 1100 S. Ashland Ave, Chicago, IL, 60607, USA
| | - Isabel Ojeda
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA
| | - Michael E Johnson
- Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA.
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13
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Sultan A, Ali R, Ishrat R, Ali S. Anti-HIV and anti-HCV small molecule protease inhibitors in-silico repurposing against SARS-CoV-2 M pro for the treatment of COVID-19. J Biomol Struct Dyn 2022; 40:12848-12862. [PMID: 34569411 DOI: 10.1080/07391102.2021.1979097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is a global health emergency warranting development and implementation of targeted treatment. The enzyme main protease (Mpro; also known as 3C-like protease) is emerging as an attractive drug target. This enzyme plays an indispensable role in processing the translated polyproteins of viral RNA. Inhibiting the activity of Mpro would wedge viral replication. To facilitate the discovery of targeted therapy for COVID-19, we carried out the structure-assisted repurposing of existing protease inhibiting small molecules to target SARS-CoV-2 Mpro. Based on the structure of SARS-CoV-2 Mpro, here we report the small drug molecule namely saquinavir as its potent inhibitor. Findings support the premise that this promising antiviral protease inhibiting small drug molecule can be validated and implemented for the treatment and clinical management of COVID-19 pandemic disease.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Armiya Sultan
- Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Rafat Ali
- Computational Laboratory, Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Romana Ishrat
- Computational Laboratory, Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Sher Ali
- Department of Life Sciences, Sharda University, Greater Noida, UP, India
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14
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Simultaneous spectrofluorimetic determination of remdesivir and simeprevir in human plasma. Sci Rep 2022; 12:21980. [PMID: 36539455 PMCID: PMC9763795 DOI: 10.1038/s41598-022-26559-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
As new infectious mutations of SARS-CoV-2 emerged throughout the world, innovative therapies to counter the virus-altered drug sensitivities were urgently needed. Several antiviral options have been in clinical trials or in compassionate use for the treatment of SARS-CoV-2 infections in an attempt to minimize both clinical severity and viral shedding. Recent research indicated that simeprevir acts synergistically with remdesivir, allowing for a multiple-fold decrease in its effective dose when used at physiologically acceptable concentrations. The goal of this work is to develop a sensitive synchronous spectrofluorimetric approach to simultaneously quantify the two drugs in biological fluids. Using this method, remdesivir and simeprevir could be measured spectrofluorimetrically at 283 and 341 nm, respectively, without interference from each other using Δλ of 90 nm. The effect of various experimental parameters on the fluorescence intensity of the two drugs was extensively explored and optimized. For each of remdesivir and simeprevir, the method exhibited a linearity range of 0.10-1.10 μg/mL, with lower detection limits of 0.01 and 0.02 μg/mL and quantification limits of 0.03 and 0.05 μg/mL, respectively. The high sensitivity of the developed method permitted the simultaneous determination of both drugs in spiked plasma samples with % recoveries ranging from 95.0 to 103.25 with acceptable standard deviation values of 1.92 and 3.04 for remdesivir and simeprevir, respectively. The validation of the approach was approved by the International Council of Harmonization (ICH) guidelines.
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15
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Viral proteases as therapeutic targets. Mol Aspects Med 2022; 88:101159. [PMID: 36459838 PMCID: PMC9706241 DOI: 10.1016/j.mam.2022.101159] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Some medically important viruses-including retroviruses, flaviviruses, coronaviruses, and herpesviruses-code for a protease, which is indispensable for viral maturation and pathogenesis. Viral protease inhibitors have become an important class of antiviral drugs. Development of the first-in-class viral protease inhibitor saquinavir, which targets HIV protease, started a new era in the treatment of chronic viral diseases. Combining several drugs that target different steps of the viral life cycle enables use of lower doses of individual drugs (and thereby reduction of potential side effects, which frequently occur during long term therapy) and reduces drug-resistance development. Currently, several HIV and HCV protease inhibitors are routinely used in clinical practice. In addition, a drug including an inhibitor of SARS-CoV-2 main protease, nirmatrelvir (co-administered with a pharmacokinetic booster ritonavir as Paxlovid®), was recently authorized for emergency use. This review summarizes the basic features of the proteases of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and SARS-CoV-2 and discusses the properties of their inhibitors in clinical use, as well as development of compounds in the pipeline.
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16
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Mosharaf MP, Kibria MK, Hossen MB, Islam MA, Reza MS, Mahumud RA, Alam K, Gow J, Mollah MNH. Meta-Data Analysis to Explore the Hub of the Hub-Genes That Influence SARS-CoV-2 Infections Highlighting Their Pathogenetic Processes and Drugs Repurposing. Vaccines (Basel) 2022; 10:vaccines10081248. [PMID: 36016137 PMCID: PMC9415433 DOI: 10.3390/vaccines10081248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 01/09/2023] Open
Abstract
The pandemic of SARS-CoV-2 infections is a severe threat to human life and the world economic condition. Although vaccination has reduced the outspread, but still the situation is not under control because of the instability of RNA sequence patterns of SARS-CoV-2, which requires effective drugs. Several studies have suggested that the SARS-CoV-2 infection causing hub differentially expressed genes (Hub-DEGs). However, we observed that there was not any common hub gene (Hub-DEGs) in our analyses. Therefore, it may be difficult to take a common treatment plan against SARS-CoV-2 infections globally. The goal of this study was to examine if more representative Hub-DEGs from published studies by means of hub of Hub-DEGs (hHub-DEGs) and associated potential candidate drugs. In this study, we reviewed 41 articles on transcriptomic data analysis of SARS-CoV-2 and found 370 unique hub genes or studied genes in total. Then, we selected 14 more representative Hub-DEGs (AKT1, APP, CXCL8, EGFR, IL6, INS, JUN, MAPK1, STAT3, TNF, TP53, UBA52, UBC, VEGFA) as hHub-DEGs by their protein-protein interaction analysis. Their associated biological functional processes, transcriptional, and post-transcriptional regulatory factors. Then we detected hHub-DEGs guided top-ranked nine candidate drug agents (Digoxin, Avermectin, Simeprevir, Nelfinavir Mesylate, Proscillaridin, Linifanib, Withaferin, Amuvatinib, Atazanavir) by molecular docking and cross-validation for treatment of SARS-CoV-2 infections. Therefore, the findings of this study could be useful in formulating a common treatment plan against SARS-CoV-2 infections globally.
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Affiliation(s)
- Md. Parvez Mosharaf
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
- School of Business, Faculty of Business, Education, Law and Arts, University of Southern Queensland, Toowoomba, QLD 4350, Australia; (K.A.); (J.G.)
| | - Md. Kaderi Kibria
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
| | - Md. Bayazid Hossen
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
| | - Md. Ariful Islam
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
| | - Md. Selim Reza
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
| | - Rashidul Alam Mahumud
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia;
| | - Khorshed Alam
- School of Business, Faculty of Business, Education, Law and Arts, University of Southern Queensland, Toowoomba, QLD 4350, Australia; (K.A.); (J.G.)
| | - Jeff Gow
- School of Business, Faculty of Business, Education, Law and Arts, University of Southern Queensland, Toowoomba, QLD 4350, Australia; (K.A.); (J.G.)
- School of Accounting, Economics and Finance, University of KwaZulu Natal, Durban 4001, South Africa
| | - Md. Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.P.M.); (M.K.K.); (M.B.H.); (M.A.I.); (M.S.R.)
- Correspondence:
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17
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Yuce M, Sarica Z, Ates B, Kurkcuoglu O. Exploring species-specific inhibitors with multiple target sites on S. aureus pyruvate kinase using a computational workflow. J Biomol Struct Dyn 2022; 41:3496-3510. [PMID: 35302925 DOI: 10.1080/07391102.2022.2051743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Experimental evidence indicated that bacterial pyruvate kinase of glycolysis can be evaluated as an alternative target to eliminate infections, while antibiotic resistance poses a global threat. Here, we use a computational workflow to reveal and investigate the potential allosteric sites of methicillin-resistant S. aureus PK, which can help in designing species-specific drugs to inhibit activity of this organism. Residue interaction networks point to a known allosteric site at the small C-C interface, a potential allosteric site near the small interface (site #1), and a second potential allosteric site at the large interface (site #2). 2 µs-long molecular dynamics (MD) simulations with AMBER16 generate different conformations of one narrow target site. Known and potential allosteric sites on the selected conformers are investigated using ensemble docking with AutoDock Vina and a library of 2447 FDA-approved drugs. We determine 18 hits, comprising ergot-alkaloids, anti-cancer-agents, antivirals, analgesics, cardiac glycosides, all with a high docking z-score for three sites. 5 selected compounds with high, average and low z-scores are subjected to 50 ns-long MD simulations for MM-GBSA calculations. ΔGbind values up to -49.3 kcal/mol at the C-C interface, up to -32.7 kcal/mol at site #1, and up to -53.3 kcal/mol at site #2 support the docking calculations. We investigate mitapivat and TT-232 as reference compounds under clinical trial, targeting human PK isomers. We suggest 18 FDA-approved hits from the docking calculations and TT-232 as potential inhibitors with multiple target sites on S. aureus PK. This study also proposes pharmacophores models for de novo drug design.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Merve Yuce
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Zehra Sarica
- Computational Science and Engineering Division, Informatics Institute, Istanbul Technical University, Istanbul, Turkey
| | - Beril Ates
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Ozge Kurkcuoglu
- Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
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18
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Cansfield AD, Ator MA, Banerjee J, Bestwick M, Bortolato A, Brown GA, Brown J, Butkovic K, Cansfield JE, Christopher JA, Congreve M, Cseke G, Deflorian F, Dugan B, Hunjadi MP, Hutinec A, Inturi TK, Landek G, Mason J, O'Brien A, Ott GR, Rupcic R, Saxty G, Southall SM, Zadravec R, Watson SP. Novel Macrocyclic Antagonists of the Calcitonin Gene-Related Peptide Receptor: Design, Realization, and Structural Characterization of Protein-Ligand Complexes. ACS Chem Neurosci 2022; 13:751-765. [PMID: 35245037 DOI: 10.1021/acschemneuro.1c00696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A series of macrocyclic calcitonin gene-related peptide (CGRP) receptor antagonists identified using structure-based design principles, exemplified by HTL0028016 (1) and HTL0028125 (2), is described. Structural characterization by X-ray crystallography of the interaction of two of the macrocycle antagonists with the CGRP receptor ectodomain is described, along with structure-activity relationships associated with point changes to the macrocyclic antagonists. The identification of non-peptidic/natural product-derived, macrocyclic ligands for a G protein coupled receptor (GPCR) is noteworthy.
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Affiliation(s)
- Andrew D Cansfield
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, U.K
| | - Mark A Ator
- Teva Pharmaceuticals, 145 Brandywine Parkway, West Chester, Pennsylvania 19380, United States
| | - Joydeep Banerjee
- Syngene International, Biocon Park, Bommasandra, Bangalore 560099, India
| | - Michael Bestwick
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, U.K
| | - Andrea Bortolato
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, U.K
| | - Giles A Brown
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, U.K
| | - Jason Brown
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, U.K
| | | | - Julie E Cansfield
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, U.K
| | - John A Christopher
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, U.K
| | - Miles Congreve
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, U.K
| | - Gabriella Cseke
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, U.K
| | - Francesca Deflorian
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, U.K
| | - Benjamin Dugan
- Teva Pharmaceuticals, 145 Brandywine Parkway, West Chester, Pennsylvania 19380, United States
| | | | - Antun Hutinec
- Fidelta d.o.o., Prilaz Baruna Filipovića 29, 10000 Zagreb, Croatia
| | | | - Goran Landek
- Fidelta d.o.o., Prilaz Baruna Filipovića 29, 10000 Zagreb, Croatia
| | - Jonathan Mason
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, U.K
| | - Alistair O'Brien
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, U.K
| | - Gregory R Ott
- Teva Pharmaceuticals, 145 Brandywine Parkway, West Chester, Pennsylvania 19380, United States
| | - Renata Rupcic
- Fidelta d.o.o., Prilaz Baruna Filipovića 29, 10000 Zagreb, Croatia
| | - Gordon Saxty
- Fidelta d.o.o., Prilaz Baruna Filipovića 29, 10000 Zagreb, Croatia
| | - Stacey M Southall
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, U.K
| | - Rahela Zadravec
- Fidelta d.o.o., Prilaz Baruna Filipovića 29, 10000 Zagreb, Croatia
| | - Stephen P Watson
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge CB21 6DG, U.K
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19
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Wang F, Chen C, Wang Z, Han X, Shi P, Zhou K, Liu X, Xiao Y, Cai Y, Huang J, Zhang L, Yang H. The Structure of the Porcine Deltacoronavirus Main Protease Reveals a Conserved Target for the Design of Antivirals. Viruses 2022; 14:v14030486. [PMID: 35336895 PMCID: PMC8949103 DOI: 10.3390/v14030486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 11/17/2022] Open
Abstract
The existing zoonotic coronaviruses (CoVs) and viral genetic variants are important microbiological pathogens that cause severe disease in humans and animals. Currently, no effective broad-spectrum antiviral drugs against existing and emerging CoVs are available. The CoV main protease (Mpro) plays an essential role in viral replication, making it an ideal target for drug development. However, the structure of the Deltacoronavirus Mpro is still unavailable. Porcine deltacoronavirus (PDCoV) is a novel CoV that belongs to the genus Deltacoronavirus and causes atrophic enteritis, severe diarrhea, vomiting and dehydration in pigs. Here, we determined the structure of PDCoV Mpro complexed with a Michael acceptor inhibitor. Structural comparison showed that the backbone of PDCoV Mpro is similar to those of alpha-, beta- and gamma-CoV Mpros. The substrate-binding pocket of Mpro is well conserved in the subfamily Coronavirinae. In addition, we also observed that Mpros from the same genus adopted a similar conformation. Furthermore, the structure of PDCoV Mpro in complex with a Michael acceptor inhibitor revealed the mechanism of its inhibition of PDCoV Mpro. Our results provide a basis for the development of broad-spectrum antivirals against PDCoV and other CoVs.
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Affiliation(s)
- Fenghua Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China; (K.Z.); (X.L.); (Y.C.)
- Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Cheng Chen
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China; (K.Z.); (X.L.); (Y.C.)
| | - Zefang Wang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China; (K.Z.); (X.L.); (Y.C.)
| | - Xu Han
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
| | - Peidian Shi
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
| | - Kaixuan Zhou
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China; (K.Z.); (X.L.); (Y.C.)
| | - Xiaomei Liu
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China; (K.Z.); (X.L.); (Y.C.)
| | - Yunjie Xiao
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
| | - Yan Cai
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China; (K.Z.); (X.L.); (Y.C.)
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
| | - Lei Zhang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
- Correspondence: (L.Z.); (H.Y.)
| | - Haitao Yang
- School of Life Sciences, Tianjin University, Tianjin 300072, China; (F.W.); (C.C.); (Z.W.); (X.H.); (P.S.); (Y.X.); (J.H.)
- Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin 300457, China; (K.Z.); (X.L.); (Y.C.)
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Correspondence: (L.Z.); (H.Y.)
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20
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Meshram RJ, Kathwate GH, Gacche RN. Progress, evolving therapeutic/diagnostic approaches, and challenges in the management of hepatitis C virus infections. Arch Virol 2022; 167:717-736. [PMID: 35089390 PMCID: PMC8795940 DOI: 10.1007/s00705-022-05375-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 12/02/2021] [Indexed: 12/11/2022]
Abstract
Hepatitis C virus (HCV) infections are emerging as one of the foremost challenges in healthcare owing to its chronicity and the virus’s quasispecies nature. Worldwide, over 170 million people are chronically infected with HCV, with an annual mortality of over 500,000 people across the world. The emerging pathophysiological evidence links HCV infections to a risk of developing liver diseases such as cirrhosis and hepatocellular carcinoma. Despite the great strides that have been made towards understanding the pathophysiology of disease progression, the tailored treatments of HCV infection remain to be established. The present review provides an update of the literature pertaining to evolving therapeutic approaches and prophylactic measures for the effective management of HCV infections. An extensive discussion of established and experimental immune prophylactic measures also sheds light on current developments in the design of vaccination strategies against HCV infection. We have also attempted to address the application of nanotechnology in formulating effective therapeutic interventions against HCV. Pointing out the limitations of the existing diagnostic methods and therapeutic approaches against HCV might inspire the design and development of novel, efficient, reliable, and cost-effective diagnostic technologies as well as novel therapeutic and immune prophylactic interventions for the effective management of HCV.
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Affiliation(s)
| | | | - Rajesh Nivarti Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, MS, 411007, India.
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21
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Effects of simeprevir on the replication of SARS-CoV-2 in vitro and in transgenic hACE2 mice. Int J Antimicrob Agents 2021; 59:106499. [PMID: 34929295 PMCID: PMC8679493 DOI: 10.1016/j.ijantimicag.2021.106499] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 12/28/2022]
Abstract
In a bid to contain the current COVID-19 (coronavirus disease 2019) pandemic, various countermeasures have been applied. To date, however, there is a lack of an effective drug for the treatment of COVID-19. Through molecular modelling studies, simeprevir, a protease inhibitor approved for the management of hepatitis C virus infection, has been predicted as a potential antiviral against SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causative agent of COVID-19. Here we assessed the efficacy of simeprevir against SARS-CoV-2 both in vitro in Vero E6 cells and in vivo in a human angiotensin-converting enzyme 2 (hACE2) transgenic mouse model. The results showed that simeprevir could inhibit SARS-CoV-2 replication in Vero E6 cells with a half-maximal effective concentration (EC50) of 1.41 ± 0.12 μM. In a transgenic hACE2 mouse model of SARS-CoV-2 infection, intraperitoneal administration of simeprevir at 10 mg/kg/day for 3 consecutive days failed to suppress viral replication. These findings collectively imply that simeprevir does not inhibit SARS-CoV-2 in vivo and therefore do not support its application as a treatment against COVID-19 at a dosage of 10 mg/kg/day.
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22
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Advances on Greener Asymmetric Synthesis of Antiviral Drugs via Organocatalysis. Pharmaceuticals (Basel) 2021; 14:ph14111125. [PMID: 34832907 PMCID: PMC8625736 DOI: 10.3390/ph14111125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022] Open
Abstract
Viral infections cause many severe human diseases, being responsible for remarkably high mortality rates. In this sense, both the academy and the pharmaceutical industry are continuously searching for new compounds with antiviral activity, and in addition, face the challenge of developing greener and more efficient methods to synthesize these compounds. This becomes even more important with drugs possessing stereogenic centers as highly enantioselective processes are required. In this minireview, the advances achieved to improve synthetic routes efficiency and sustainability of important commercially antiviral chiral drugs are discussed, highlighting the use of organocatalytic methods.
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23
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Subbaiah MAM, Meanwell NA. Bioisosteres of the Phenyl Ring: Recent Strategic Applications in Lead Optimization and Drug Design. J Med Chem 2021; 64:14046-14128. [PMID: 34591488 DOI: 10.1021/acs.jmedchem.1c01215] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The benzene moiety is the most prevalent ring system in marketed drugs, underscoring its historic popularity in drug design either as a pharmacophore or as a scaffold that projects pharmacophoric elements. However, introspective analyses of medicinal chemistry practices at the beginning of the 21st century highlighted the indiscriminate deployment of phenyl rings as an important contributor to the poor physicochemical properties of advanced molecules, which limited their prospects of being developed into effective drugs. This Perspective deliberates on the design and applications of bioisosteric replacements for a phenyl ring that have provided practical solutions to a range of developability problems frequently encountered in lead optimization campaigns. While the effect of phenyl ring replacements on compound properties is contextual in nature, bioisosteric substitution can lead to enhanced potency, solubility, and metabolic stability while reducing lipophilicity, plasma protein binding, phospholipidosis potential, and inhibition of cytochrome P450 enzymes and the hERG channel.
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Affiliation(s)
- Murugaiah A M Subbaiah
- Department of Medicinal Chemistry, Biocon-Bristol Myers Squibb Research and Development Centre, Biocon Park, Bommasandra IV Phase, Jigani Link Road, Bangalore, Karnataka 560099, India
| | - Nicholas A Meanwell
- Department of Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
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24
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Muhammed Y, Yusuf Nadabo A, Pius M, Sani B, Usman J, Anka Garba N, Mohammed Sani J, Opeyemi Olayanju B, Zeal Bala S, Garba Abdullahi M, Sambo M. SARS-CoV-2 spike protein and RNA dependent RNA polymerase as targets for drug and vaccine development: A review. BIOSAFETY AND HEALTH 2021; 3:249-263. [PMID: 34396086 PMCID: PMC8346354 DOI: 10.1016/j.bsheal.2021.07.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/04/2021] [Accepted: 07/18/2021] [Indexed: 01/18/2023] Open
Abstract
The present pandemic has posed a crisis to the economy of the world and the health sector. Therefore, the race to expand research to understand some good molecular targets for vaccine and therapeutic development for SARS-CoV-2 is inevitable. The newly discovered coronavirus 2019 (COVID-19) is a positive sense, single-stranded RNA, and enveloped virus, assigned to the beta CoV genus. The virus (SARS-CoV-2) is more infectious than the previously detected coronaviruses (MERS and SARS). Findings from many studies have revealed that S protein and RdRp are good targets for drug repositioning, novel therapeutic development (antibodies and small molecule drugs), and vaccine discovery. Therapeutics such as chloroquine, convalescent plasma, monoclonal antibodies, spike binding peptides, and small molecules could alter the ability of S protein to bind to the ACE-2 receptor, and drugs such as remdesivir (targeting SARS-CoV-2 RdRp), favipir, and emetine could prevent SASR-CoV-2 RNA synthesis. The novel vaccines such as mRNA1273 (Moderna), 3LNP-mRNAs (Pfizer/BioNTech), and ChAdOx1-S (University of Oxford/Astra Zeneca) targeting S protein have proven to be effective in combating the present pandemic. Further exploration of the potential of S protein and RdRp is crucial in fighting the present pandemic.
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Affiliation(s)
- Yusuf Muhammed
- Department of Biochemistry, Federal University, Gusau, Nigeria,Corresponding author: Department of Biochemistry, Federal University, Gusau, Nigeria
| | | | - Mkpouto Pius
- Department of Medical Genetics, University of Cambridge, CB2 1TN, United Kingdom
| | - Bashiru Sani
- Department of Microbiology, Federal University of Lafia, Nigeria
| | - Jafar Usman
- Department of Biochemistry, Federal University, Gusau, Nigeria
| | | | | | - Basit Opeyemi Olayanju
- Department of Chemistry and Biochemistry, Florida International University, FL 33199, USA
| | | | | | - Misbahu Sambo
- Department of Biochemistry, Abubakar Tafawa Balewa University Bauchi, Nigeria
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25
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Skwarecki AS, Nowak MG, Milewska MJ. Amino Acid and Peptide-Based Antiviral Agents. ChemMedChem 2021; 16:3106-3135. [PMID: 34254457 DOI: 10.1002/cmdc.202100397] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Indexed: 01/10/2023]
Abstract
A significant number of antiviral agents used in clinical practice are amino acids, short peptides, or peptidomimetics. Among them, several HIV protease inhibitors (e. g. lopinavir, atazanavir), HCV protease inhibitors (e. g. grazoprevir, glecaprevir), and HCV NS5A protein inhibitors have contributed to a significant decrease in mortality from AIDS and hepatitis. However, there is an ongoing need for the discovery of new antiviral agents and the development of existing drugs; amino acids, both proteinogenic and non-proteinogenic in nature, serve as convenient building blocks for this purpose. The synthesis of non-proteinogenic amino acid components of antiviral agents could be challenging due to the need for enantiomerically or diastereomerically pure products. Herein, we present a concise review of antiviral agents whose structures are based on amino acids of both natural and unnatural origin. Special attention is paid to the synthetic aspects of non-proteinogenic amino acid components of those agents.
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Affiliation(s)
- Andrzej S Skwarecki
- Department of Pharmaceutical Technology and Biochemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
| | - Michał G Nowak
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
| | - Maria J Milewska
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
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26
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Sun MR, Li HL, Ba MY, Cheng W, Zhu HL, Duan YT. Cyclopropyl Scaffold: A Generalist for Marketed Drugs. Mini Rev Med Chem 2021; 21:150-170. [PMID: 32727325 DOI: 10.2174/1389557520666200729161150] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/23/2019] [Accepted: 04/26/2020] [Indexed: 11/22/2022]
Abstract
In recent decades, much attention has been given to cyclopropyl scaffolds, which commonly exist in natural products and synthetic organic molecules. Clinical drug molecules with cyclopropyl rings are an area of focus in therapeutic research due to their interesting chemical properties and unique pharmacology activity. These molecular drugs against different targets are applicable in some therapeutic treatment fields including cancer, infection, respiratory disorder, cardiovascular and cerebrovascular diseases, dysphrenia, nervous system disorders, endocrine and metabolic disorders, skin disease, digestive disorders, urogenital diseases, otolaryngological and dental diseases, and eye diseases. This review is a guide for pharmacologists who are in search of valid preclinical/clinical drug compounds where the progress, from 1961 to the present day, of approved marketed drugs containing cyclopropyl scaffold is examined.
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Affiliation(s)
- Mo-Ran Sun
- School of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan450001, China
| | - Hong-Liang Li
- School of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan450001, China
| | - Meng-Yu Ba
- School of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan450001, China
| | - Weyland Cheng
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou University, Zhengzhou 450018, China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, China
| | - Yong-Tao Duan
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou University, Zhengzhou 450018, China
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27
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Ghiasi T, Ahmadi S, Ahmadi E, Talei Bavil Olyai MR, Khodadadi Z. The index of ideality of correlation: QSAR studies of hepatitis C virus NS3/4A protease inhibitors using SMILES descriptors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:495-520. [PMID: 34074200 DOI: 10.1080/1062936x.2021.1925344] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
Robust and reliable QSAR models were developed to predict half-maximal inhibitory concentration (IC50) values of hepatitis C virus NS3/4A protease inhibitors from the Monte Carlo technique. 524 HCV NS3/4A protease inhibitors were extracted from the scientific literature to create a reasonably large set. The models were developed using CORAL software by using two target functions namely target function 1 (TF1) without applying the index of ideality of correlation (IIC) and target function 2 (TF2) that uses IIC. The constructed models based on TF2 were statistically more significant and robust than the models based on TF1. The determination coefficients (r2) of training and test sets were 0.86 and 0.88 for the best split based on TF2. The promoters of the increase/decrease of activity were also extracted and interpreted in detail. The model interpretation results explain the role of different structural attributes in predicting the pIC50 values of hepatitis C virus NS3/4A protease inhibitors. Based on the mechanistic model interpretation results, eight new compounds were designed and their pIC50 values were predicted based on the average prediction of ten models.
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Affiliation(s)
- T Ghiasi
- Department of Chemistry, Faculty of Science, Islamic Azad University, South Tehran Branch, Tehran, Iran
| | - S Ahmadi
- Department of Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - E Ahmadi
- Department of Chemistry, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran
| | - M R Talei Bavil Olyai
- Department of Chemistry, Faculty of Science, Islamic Azad University, South Tehran Branch, Tehran, Iran
| | - Z Khodadadi
- Department of Chemistry, Faculty of Science, Islamic Azad University, South Tehran Branch, Tehran, Iran
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28
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Lo HS, Hui KPY, Lai HM, He X, Khan KS, Kaur S, Huang J, Li Z, Chan AKN, Cheung HHY, Ng KC, Ho JCW, Chen YW, Ma B, Cheung PMH, Shin D, Wang K, Lee MH, Selisko B, Eydoux C, Guillemot JC, Canard B, Wu KP, Liang PH, Dikic I, Zuo Z, Chan FKL, Hui DSC, Mok VCT, Wong KB, Mok CKP, Ko H, Aik WS, Chan MCW, Ng WL. Simeprevir Potently Suppresses SARS-CoV-2 Replication and Synergizes with Remdesivir. ACS CENTRAL SCIENCE 2021; 7:792-802. [PMID: 34075346 PMCID: PMC8056950 DOI: 10.1021/acscentsci.0c01186] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Indexed: 05/08/2023]
Abstract
The outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global threat to human health. Using a multidisciplinary approach, we identified and validated the hepatitis C virus (HCV) protease inhibitor simeprevir as an especially promising repurposable drug for treating COVID-19. Simeprevir potently reduces SARS-CoV-2 viral load by multiple orders of magnitude and synergizes with remdesivir in vitro. Mechanistically, we showed that simeprevir not only inhibits the main protease (Mpro) and unexpectedly the RNA-dependent RNA polymerase (RdRp) but also modulates host immune responses. Our results thus reveal the possible anti-SARS-CoV-2 mechanism of simeprevir and highlight the translational potential of optimizing simeprevir as a therapeutic agent for managing COVID-19 and future outbreaks of CoV.
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Affiliation(s)
- Ho Sing Lo
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Shatin, Hong Kong
| | - Kenrie Pui Yan Hui
- School
of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
- Centre
for Immunology and Infection (C2I), Hong
Kong Science Park, Hong Kong, SAR, China
| | - Hei-Ming Lai
- Department
of Psychiatry, Faculty of Medicine, The
Chinese University of Hong Kong, Shatin, Hong Kong
- Department
of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
- Li
Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xu He
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Shatin, Hong Kong
| | - Khadija Shahed Khan
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Shatin, Hong Kong
| | - Simranjeet Kaur
- Department
of Chemistry, Faculty of Science, Hong Kong
Baptist University, Kowloon
Tong, Hong Kong
| | - Junzhe Huang
- Department
of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
- Li
Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Zhongqi Li
- Department
of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
- Li
Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Anthony K. N. Chan
- Department
of Systems Biology, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - Hayley Hei-Yin Cheung
- School
of Life Sciences, Centre for Protein Science and Crystallography,
State Key Laboratory of Agrobiotechnology, Faculty of Science, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ka-Chun Ng
- School
of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - John Chi Wang Ho
- School
of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Yu Wai Chen
- Department
of Applied Biology and Chemical
Technology and the State Key Laboratory of Chemical Biology and Drug
Discovery, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Bowen Ma
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Shatin, Hong Kong
| | - Peter Man-Hin Cheung
- School
of Public Health, Faculty of Medicine, The
Chinese University of Hong Kong, Shatin, Hong Kong
| | - Donghyuk Shin
- Buchmann
Institute for Molecular Life Sciences, Goethe
University, 60323 Frankfurt am Main, Germany
- Department
of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic
of Korea
| | - Kaidao Wang
- Protein
Production Department, GenScript Biotech
Corporation, Nanjing, Jiangsu Province 211100, China
| | - Meng-Hsuan Lee
- Institute
of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - Barbara Selisko
- Laboratoire
d’Architecture et Fonction des Macromolécules Biologiques
(AFMB), Centre National de la Recherche Scientifique, Aix-Marseille Université, 13007 Marseille, France
| | - Cecilia Eydoux
- Laboratoire
d’Architecture et Fonction des Macromolécules Biologiques
(AFMB), Centre National de la Recherche Scientifique, Aix-Marseille Université, 13007 Marseille, France
| | - Jean-Claude Guillemot
- Laboratoire
d’Architecture et Fonction des Macromolécules Biologiques
(AFMB), Centre National de la Recherche Scientifique, Aix-Marseille Université, 13007 Marseille, France
| | - Bruno Canard
- Laboratoire
d’Architecture et Fonction des Macromolécules Biologiques
(AFMB), Centre National de la Recherche Scientifique, Aix-Marseille Université, 13007 Marseille, France
| | - Kuen-Phon Wu
- Institute
of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - Po-Huang Liang
- Institute
of Biological Chemistry, Academia Sinica, Taipei, Taiwan 115
| | - Ivan Dikic
- Buchmann
Institute for Molecular Life Sciences, Goethe
University, 60323 Frankfurt am Main, Germany
| | - Zhong Zuo
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Shatin, Hong Kong
| | - Francis K. L. Chan
- Department
of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
- Institute
of Digestive Disease, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - David S. C. Hui
- Department
of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
- Stanley
Ho Center for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Vincent C. T. Mok
- Department
of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
- Gerald
Choa Neuroscience Centre, Margaret K. L. Cheung Research Centre for
Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kam-Bo Wong
- School
of Life Sciences, Centre for Protein Science and Crystallography,
State Key Laboratory of Agrobiotechnology, Faculty of Science, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chris Ka Pun Mok
- HKU-Pasteur
Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Shatin, Hong Kong
| | - Ho Ko
- Department
of Psychiatry, Faculty of Medicine, The
Chinese University of Hong Kong, Shatin, Hong Kong
- Department
of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
- Li
Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
- Gerald
Choa Neuroscience Centre, Margaret K. L. Cheung Research Centre for
Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
- School
of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
- Peter
Hung Pain Research Institute, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wei Shen Aik
- Department
of Chemistry, Faculty of Science, Hong Kong
Baptist University, Kowloon
Tong, Hong Kong
| | - Michael Chi Wai Chan
- School
of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
- Centre
for Immunology and Infection (C2I), Hong
Kong Science Park, Hong Kong, SAR, China
| | - Wai-Lung Ng
- School
of Pharmacy, Faculty of Medicine, The Chinese
University of Hong Kong, Shatin, Hong Kong
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29
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Wu X, Ren J, Shao Z, Yang X, Qian D. Transition-Metal-Catalyzed Asymmetric Couplings of α-Aminoalkyl Fragments to Access Chiral Alkylamines. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01545] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xiaomei Wu
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, People’s Republic of China
| | - Jiangtao Ren
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, People’s Republic of China
| | - Zhihui Shao
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, People’s Republic of China
| | - Xiaodong Yang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, People’s Republic of China
| | - Deyun Qian
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education and Yunnan Province; Yunnan Provincial Center for Research & Development of Natural Products; School of Chemical Science and Technology, Yunnan University, Kunming 650091, People’s Republic of China
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30
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Tabrez S, Rahman F, Ali R, Muhammad F, Alshehri BM, Alaidarous MA, Banawas S, Dukhyil AAB, Rub A. Repurposing of FDA-approved drugs as inhibitors of sterol C-24 methyltransferase of Leishmania donovani to fight against leishmaniasis. Drug Dev Res 2021; 82:1154-1161. [PMID: 33929761 DOI: 10.1002/ddr.21820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/08/2021] [Accepted: 04/15/2021] [Indexed: 12/30/2022]
Abstract
Leishmaniasis is a vector-borne disease caused by around 20 species of Leishmania. The main clinical forms of leishmaniasis are cutaneous leishmaniasis (CL) and visceral leishmaniasis (VL). VL is caused by Leishmania infantum in Central and South America, Mediterranean Basin, Middle East, and by L. donovani in Asia and Africa. Sterol C-24 methyltransferase (LdSMT) of L. donovani is a transferase enzyme of the sterol biosynthesis pathway. This pathway is one of the major targets for drug developments in Leishmania. Due to insufficient evidence about the exact function of SMT inside the cell and the uniqueness of the SMT enzyme in the Leishmania parasites made it a significant target for an effective drug development approach. We performed virtual screening of the Food and Drug Administration (FDA)-approved drug library against LdSMT and found simeprevir, an antiviral drug on top in the binding score. It showed a significant binding affinity with LdSMT. The binding was supported by hydrogen bonds and several other interactions. Simeprevir inhibited L. donovani growth of promastigotes with 50% inhibitory concentration (IC50 ) of 51.49 ± 5.87 μM. Further studies showed that simeprevir induced ROS generation in 44.7% of parasites at 125-μM concentration. Here, we for the first time reported simeprevir as an antileishmanial lead molecule using a drug repurposing approach.
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Affiliation(s)
- Shams Tabrez
- Infection and Immunity Lab (414), Department of Biotechnology, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Fazlur Rahman
- Infection and Immunity Lab (414), Department of Biotechnology, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Rahat Ali
- Infection and Immunity Lab (414), Department of Biotechnology, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Fida Muhammad
- Infection and Immunity Lab (414), Department of Biotechnology, Jamia Millia Islamia (A Central University), New Delhi, India
| | - Bader Mohammed Alshehri
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Mohammed A Alaidarous
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia.,Health and Basic Sciences Research Center, Majmaah University, Al Majmaah, Saudi Arabia
| | - Saeed Banawas
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia.,Health and Basic Sciences Research Center, Majmaah University, Al Majmaah, Saudi Arabia.,Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon, USA
| | - Abdul Aziz Bin Dukhyil
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Abdur Rub
- Infection and Immunity Lab (414), Department of Biotechnology, Jamia Millia Islamia (A Central University), New Delhi, India
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31
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Zhang H, Zheng X, Li J, Liu Q, Huang XX, Ding H, Suzuki R, Muramatsu M, Song SJ. Flavonoid-triazolyl hybrids as potential anti-hepatitis C virus agents: Synthesis and biological evaluation. Eur J Med Chem 2021; 218:113395. [PMID: 33838584 DOI: 10.1016/j.ejmech.2021.113395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/06/2021] [Accepted: 03/17/2021] [Indexed: 12/15/2022]
Abstract
A series of flavonoid-triazolyl hybrids were synthesized and evaluated as novel inhibitors of hepatitis C virus (HCV). The results of anti-HCV activity assays showed that most of the synthesized derivatives at a concentration of 100 μg/mL inhibited the generation of progeny virus. Among these derivatives, 10m and 10r exhibited the most potent anti-HCV activity and inhibited the production of HCV in a dose-dependent manner. Interestingly, 10m and 10r had no significant inhibitory effect on viral translation or replication. Additional action mechanism studies revealed that the most potent compounds, 10m and 10r, significantly inhibited viral entry to 34.0% and 52.0%, respectively, at 10 μM. These results suggest further effective application of 10m and 10r as potential HCV preventive agents.
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Affiliation(s)
- Han Zhang
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Xin Zheng
- Department of Cardiology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China; Department of Virology II, National Institute of Infectious Diseases, 162-8640, Tokyo, Japan
| | - Jichong Li
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Qingbo Liu
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Xiao-Xiao Huang
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Huaiwei Ding
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Diseases, 162-8640, Tokyo, Japan
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, 162-8640, Tokyo, Japan.
| | - Shao-Jiang Song
- Key Laboratory of Computational Chemistry Based Natural Antitumor Drug Research & Development, Liaoning Province, School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
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32
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Zhong YJ, Qi T, Ji YL, Huang H, Zhang X, Leng HJ, Peng C, Li JL, Han B. Highly Chemoselective [2+1] Annulation of α-Alkylidene Pyrazolones with α-Bromonitroalkenes: Synthesis of Pyrazolone-Based Vinylcyclopropanes and Computational Studies. J Org Chem 2021; 86:2582-2592. [PMID: 33423501 DOI: 10.1021/acs.joc.0c02674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A highly chemoselective [2+1] annulation of α-alkylidene pyrazolones with α-bromonitroalkenes has been achieved under mild conditions. α-Alkylidene pyrazolones were unprecedentedly used as a C1 synthon to participate in annulation reactions, providing access to diverse vinylcyclopropane-based pyrazolone products. In addition, a spectrum of pharmaceutically interesting pyrazole-fused pyranone oximes could be rapidly obtained through a [2+1] annulation/rearrangement sequential process. Computational studies disclosed the origin of the observed chemoselectivity of the [2+1] cycloaddition.
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Affiliation(s)
- Ya-Jun Zhong
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Ting Qi
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610052, People's Republic of China
| | - Yan-Ling Ji
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Hua Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China.,Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610052, People's Republic of China
| | - Xiang Zhang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610052, People's Republic of China
| | - Hai-Jun Leng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China.,Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610052, People's Republic of China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Jun-Long Li
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610052, People's Republic of China
| | - Bo Han
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
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33
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Slagman S, Fessner WD. Biocatalytic routes to anti-viral agents and their synthetic intermediates. Chem Soc Rev 2021; 50:1968-2009. [DOI: 10.1039/d0cs00763c] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An assessment of biocatalytic strategies for the synthesis of anti-viral agents, offering guidelines for the development of sustainable production methods for a future COVID-19 remedy.
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Affiliation(s)
- Sjoerd Slagman
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
| | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
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34
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Affiliation(s)
- Nicholas A Meanwell
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Gunda I Georg
- College of Pharmacy, University of Minnesota, 717 Delaware Street SE, Minneapolis, Minnesota 55414, United States
| | - Shaomeng Wang
- University of Michigan, Departments of Internal Medicine, Pharmacology and Medicinal Chemistry and Michigan Center for Therapeutic Innovation, Ann Arbor, Michigan 48109, United States
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35
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Ahmed RM, Fayed MAA, El-Behairy MF, Abdallah IA. Identification, isolation, structural characterization, in silico toxicity prediction and in vitro cytotoxicity assay of simeprevir acidic and oxidative degradation products. RSC Adv 2020; 10:42816-42826. [PMID: 35514884 PMCID: PMC9057948 DOI: 10.1039/d0ra09253c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022] Open
Abstract
Simeprevir is a new direct-acting antiviral drug used for the treatment of chronic hepatitis C. In this work, a simple, fast and economical chromatographic method was developed for the determination of simeprevir in the presence of its acidic and oxidative degradation products. The stress studies performed herein showed that simeprevir degraded under acidic and oxidative conditions but was stable under thermal and alkaline conditions. Chromatographic separation was achieved on a reversed-phase Eclipse XDB C18 column (4.6 × 150 mm, 5 μm). The mobile phase consisted of methanol-0.05 M ammonium acetate (pH 4) (90 : 10, v/v) and was used at a flow rate of 1 mL min−1. The column effluent was monitored at 237 nm. The calibration curve was linear over the concentration range of 0.1–20 μg mL−1. The relative standard deviations for the intra-day and inter-day precision were less than 2%, and good percentage recoveries that met the acceptance criteria of the International Conference on Harmonization (ICH) guidelines were obtained. The robustness was assessed using the Plackett–Burman design. The simeprevir degradation products were isolated by flash chromatography and confirmed by 1H NMR and LC-MS/MS techniques. The fully validated chromatographic method can be applied as a stability-indicating method for simeprevir and for routine analysis during quality control. Additionally, in silico toxicity prediction of the degradation products demonstrated a hepatotoxicity alert for DP 1, DP 2, DP 4 and DP 5 and a carcinogenicity alert for DP 3. In view of safety aspects, an in vitro cytotoxicity assay was carried out for simeprevir degradation products. They were found to be non-toxic in vitro at the tested concentrations. Simeprevir is a new direct-acting antiviral drug used for the treatment of chronic hepatitis C.![]()
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Affiliation(s)
- Rasha M Ahmed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Misr International University Cairo 11341 Egypt
| | - Marwa A A Fayed
- Department of Pharmacognosy, Faculty of Pharmacy, University of Sadat City Sadat City 32897 Egypt
| | - Mohammed F El-Behairy
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Sadat City Sadat City 32897 Egypt
| | - Inas A Abdallah
- Department of Analytical Chemistry, Faculty of Pharmacy, University of Sadat City Sadat City 32897 Egypt
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36
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Faucher F, Bennett JM, Bogyo M, Lovell S. Strategies for Tuning the Selectivity of Chemical Probes that Target Serine Hydrolases. Cell Chem Biol 2020; 27:937-952. [PMID: 32726586 PMCID: PMC7484133 DOI: 10.1016/j.chembiol.2020.07.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 02/08/2023]
Abstract
Serine hydrolases comprise a large family of enzymes that have diverse roles in key cellular processes, such as lipid metabolism, cell signaling, and regulation of post-translation modifications of proteins. They are also therapeutic targets for multiple human pathologies, including viral infection, diabetes, hypertension, and Alzheimer disease; however, few have well-defined substrates and biological functions. Activity-based probes (ABPs) have been used as effective tools to both profile activity and screen for selective inhibitors of serine hydrolases. One broad-spectrum ABP containing a fluorophosphonate electrophile has been used extensively to advance our understanding of diverse serine hydrolases. Due to the success of this single reagent, several robust chemistries have been developed to further diversify and tune the selectivity of ABPs used to target serine hydrolases. In this review, we highlight approaches to identify selective serine hydrolase ABPs and suggest new synthetic methodologies that could be applied to further advance probe development.
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Affiliation(s)
- Franco Faucher
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - John M Bennett
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Scott Lovell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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37
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Patel ND, Wei X, Byrne D, Narayanan BA, Pennino S, Sarvestani M, Saha A, Haddad N, Kapadia S, Lorenz JC, DeCroos P, Ye A, Lee H, Grinberg N, Hossain A, Busacca CA, Yee NK, Senanayake CH. Sulfone-Mediated S NAr Reaction as a Powerful Tool for the Synthesis of 4-Quinolinyl Ethers and More-Application to the Synthesis of HCV NS3/4a Protease Inhibitor BI 201420. J Org Chem 2020; 85:8339-8351. [PMID: 32462862 DOI: 10.1021/acs.joc.0c00554] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
An efficient general methodology for the synthesis of 4-quinolinyl ethers is demonstrated via a highly reactive SNAr reaction of 4-quinolinyl sulfones with a range of structurally diversified 1°, 2°, and 3° alcohols with a wide substrate scope and high yields. By adapting this methodology, a convergent synthesis of a complex target of HCV NS3/4a protease inhibitor BI 201420 was accomplished.
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Affiliation(s)
- Nitinchandra D Patel
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Xudong Wei
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Denis Byrne
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Bikshandarkoil A Narayanan
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Scott Pennino
- Material and Analytical Sciences US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Max Sarvestani
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Anjan Saha
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Nizar Haddad
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Suresh Kapadia
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Jon C Lorenz
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Philomen DeCroos
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Andrew Ye
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Heewon Lee
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Nelu Grinberg
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Azad Hossain
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Carl A Busacca
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Nathan K Yee
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
| | - Chris H Senanayake
- Chemical Development US, Boehringer-Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, P.O. Box 368, Ridgefield, Connecticut 06877-0368, United States
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38
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Aguiar BF, Campos GRF, Rodrigues JPV, Marques NN, Molina BF, Bittar C, Souza FF, Martinelli ADLC, Rahal P, Pereira LRL. Baseline resistance associated substitutions in HCV genotype 1 infected cohort treated with Simeprevir, Daclatasvir and Sofosbuvir in Brazil. Clin Res Hepatol Gastroenterol 2020; 44:329-339. [PMID: 31523019 DOI: 10.1016/j.clinre.2019.07.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 07/18/2019] [Indexed: 02/04/2023]
Abstract
BACKGROUND The World Health Organization estimates that 1% of the world population (71 million) is infected with hepatitis C virus (HCV). In 2015, three direct-acting antivirals (DAAs), simeprevir (SMV), sofosbuvir (SOF) and daclatasvir (DCV) were included in the Brazilian protocol for the treatment of chronic hepatitis C. Despite the fact that the use of these drugs is associated with higher treatment response rates and with lower incidence of side effects, studies have shown the association between the presence of viral resistance mutations and the failure of pharmacological treatment. AIM This way, this study aimed to evaluate the safety and effectiveness of treatment for HCV genotypes 1a and 1b infected patients with these DAAs, also analyzing the occurrence and prevalence of baseline resistance associated substitutions (RAS), observing the impact of these mutations into the treatment success. METHODS Clinical data were collected from all the 262 HCV infected patients included for comparative analysis, while serum samples collected from 144 of these individuals, before treatment, were submitted to molecular biology approaches for mutation analysis into NS3, NS5A and NS5B regions. RESULTS Regarding the treatment regimens, 49.6% of the patients received SOF+DCV±ribavirin and 50.4% used SOF+SMV±ribavirin. The sustained virological response at 12 weeks post-treatment (SVR12) rate was 92.7% (93.9% for SOF plus DCV and 91.7% for SOF plus SMV). No clinical or laboratorial factor was statistically associated with SVR. The most common adverse reactions were haematological events, nausea/vomiting, headache and asthenia. Out of 144 blood samples, 70 (48.6%) had detected RAS, 34.8% treated with SOF+DCV±ribavirin and 61.3% SOF+SMV±ribavirin. The resistance mutations against SMV were detected into NS3: substitutions G122S (28%), I170V (22.7%), Y56F (17.3%) and V132I (14.7%). The mutations against DCV R30Q (9.1%), P58H (6.1%) and Q62E (6.1%) were observed into NS5A, and for SOF the mutations A421V (10.6%), L159F (6.4%) and C316N (6.4%) were present inside NS5B viral protein. Four patients did not reach SVR, three of them presented viruses carrying RAS (1 treated with SOF+DCV and 2 with SOF+SMV). Some of these mutations, like R30Q (present in relapsing samples) and L159F, are well known by their influence on antiviral resistance, while others, like C316N, have a compensatory effect on viral fitness, maintaining these baseline RAS. CONCLUSION The use of treatment regimens composed of SOF and DCV or SOF and SMV showed a high SVR rate, despite of a high rate of RAS, and a good tolerability profile in patients with HCV genotype 1. However, the high occurrence of baseline RAS observed in this casuistic is still a concern and studies like this show the necessity to understand how they are maintained in the population and to direct more efficiently the use of DAAs.
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Affiliation(s)
- Bruna Forte Aguiar
- FCFRP-USP - University of São Paulo, Ribeirão Preto Faculty of Pharmaceutical Sciences-Café avenue, 14040-903 Ribeirão Preto, SP, Brazil.
| | - Guilherme Rodrigues Fernandes Campos
- UNESP - São Paulo State University, Institute of Bioscience, Language and Exact Science-IBILCE, Department of Biology, Cristóvão Colombo Street, 2265, 15054-000 São José do Rio Preto, SP, Brazil.
| | - João Paulo Vilela Rodrigues
- FCFRP-USP - University of São Paulo, Ribeirão Preto Faculty of Pharmaceutical Sciences-Café avenue, 14040-903 Ribeirão Preto, SP, Brazil.
| | - Nayara Nathie Marques
- UNESP - São Paulo State University, Institute of Bioscience, Language and Exact Science-IBILCE, Department of Biology, Cristóvão Colombo Street, 2265, 15054-000 São José do Rio Preto, SP, Brazil.
| | - Bárbara Floriano Molina
- UNESP - São Paulo State University, Institute of Bioscience, Language and Exact Science-IBILCE, Department of Biology, Cristóvão Colombo Street, 2265, 15054-000 São José do Rio Preto, SP, Brazil.
| | - Cintia Bittar
- UNESP - São Paulo State University, Institute of Bioscience, Language and Exact Science-IBILCE, Department of Biology, Cristóvão Colombo Street, 2265, 15054-000 São José do Rio Preto, SP, Brazil.
| | - Fernanda Fernandes Souza
- FMRP-USP-University of São Paulo, Ribeirão Preto School of Medicine, Bandeirantes Avenue, 3900, 14049-900 Ribeirão Preto, SP, Brazil.
| | - Ana de Lourdes Candolo Martinelli
- FMRP-USP-University of São Paulo, Ribeirão Preto School of Medicine, Bandeirantes Avenue, 3900, 14049-900 Ribeirão Preto, SP, Brazil.
| | - Paula Rahal
- UNESP - São Paulo State University, Institute of Bioscience, Language and Exact Science-IBILCE, Department of Biology, Cristóvão Colombo Street, 2265, 15054-000 São José do Rio Preto, SP, Brazil.
| | - Leonardo Régis Leira Pereira
- FCFRP-USP - University of São Paulo, Ribeirão Preto Faculty of Pharmaceutical Sciences-Café avenue, 14040-903 Ribeirão Preto, SP, Brazil.
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39
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Jiang X, Tan J, Wang Y, Chen J, Li J, Jiang Z, Quan Y, Jin J, Li Y, Cen S, Li Y, Peng Z, Li Z. 2-((4-Arylpiperazin-1-yl)methyl)benzonitrile Derivatives as Orally Available Inhibitors of Hepatitis C Virus with a Novel Mechanism of Action. J Med Chem 2020; 63:5972-5989. [PMID: 32378892 DOI: 10.1021/acs.jmedchem.0c00232] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Although the direct-acting antivirals revolutionized the hepatitis C virus (HCV) infection treatment in the last decade, more efforts are needed to reach the elimination of HCV in the absence of a vaccine. 4-(Piperazin-1-yl)-2-((p-tolylamino)methyl)-benzonitrile (1) is a modest HCV inhibitor identified from an in-house screening using a HCV-infected Huh7.5 cell culture. Starting from it, the chemical optimization afforded a new 2-((4-arylpiperazin-1-yl)methyl)benzonitrile scaffold with significantly increased antiviral activity against HCV. A highly effective HCV inhibitor, 35 (L0909, EC50 = 0.022 μM, SI > 600), was identified by the structure-activity relationship study. The biological study revealed that L0909 could block HCV replication by acting on the HCV entry stage. The high sensitivity to clinical resistant HCV mutants and synergistic effect with clinical drugs were observed for this compound. The further pharmaceutical studies demonstrated that L0909 is long-lasting, is orally available, and has low toxicity in vivo. These results show L0909 as a promising HCV entry inhibitor for single or combinational therapeutic potential.
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Affiliation(s)
- Xinbei Jiang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jiali Tan
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yixuan Wang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jinhua Chen
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jianrui Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.,Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhi Jiang
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yanni Quan
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jie Jin
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yuhuan Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.,Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Shan Cen
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Yanping Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zonggen Peng
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.,Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhuorong Li
- CAMS Key Laboratory of Antiviral Drug Research, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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40
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Chinthakindi PK, Benediktsdottir A, Arvidsson PI, Chen Y, Sandström A. Solid Phase Synthesis of Sulfonimidamide Pseudopeptides and Library Generation. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Praveen K. Chinthakindi
- The Beijer Laboratory; Department of Medicinal Chemistry; Uppsala University; Box 574 75123 Uppsala Sweden
| | - Andrea Benediktsdottir
- The Beijer Laboratory; Department of Medicinal Chemistry; Uppsala University; Box 574 75123 Uppsala Sweden
| | - Per I. Arvidsson
- Science for Life Laboratory; Drug Discovery and Development Platform and Division of Translational Medicine and Chemical Biology; Karolinska Institutet; 17177 Stockholm Sweden
- Catalysis and Peptide Research Unit; Drug Discovery and Development Platform and Division of Translational Medicine and Chemical Biology; University of KwaZulu-Natal; 4000 Durban South Africa
| | - Yantao Chen
- Medicinal Chemistry; Research and Early Development, Cardiovascular, Renal and Metabolism; AstraZeneca; 43183 Gothenburg Sweden
| | - Anja Sandström
- The Beijer Laboratory; Department of Medicinal Chemistry; Uppsala University; Box 574 75123 Uppsala Sweden
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41
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Barlow N, Vanga SR, Sävmarker J, Sandström A, Burns P, Hallberg A, Åqvist J, Gutiérrez-de-Terán H, Hallberg M, Larhed M, Chai SY, Thompson PE. Macrocyclic peptidomimetics as inhibitors of insulin-regulated aminopeptidase (IRAP). RSC Med Chem 2020; 11:234-244. [PMID: 33479630 DOI: 10.1039/c9md00485h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 11/21/2019] [Indexed: 12/25/2022] Open
Abstract
Macrocyclic analogues of the linear hexapeptide, angiotensin IV (AngIV) have proved to be potent inhibitors of insulin-regulated aminopeptidase (IRAP, oxytocinase, EC 3.4.11.3). Along with higher affinity, macrocycles may also offer better metabolic stability, membrane permeability and selectivity, however predicting the outcome of particular cycle modifications is challenging. Here we describe the development of a series of macrocyclic IRAP inhibitors with either disulphide, olefin metathesis or lactam bridges and variations of ring size and other functionality. The binding mode of these compounds is proposed based on molecular dynamics analysis. Estimation of binding affinities (ΔG) and relative binding free energies (ΔΔG) with the linear interaction energy (LIE) method and free energy perturbation (FEP) method showed good general agreement with the observed inhibitory potency. Experimental and calculated data highlight the cumulative importance of an intact N-terminal peptide, the specific nature of the macrocycle, the phenolic oxygen and the C-terminal functionality.
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Affiliation(s)
- Nicholas Barlow
- Department of Medicinal Chemistry , BMC , Uppsala University , P.O. Box 574 , SE-751 23 Uppsala , Sweden.,Medicinal Chemistry , Monash Institute of Pharmaceutical Sciences , Parkville , Victoria 3052 , Australia .
| | - Sudarsana Reddy Vanga
- Department of Cell and Molecular Biology , BMC , Uppsala University , Box 596 , SE-751 24 Uppsala , Sweden
| | - Jonas Sävmarker
- The Beijer Laboratory , Department of Medicinal Chemistry , BMC , Uppsala University , P.O. Box 574 , SE-751 23 Uppsala , Sweden
| | - Anja Sandström
- The Beijer Laboratory , Department of Medicinal Chemistry , BMC , Uppsala University , P.O. Box 574 , SE-751 23 Uppsala , Sweden
| | - Peta Burns
- Biomedicine Discovery Institute , Department of Physiology , Monash University , Clayton , Victoria 3800 , Australia
| | - Anders Hallberg
- Department of Medicinal Chemistry , BMC , Uppsala University , P.O. Box 574 , SE-751 23 Uppsala , Sweden
| | - Johan Åqvist
- Department of Cell and Molecular Biology , BMC , Uppsala University , Box 596 , SE-751 24 Uppsala , Sweden
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology , BMC , Uppsala University , Box 596 , SE-751 24 Uppsala , Sweden
| | - Mathias Hallberg
- The Beijer Laboratory , Department of Pharmaceutical Biosciences , Division of Biological Research on Drug Dependence , BMC , Uppsala University , P.O. Box 591 , SE-751 24 Uppsala , Sweden
| | - Mats Larhed
- Department of Medicinal Chemistry , BMC , Uppsala University , P.O. Box 574 , SE-751 23 Uppsala , Sweden.,Science for Life Laboratory , Department of Medicinal Chemistry , BMC , Uppsala University , SE-751 24 Uppsala , Sweden
| | - Siew Yeen Chai
- Biomedicine Discovery Institute , Department of Physiology , Monash University , Clayton , Victoria 3800 , Australia
| | - Philip E Thompson
- Medicinal Chemistry , Monash Institute of Pharmaceutical Sciences , Parkville , Victoria 3052 , Australia .
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42
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Girvin ZC, Andrews MK, Liu X, Gellman SH. Foldamer-templated catalysis of macrocycle formation. Science 2019; 366:1528-1531. [PMID: 31857487 DOI: 10.1126/science.aax7344] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 09/13/2019] [Accepted: 11/04/2019] [Indexed: 12/19/2022]
Abstract
Macrocycles, compounds containing a ring of 12 or more atoms, find use in human medicine, fragrances, and biological ion sensing. The efficient preparation of macrocycles is a fundamental challenge in synthetic organic chemistry because the high entropic cost of large-ring closure allows undesired intermolecular reactions to compete. Here, we present a bioinspired strategy for macrocycle formation through carbon-carbon bond formation. The process relies on a catalytic oligomer containing α- and β-amino acid residues to template the ring-closing process. The α/β-peptide foldamer adopts a helical conformation that displays a catalytic primary amine-secondary amine diad in a specific three-dimensional arrangement. This catalyst promotes aldol reactions that form rings containing 14 to 22 atoms. Utility is demonstrated in the synthesis of the natural product robustol.
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Affiliation(s)
- Zebediah C Girvin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Xinyu Liu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
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43
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Tyagi M, Begnini F, Poongavanam V, Doak BC, Kihlberg J. Drug Syntheses Beyond the Rule of 5. Chemistry 2019; 26:49-88. [DOI: 10.1002/chem.201902716] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/20/2019] [Indexed: 01/26/2023]
Affiliation(s)
- Mohit Tyagi
- Department of Chemistry–BMC Uppsala University Box 576 75123 Uppsala Sweden
| | - Fabio Begnini
- Department of Chemistry–BMC Uppsala University Box 576 75123 Uppsala Sweden
| | | | - Bradley C. Doak
- Department of Medicinal Chemistry, MIPS Monash University 381 Royal Parade Parkville Victoria 3052 Australia
| | - Jan Kihlberg
- Department of Chemistry–BMC Uppsala University Box 576 75123 Uppsala Sweden
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44
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Campos KR, Coleman PJ, Alvarez JC, Dreher SD, Garbaccio RM, Terrett NK, Tillyer RD, Truppo MD, Parmee ER. The importance of synthetic chemistry in the pharmaceutical industry. Science 2019; 363:363/6424/eaat0805. [PMID: 30655413 DOI: 10.1126/science.aat0805] [Citation(s) in RCA: 231] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Innovations in synthetic chemistry have enabled the discovery of many breakthrough therapies that have improved human health over the past century. In the face of increasing challenges in the pharmaceutical sector, continued innovation in chemistry is required to drive the discovery of the next wave of medicines. Novel synthetic methods not only unlock access to previously unattainable chemical matter, but also inspire new concepts as to how we design and build chemical matter. We identify some of the most important recent advances in synthetic chemistry as well as opportunities at the interface with partner disciplines that are poised to transform the practice of drug discovery and development.
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Affiliation(s)
- Kevin R Campos
- Global Chemistry, Merck & Co. Inc., Kenilworth, NJ 07033, USA.
| | - Paul J Coleman
- Global Chemistry, Merck & Co. Inc., Kenilworth, NJ 07033, USA.
| | - Juan C Alvarez
- Global Chemistry, Merck & Co. Inc., Kenilworth, NJ 07033, USA
| | | | | | | | | | | | - Emma R Parmee
- Global Chemistry, Merck & Co. Inc., Kenilworth, NJ 07033, USA
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Cummings MD, Sekharan S. Structure-Based Macrocycle Design in Small-Molecule Drug Discovery and Simple Metrics To Identify Opportunities for Macrocyclization of Small-Molecule Ligands. J Med Chem 2019; 62:6843-6853. [DOI: 10.1021/acs.jmedchem.8b01985] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Maxwell D. Cummings
- Janssen Research and Development, LLC, Welsh and McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Sivakumar Sekharan
- Cambridge Crystallographic Data Centre, 252 Nassau Street, Princeton, New Jersey 08542, United States
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Mohamed SH, Issa YM, Salim AI. Simultaneous quantification of simeprevir sodium: A hepatitis C protease inhibitor in binary and ternary mixtures with sofosbuvir and/or ledipasvir utilizing direct and H-point standard addition strategies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 210:290-297. [PMID: 30469132 DOI: 10.1016/j.saa.2018.07.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/18/2018] [Accepted: 07/05/2018] [Indexed: 05/24/2023]
Abstract
Simeprevir sodium (SMV); a novel hepatitis C inhibitor, quells hepatitis C viral replication by binding to and repressing the protease, hepatitis C infection (HCV) NS3/4A. In this way, it is known as a prompt acting antiviral agent. Calibration curves of SMV were built in various solvents; ethanol, methanol, acetonitrile, chloroform and dichloromethane. It is obeyed up to 60.0 μg/mL; in all solvents at two maximum wavelengths (280 and 327 nm). Several investigations show that, SMV might be present in a mixture of Sofosbuvir (SOF) and/or Ledipasvir (LDP). So far as that is concerned, H-point standard addition strategy (HPSAS) is made to identify it in binary or ternary mixtures. Recovery studies are in the prevalent range (93.0-107.0%) with relative standard deviation <1.5%. A correlation between the developed techniques is carried out and it demonstrates that these strategies are effectively applied for the simultaneous analysis of SMV, SOF and LDP in several synthetic samples and pharmaceutics. Statistical treatment of the acquired data is carried out against a newly published HPLC technique using F- and t-treatments.
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Affiliation(s)
- Sabrein H Mohamed
- Chemistry Department, Faculty of Science, Cairo University, 12613, Giza, Egypt.
| | - Yousry M Issa
- Chemistry Department, Faculty of Science, Cairo University, 12613, Giza, Egypt
| | - Alyaa I Salim
- Basic Science Department, Faculty of Engineering, Madina High Institute for Engineering and Technology, Giza, Egypt
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Özen A, Prachanronarong K, Matthew AN, Soumana DI, Schiffer CA. Resistance outside the substrate envelope: hepatitis C NS3/4A protease inhibitors. Crit Rev Biochem Mol Biol 2019; 54:11-26. [PMID: 30821513 DOI: 10.1080/10409238.2019.1568962] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Direct acting antivirals have dramatically increased the efficacy and tolerability of hepatitis C treatment, but drug resistance has emerged with some of these inhibitors, including nonstructural protein 3/4 A protease inhibitors (PIs). Although many co-crystal structures of PIs with the NS3/4A protease have been reported, a systematic review of these crystal structures in the context of the rapidly emerging drug resistance especially for early PIs has not been performed. To provide a framework for designing better inhibitors with higher barriers to resistance, we performed a quantitative structural analysis using co-crystal structures and models of HCV NS3/4A protease in complex with natural substrates and inhibitors. By comparing substrate structural motifs and active site interactions with inhibitor recognition, we observed that the selection of drug resistance mutations correlates with how inhibitors deviate from viral substrates in molecular recognition. Based on this observation, we conclude that guiding the design process with native substrate recognition features is likely to lead to more robust small molecule inhibitors with decreased susceptibility to resistance.
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Affiliation(s)
- Ayşegül Özen
- a Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , MA , USA
| | - Kristina Prachanronarong
- a Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , MA , USA
| | - Ashley N Matthew
- a Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , MA , USA
| | - Djade I Soumana
- a Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , MA , USA
| | - Celia A Schiffer
- a Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , MA , USA
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Horváth A, Depré D, A Vermeulen WA, Wuyts SL, Harutyunyan SR, Binot G, Cuypers J, Couck W, Den Heuvel DV. Ring-Closing Metathesis on Commercial Scale: Synthesis of HCV Protease Inhibitor Simeprevir. J Org Chem 2019; 84:4932-4939. [PMID: 30721066 DOI: 10.1021/acs.joc.8b03124] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The key macrocyclization step in the synthesis of simeprevir, a hepatitis C virus (HCV) antiviral drug, was studied. N-Boc substitution on the diene precursor changes the site of insertion of the metathesis catalyst and, consequently, the kinetic model of the ring closing metathesis (RCM), enabling a further increase in the macrocyclization efficiency under simulated high dilution (SHD) conditions. NMR of the inserted species of both first and second generation RCM catalysts are reported and discussed.
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Affiliation(s)
- András Horváth
- Janssen Pharmaceutica N.V. , 30 Turnhoutseweg , B-2340 Beerse , Belgium
| | - Dominique Depré
- Janssen Pharmaceutica N.V. , 30 Turnhoutseweg , B-2340 Beerse , Belgium
| | - Wim A A Vermeulen
- Janssen Pharmaceutica N.V. , 30 Turnhoutseweg , B-2340 Beerse , Belgium
| | - Stijn L Wuyts
- Janssen Pharmaceutica N.V. , 30 Turnhoutseweg , B-2340 Beerse , Belgium
| | | | - Grégori Binot
- Janssen Pharmaceutica N.V. , 30 Turnhoutseweg , B-2340 Beerse , Belgium
| | - Jef Cuypers
- Janssen Pharmaceutica N.V. , 30 Turnhoutseweg , B-2340 Beerse , Belgium
| | - Wouter Couck
- Janssen Pharmaceutica N.V. , 30 Turnhoutseweg , B-2340 Beerse , Belgium
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Kurpil B, Markushyna Y, Savateev A. Visible-Light-Driven Reductive (Cyclo)Dimerization of Chalcones over Heterogeneous Carbon Nitride Photocatalyst. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04182] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Bogdan Kurpil
- Max-Planck Institute of Colloids and Interfaces, Department of Colloid Chemistry, Research Campus Golm, 14424 Potsdam, Germany
| | - Yevheniia Markushyna
- Max-Planck Institute of Colloids and Interfaces, Department of Colloid Chemistry, Research Campus Golm, 14424 Potsdam, Germany
| | - Aleksandr Savateev
- Max-Planck Institute of Colloids and Interfaces, Department of Colloid Chemistry, Research Campus Golm, 14424 Potsdam, Germany
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50
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Liverton NJ. Evolution of HCV NS3/4a Protease Inhibitors. TOPICS IN MEDICINAL CHEMISTRY 2019. [DOI: 10.1007/7355_2018_39] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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