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Chaibi FZ, Brier L, Carré P, Landry V, Desmarets L, Tarricone A, Cantrelle FX, Moschidi D, Herledan A, Biela A, Bourgeois F, Ribes C, Ikherbane S, Malessan M, Dubuisson J, Belouzard S, Hanoulle X, Leroux F, Deprez B, Charton J. N-acylbenzimidazoles as selective Acylators of the catalytic cystein of the coronavirus 3CL protease. Eur J Med Chem 2024; 276:116707. [PMID: 39068863 DOI: 10.1016/j.ejmech.2024.116707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/16/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
The 3CL protease (3CLpro, Mpro) plays a key role in the replication of the SARS-CoV-2 and was validated as therapeutic target by the development and approval of specific antiviral drugs (nirmatrelvir, ensitrelvir), inhibitors of this protease. Moreover, its high conservation within the coronavirus family renders it an attractive therapeutic target for the development of anti-coronavirus compounds with broad spectrum activity to control COVID-19 and future coronavirus diseases. Here we report on the design, synthesis and structure-activity relationships of a new series of small covalent reversible inhibitors of the SARS-CoV-2 3CLpro. As elucidated thanks to the X-Ray structure of some inhibitors with the 3CLpro, the mode of inhibition involves acylation of the thiol of the catalytic cysteine. The synthesis of 60 analogs led to the identification of compound 56 that inhibits the SARS-CoV-2 3CLpro with high potency (IC50 = 70 nM) and displays antiviral activity in cells (EC50 = 3.1 μM). Notably, compound 56 inhibits the 3CLpro of three other human coronaviruses and exhibit a good selectivity against two human cysteine proteases. These results demonstrate the potential of this electrophilic N-acylbenzimidazole series as a basis for further optimization.
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Affiliation(s)
- Fatima-Zahra Chaibi
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Lucile Brier
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Paul Carré
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Valérie Landry
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Lowiese Desmarets
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Audrey Tarricone
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - François-Xavier Cantrelle
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Danai Moschidi
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Alexandre Biela
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Fanny Bourgeois
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Chloé Ribes
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Sarah Ikherbane
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Mathilde Malessan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Jean Dubuisson
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Sandrine Belouzard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Xavier Hanoulle
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France.
| | - Julie Charton
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France
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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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Khurshid R, Schulz JM, Hu J, Snowden TS, Reynolds RC, Schürer SC. Targeted degrader technologies as prospective SARS-CoV-2 therapies. Drug Discov Today 2024; 29:103847. [PMID: 38029836 PMCID: PMC10836335 DOI: 10.1016/j.drudis.2023.103847] [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: 09/30/2023] [Revised: 11/10/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023]
Abstract
COVID-19 remains a severe public health threat despite the WHO declaring an end to the public health emergency in May 2023. Continual development of SARS-CoV-2 variants with resistance to vaccine-induced or natural immunity necessitates constant vigilance as well as new vaccines and therapeutics. Targeted protein degradation (TPD) remains relatively untapped in antiviral drug discovery and holds the promise of attenuating viral resistance development. From a unique structural design perspective, this review covers antiviral degrader merits and challenges by highlighting key coronavirus protein targets and their co-crystal structures, specifically illustrating how TPD strategies can refine existing SARS-CoV-2 3CL protease inhibitors to potentially produce superior protease-degrading agents.
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Affiliation(s)
- Rabia Khurshid
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Joseph M Schulz
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jiaming Hu
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Timothy S Snowden
- The University of Alabama, Department of Chemistry and Biochemistry and Center for Convergent Bioscience and Medicine, 250 Hackberry Lane, Tuscaloosa, AL 35487-0336, USA
| | - Robert C Reynolds
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35205, USA
| | - Stephan C Schürer
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Institute for Data Science & Computing, University of Miami, Coral Gables, FL 33146, USA.
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4
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Brier L, Hassan H, Hanoulle X, Landry V, Moschidi D, Desmarets L, Rouillé Y, Dumont J, Herledan A, Warenghem S, Piveteau C, Carré P, Ikherbane S, Cantrelle FX, Dupré E, Dubuisson J, Belouzard S, Leroux F, Deprez B, Charton J. Novel dithiocarbamates selectively inhibit 3CL protease of SARS-CoV-2 and other coronaviruses. Eur J Med Chem 2023; 250:115186. [PMID: 36796300 PMCID: PMC9901219 DOI: 10.1016/j.ejmech.2023.115186] [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: 12/05/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023]
Abstract
Since end of 2019, the global and unprecedented outbreak caused by the coronavirus SARS-CoV-2 led to dramatic numbers of infections and deaths worldwide. SARS-CoV-2 produces two large viral polyproteins which are cleaved by two cysteine proteases encoded by the virus, the 3CL protease (3CLpro) and the papain-like protease, to generate non-structural proteins essential for the virus life cycle. Both proteases are recognized as promising drug targets for the development of anti-coronavirus chemotherapy. Aiming at identifying broad spectrum agents for the treatment of COVID-19 but also to fight emergent coronaviruses, we focused on 3CLpro that is well conserved within this viral family. Here we present a high-throughput screening of more than 89,000 small molecules that led to the identification of a new chemotype, potent inhibitor of the SARS-CoV-2 3CLpro. The mechanism of inhibition, the interaction with the protease using NMR and X-Ray, the specificity against host cysteine proteases and promising antiviral properties in cells are reported.
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Affiliation(s)
- Lucile Brier
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Haitham Hassan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Xavier Hanoulle
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Valerie Landry
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Danai Moschidi
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Lowiese Desmarets
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Yves Rouillé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Julie Dumont
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Sandrine Warenghem
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Paul Carré
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Sarah Ikherbane
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - François-Xavier Cantrelle
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Elian Dupré
- CNRS, EMR9002 - BSI - Integrative Structural Biology, F-59000, Lille, France; Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000, Lille, France
| | - Jean Dubuisson
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Sandrine Belouzard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France; Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000, Lille, France.
| | - Julie Charton
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, EGID, F-59000, Lille, France
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Rudra Paul A, Debnath S, Majumdar S. Water‐SDS‐Ionic Liquid Catalytic System for the Synthesis of Pyrano‐chromenes and in‐silicio Approach to Predict Inhibitory Activity Against Mpro of SARS‐CoV‐2**. ChemistrySelect 2023. [DOI: 10.1002/slct.202300007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Abhijit Rudra Paul
- Department of Chemistry Tripura University Suryamaninagar 799 022 Tripura INDIA
| | - Sudhan Debnath
- Department of Chemistry Netaji Subhash Mahavidyalaya Tripura 799114 India
| | - Swapan Majumdar
- Department of Chemistry Tripura University Suryamaninagar 799 022 Tripura INDIA
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Chaube U, Patel BD, Bhatt HG. A hypothesis on designing strategy of effective RdRp inhibitors for the treatment of SARS-CoV-2. 3 Biotech 2023; 13:12. [PMID: 36532857 PMCID: PMC9755803 DOI: 10.1007/s13205-022-03430-w] [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: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Vaccines are used as one of the major weapons for the eradication of pandemic. However, the rise of different variants of the SARS-CoV-2 virus is creating doubts regarding the end of the pandemic. Hence, there is an urgent need to develop more drug candidates which can be useful for the treatment of COVID-19. In the present research for the scientific hypothesis, emphasis was given on the direct antiviral therapy available for the treatment of COVID-19. In lieu of this, the available molecular targets which include Severe Acute Respiratory Syndrome Chymotrypsin-like Protease (SARS-3CLpro), Papain-Like Cysteine Protease (PLpro), and RNA-Dependent RNA Polymerase (RdRp) were explored. As per the current scientific reports and literature, among all the available molecular targets, RNA-Dependent RNA Polymerase (RdRp) was found to be a crucial molecular target for the treatment of COVID-19. Most of the inhibitors which are reported against this target consisted of the free amine group and carbonyl group which might be playing an important role in the binding interaction with the RdRp protein. Among all the reported RdRp inhibitors, remdesivir, favipiravir, and molnupiravir were found to be the most promising drugs against COVID-19. Overall, the structural features of this RNA-Dependent RNA Polymerase (RdRp) inhibitors proved the importance of pyrrolo-triazine and pyrimidine scaffolds. Previous computational models of these drug molecules indicated that substitution with the polar functional group, hydrogen bond donor, and electronegative atoms on these scaffolds may increase the activity against the RdRp protein. Hence, in line with the proposed hypothesis, in the present research work for the evaluation of the hypothesis, new molecules were designed from the pyrrolo-triazine and pyrimidine scaffolds. Further, molecular docking and MD simulation studies were performed with these designed molecules. All these designed molecules (DM-1, DM-2, and DM-3) showed the results as per the proposed hypothesis. Among all the designed molecules, DM-1 showed promising results against the RdRp protein of SARS-CoV-2. In the future, these structural features can be used for the development of new RdRp inhibitors with improved activity. Also, in the future lead compound DM-1 can be explored against the RdRp protein for the treatment of COVID-19.
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Affiliation(s)
- Udit Chaube
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481 India
| | - Bhumika D. Patel
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481 India
| | - Hardik G. Bhatt
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat 382481 India
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Wang S, Ren Y, Wang Z, Jiang X, Xu S, Zhang X, Zhao S, Zalloum WA, Liu X, Zhan P. The current progress in the use of boron as a platform for novel antiviral drug design. Expert Opin Drug Discov 2022; 17:1329-1340. [PMID: 36448326 DOI: 10.1080/17460441.2023.2153829] [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: 12/02/2022]
Abstract
INTRODUCTION Boron has attracted extensive interest due to several FDA-approved boron-containing drugs and other pharmacological agents in clinical trials. As a semimetal, it has peculiar biochemical characteristics which could be utilized in designing novel drugs against drug-resistant viruses. Emerging and reemerging viral pandemics are major threats to human health. Accordingly, we aim to comprehensively review the current status of antiviral boron-containing compounds. AREAS COVERED This review focuses on the utilization of boron to design molecules against viruses from two perspectives: (i) single boron atom-containing compounds acting on miscellaneous viral targets and (ii) boron clusters. The peculiar properties of antiviral boron-containing compounds and their diverse binding modes with viral targets are described in detail in this review. EXPERT OPINION Compounds bearing boronic acid can interact with viral targets by forming covalent or robust hydrogen bonds. This feature is valuable for combating resistant viruses. Furthermore, boron clusters can form dihydrogen bonds and bear features such as three-dimensional aromaticity, hydrophobicity, and biological stability. All these features demonstrated boron as a probable essential element with immense potential for drug design.
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Affiliation(s)
- Shuo Wang
- 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, PR China
| | - Yujie Ren
- 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, PR China
| | - Zhao Wang
- 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, PR China
| | - Xiangyi Jiang
- 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, 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, PR China
| | - Xujie Zhang
- 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, PR China
| | - Shujie Zhao
- 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, PR China
| | - Waleed A Zalloum
- Department of Pharmacy, Faculty of Health Science, American University of Madaba, P.O Box 2882 11821, Amman, Jordan
| | - 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, 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, PR China
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Samrat SK, Xu J, Xie X, Gianti E, Chen H, Zou J, Pattis JG, Elokely K, Lee H, Li Z, Klein ML, Shi PY, Zhou J, Li H. Allosteric inhibitors of the main protease of SARS-CoV-2. Antiviral Res 2022; 205:105381. [PMID: 35835291 PMCID: PMC9272661 DOI: 10.1016/j.antiviral.2022.105381] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 12/19/2022]
Abstract
SARS-CoV-2 has raised the alarm to search for effective therapy for this virus. To date several vaccines have been approved but few available drugs reported recently still need approval from FDA. Remdesivir was approved for emergency use only. In this report, the SARS-CoV-2 3CLpro was expressed and purified. By using a FRET-based enzymatic assay, we have screened a library consisting of more than 300 different niclosamide derivatives and identified three molecules JMX0286, JMX0301, and JMX0941 as potent allosteric inhibitors against SARS-CoV-2 3CLpro, with IC50 values similar to that of known covalent inhibitor boceprevir. In a cell-based antiviral assay, these inhibitors can inhibit the virus growth with EC50 in the range of 2-3 μM. The mechanism of action of JMX0286, JMX0301, and JMX0941 were characterized by enzyme kinetics, affinity binding and protein-based substrate digestion. Molecular docking, molecular dynamics (MD) simulations and hydration studies suggested that JMX0286, JMX0301, JMX0941 bind specifically to an allosteric pocket of the SARS-CoV-2 3CL protease. This study provides three potent compounds for further studies.
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Affiliation(s)
- Subodh Kumar Samrat
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ, 85721-0207, USA.
| | - Jimin Xu
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Eleonora Gianti
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jason G Pattis
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Khaled Elokely
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Hyun Lee
- Department of Pharmaceutical Sciences at College of Pharmacy and Biophysics Core at Research Resources Center, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Zhong Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ, 85721-0207, USA
| | - Michael L Klein
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA, 19122, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA; Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, 77555, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, 77555, USA.
| | - Hongmin Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ, 85721-0207, USA; BIO5 Institute, The University of Arizona, Tucson, Tucson, AZ, 85721, USA.
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9
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Sahoo R, Sahu P, Swargam S, Kumari I, Behera B. Repurposing small molecules of Tephrosia purpurea against SARS-CoV-2 main protease. J Biomol Struct Dyn 2022:1-12. [PMID: 35983619 DOI: 10.1080/07391102.2022.2112616] [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: 10/15/2022]
Abstract
Coronavirus infection is a communicable disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which emerged as a global pandemic with deteriorating effect on the world's population. Main protease (Mpro) of SARS-CoV-2 plays a significant role in the viral replication, transcription and disease propagation as well as a potential candidate for drug discovery and development for COVID-19 infection. The current study employed state of art structure-based drug discovery to decipher the role of phytochemicals of Tephrosia purpurea against Mpro. Tephrosia purpurea is being used as a traditional medicinal plant for the treatment of cough, breathlessness and fever as per the Indian Materia Medica. Screening of the phytochemicals of Tephrosia purpurea against Mpro was performed using molecular docking approach to identify the top 5 hits (+)-tephrorin B, deguelin, vitamin p, lanceolarin and 3beta-hydroxy-20(29)-lupene with binding energy of -8.4, -8.1, -8.0, -7.8, and -7.8 kcal/mol, respectively. Furthermore, identified top 5 hits were subjected to drug-likeness and toxicity prediction as well as MM-GBSA calculation. Out of the five molecules four molecules were predicted not to comprise any mutagenic and carcinogenic effects. Top two molecules based on the drug-likeness properties for oral bio-availability were further analysed by molecular dynamics simulation at 100 ns timescale. It was observed from the dynamic behaviour of the two complexes that the addition of these molecules changed the conformation and stability of the apo protein; thus may act as inhibitors for Mpro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rosaleen Sahoo
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.,Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Parameswar Sahu
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education & Research, New Delhi, India
| | - Sandeep Swargam
- Genomics and Epidemiology Division, National Centre for Disease Control, Civil Lines, New Delhi, India
| | - Indu Kumari
- Department of Environmental Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Banshidhar Behera
- Department of Dravyaguna, Ayurvedic and Unani Tibbia College, New Delhi, India
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10
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Design, synthesis and docking study of Vortioxetine derivatives as a SARS-CoV-2 main protease inhibitor. DARU : JOURNAL OF FACULTY OF PHARMACY, TEHRAN UNIVERSITY OF MEDICAL SCIENCES 2022; 30:139-152. [PMID: 35508799 PMCID: PMC9067898 DOI: 10.1007/s40199-022-00441-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 04/09/2022] [Indexed: 12/02/2022]
Abstract
Purpose Vortioxetine an anti-depressant FDA-drug recently reported showing better in vitro efficacy against SARS-CoV-2. Methods In this study, we have synthesized ten new derivatives having alkenes, alkynes, benzyl, aryl, and mixed carbamate at the N-terminal of vortioxetine. Then the binding energy and interactions with the crucial amino acid residues in the binding pocket of main protease (Mpro) of SARS-CoV-2, of reported and ten newly synthesized vortioxetine derivatives (total thirty-one) in comparison with remdesivir are analyzed and presented in this paper. Results Based on the docking scores predicted by ADV and AD, most vortioxetine derivatives showed better binding efficiency towards Mpro of SARS-CoV-2 in comparison with remdesivir (an EUA approved drug against SARS-CoV-2 Mpro) and vortioxetine. Conclusion This study shows that some vortioxetine derivatives can be developed into promising drugs for COVID-19 treatment. Supplementary Information The online version contains supplementary material available at 10.1007/s40199-022-00441-z.
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11
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Bogdanov AV, Sirazieva AR, Voloshina AD, Abzalilov TA, Samorodov AV, Mironov VF. Synthesis and Antimicrobial, Antiplatelet, and Anticoagulant Activities of New Isatin Deivatives Containing a Hetero-Fused Imidazole Fragment. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2022. [PMCID: PMC9007260 DOI: 10.1134/s1070428022030101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A series of isatin derivatives containing an adenine or theophylline fragment have been synthesized. The corresponding N′-[2-(trimethylammonio)acetyl] and N′-(2-pyridinioacetyl) hydrazones have been found to exhibit neither cytotoxicity nor hemotoxicity. Quaternary salts based on adenine derivatives of 5-methyl- and 5-ethylisatins showed the highest antiplatelet activity which exceeded the activity of acetylsalicylic acid by a factor of 1.5.
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Affiliation(s)
- A. V. Bogdanov
- Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, 420088 Kazan, Russia
- Kazan (Volga region) Federal University, 420008 Kazan, Russia
| | - A. R. Sirazieva
- Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, 420088 Kazan, Russia
| | - A. D. Voloshina
- Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, 420088 Kazan, Russia
| | - T. A. Abzalilov
- Bashkir State Medical University, Ministry of Health of the Russian Federation, 450008 Ufa, Russia
| | - A. V. Samorodov
- Bashkir State Medical University, Ministry of Health of the Russian Federation, 450008 Ufa, Russia
| | - V. F. Mironov
- Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, 420088 Kazan, Russia
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12
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Meyer CC, Dubey ZJ, Krische MJ. Enantioselective Iridium-Catalyzed Reductive Coupling of Dienes with Oxetanones and N-Acyl-Azetidinones Mediated by 2-Propanol. Angew Chem Int Ed Engl 2022; 61:e202115959. [PMID: 35119714 PMCID: PMC8940717 DOI: 10.1002/anie.202115959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Indexed: 12/26/2022]
Abstract
Cyclometallated iridium-PhanePhos complexes generated in situ from [Ir(cod)Cl]2 and (R)-PhanePhos catalyze 2-propanol-mediated reductive couplings of 2-substituted dienes with oxetanone and N-acyl-azetidinones to form branched homoallylic oxetanols and azetidinols with excellent control of regio- and enantioselectivity without C-C cleavage of the strained ring via enantiotopic π-facial selection of transient allyliridium nucleophiles. This work represents the first systematic study of enantioselective additions to symmetric ketones.
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Affiliation(s)
- Cole C. Meyer
- University of Texas at Austin, Department of Chemistry, 105 E 24th St. (A5300), Austin, TX 78712-1167 (USA)
| | - Zachary J. Dubey
- University of Texas at Austin, Department of Chemistry, 105 E 24th St. (A5300), Austin, TX 78712-1167 (USA)
| | - Michael J. Krische
- University of Texas at Austin, Department of Chemistry, 105 E 24th St. (A5300), Austin, TX 78712-1167 (USA)
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13
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Jawarkar RD, Bakal RL, Zaki MEA, Al-Hussain S, Ghosh A, Gandhi A, Mukerjee N, Samad A, Masand VH, Lewaa I. QSAR based virtual screening derived identification of a novel hit as a SARS CoV-229E 3CL pro Inhibitor: GA-MLR QSAR modeling supported by molecular Docking, molecular dynamics simulation and MMGBSA calculation approaches. ARAB J CHEM 2022; 15:103499. [PMID: 34909066 PMCID: PMC8524701 DOI: 10.1016/j.arabjc.2021.103499] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/10/2021] [Indexed: 12/26/2022] Open
Abstract
Congruous coronavirus drug targets and analogous lead molecules must be identified as quickly as possible to produce antiviral therapeutics against human coronavirus (HCoV SARS 3CLpro) infections. In the present communication, we bear recognized a HIT candidate for HCoV SARS 3CLpro inhibition. Four Parametric GA-MLR primarily based QSAR model (R2:0.84, R2adj:0.82, Q2loo: 0.78) was once promoted using a dataset over 37 structurally diverse molecules along QSAR based virtual screening (QSAR-VS), molecular docking (MD) then molecular dynamic simulation (MDS) analysis and MMGBSA calculations. The QSAR-based virtual screening was utilized to find novel lead molecules from an in-house database of 100 molecules. The QSAR-vS successfully offered a hit molecule with an improved PEC50 value from 5.88 to 6.08. The benzene ring, phenyl ring, amide oxygen and nitrogen, and other important pharmacophoric sites are revealed via MD and MDS studies. Ile164, Pro188, Leu190, Thr25, His41, Asn46, Thr47, Ser49, Asn189, Gln191, Thr47, and Asn141 are among the key amino acid residues in the S1 and S2 pocket. A stable complex of a lead molecule with the HCoV SARS 3CLpro was discovered using MDS. MM-GBSA calculations resulted from MD simulation results well supported with the binding energies calculated from the docking results. The results of this study can be exploited to develop a novel antiviral target, such as an HCoV SARS 3CLpro Inhibitor.
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Key Words
- 3CLpro, 3C like Protease
- FDA, Food and Drug Administration
- GA-MLR
- GA-MLR, Genetic Algorithm Multilinear Regression
- HCoV SARS 3CLpro
- HCoV-HKU1, Human coronavirus HKU1
- HCoV-NL63, Human coronavirus NL63
- HCoVs, human coronaviruses
- Lead
- MD, Molecular Docking
- MDS, molecular dynamic simulation
- MERS, Middle East Respiratory Syndrome
- MMGBSA calculations
- MMGBSA, Molecular Mechanics Generalized Born and Surface Area
- Molecular docking and MD simulation
- OECD, Organization for Economic Corporation and Development
- QSAR based virtual screening
- QSAR, Quantitative Structure Activity Relationship
- RNA, Ribo-nucleic acid
- SARS, severe acute respiratory sign
- VS, Virtual Screening
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Affiliation(s)
- R D Jawarkar
- Department of Medicinal Chemistry, Dr. Rajendra Gode Institute of Pharmacy, University-Mardi Road, Amravati, Maharashtra, 444603, India
| | - Ravindrakumar L Bakal
- Department of Medicinal Chemistry, Dr. Rajendra Gode Institute of Pharmacy, University-Mardi Road, Amravati, Maharashtra, 444603, India
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Al-Imam Mohammad Ibn Saud Islamic university, Riyadh 13318, Saudi Arabia
| | - Sami Al-Hussain
- Department of Chemistry, Faculty of Science, Al-Imam Mohammad Ibn Saud Islamic university, Riyadh 13318, Saudi Arabia
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, Assam 781014, India
| | - Ajaykumar Gandhi
- Department of Chemistry, Government College of Arts and Science, Aurangabad, Maharashtra 431 004, India
| | - Nobendu Mukerjee
- Department of Microbiology; Ramakrishna Mission Vivekananda Centenary College, Akhil Mukherjee Rd, Chowdhary Para, Rahara, Khardaha, Kolkata, West Bengal 700118, India
| | - Abdul Samad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Vijay H Masand
- Department of Chemistry, Vidyabharti Mahavidyalaya, Camp Road, Amravati Maharashtra, India
| | - Israa Lewaa
- Department of Business Administration, Faculty of Business Administration, Economics & Political Science, The British University in Egypt (BUE), Cairo, Egypt
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14
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Dampalla CS, Rathnayake AD, Perera KD, Jesri ARM, Nguyen HN, Miller MJ, Thurman HA, Zheng J, Kashipathy MM, Battaile KP, Lovell S, Perlman S, Kim Y, Groutas WC, Chang KO. Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies. J Med Chem 2021; 64:17846-17865. [PMID: 34865476 PMCID: PMC8673480 DOI: 10.1021/acs.jmedchem.1c01037] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 12/21/2022]
Abstract
The COVID-19 pandemic is having a major impact on public health worldwide, and there is an urgent need for the creation of an armamentarium of effective therapeutics, including vaccines, biologics, and small-molecule therapeutics, to combat SARS-CoV-2 and emerging variants. Inspection of the virus life cycle reveals multiple viral- and host-based choke points that can be exploited to combat the virus. SARS-CoV-2 3C-like protease (3CLpro), an enzyme essential for viral replication, is an attractive target for therapeutic intervention, and the design of inhibitors of the protease may lead to the emergence of effective SARS-CoV-2-specific antivirals. We describe herein the results of our studies related to the application of X-ray crystallography, the Thorpe-Ingold effect, deuteration, and stereochemistry in the design of highly potent and nontoxic inhibitors of SARS-CoV-2 3CLpro.
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Affiliation(s)
| | - Athri D. Rathnayake
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Krishani Dinali Perera
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | | | - Harry Nhat Nguyen
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Matthew J. Miller
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Hayden A. Thurman
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Jian Zheng
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | | | | | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA 52242, USA
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
| | - William C. Groutas
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506, USA
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15
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Deb B, Debnath S, Chakraborty A, Majumdar S. Bis-indolylation of aldehydes and ketones using silica-supported FeCl 3: molecular docking studies of bisindoles by targeting SARS-CoV-2 main protease binding sites. RSC Adv 2021; 11:30827-30839. [PMID: 35498942 PMCID: PMC9041420 DOI: 10.1039/d1ra05679d] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
We report herein an operationally simple, efficient and versatile procedure for the synthesis of bis-indolylmethanes via the reaction of indoles with aldehydes or ketones in the presence of silica-supported ferric chloride under grindstone conditions. The prepared supported catalyst was characterized by SEM and EDX spectroscopy. The present protocol has several advantages such as shorter reaction time, high yield, avoidance of using harmful organic solvents during the reaction and tolerance of a wide range of functional groups. Molecular docking studies targeted toward the binding site of SARS-CoV-2 main protease (3CLpro or Mpro) enzymes were investigated with the synthesized bis-indoles. Our study revealed that some of the synthesized compounds have potentiality to inhibit the SARS-CoV-2 Mpro enzyme by interacting with key amino acid residues of the active sites via hydrophobic as well as hydrogen bonding interactions.
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Affiliation(s)
- Barnali Deb
- Department of Chemistry, Tripura University Suryamaninagar 799 022 India +91-381-237-4802 +91-381-237-9070
| | - Sudhan Debnath
- Department of Chemistry, Netaji Subhash Mahavidalaya Tripura 799114 India
| | - Ankita Chakraborty
- Department of Chemistry, Tripura University Suryamaninagar 799 022 India +91-381-237-4802 +91-381-237-9070
| | - Swapan Majumdar
- Department of Chemistry, Tripura University Suryamaninagar 799 022 India +91-381-237-4802 +91-381-237-9070
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16
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Godinho PIC, Soengas RG, Silva VLM. Therapeutic Potential of Glycosyl Flavonoids as Anti-Coronaviral Agents. Pharmaceuticals (Basel) 2021; 14:546. [PMID: 34200456 PMCID: PMC8227519 DOI: 10.3390/ph14060546] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 12/26/2022] Open
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread all over the world, creating a devastating socio-economic impact. Even though protective vaccines are starting to be administered, an effective antiviral agent for the prevention and treatment of COVID-19 is not available yet. Moreover, since new and deadly CoVs can emerge at any time with the potential of becoming pandemics, the development of therapeutic agents against potentially deadly CoVs is a research area of much current interest. In the search for anti-coronaviral drugs, researchers soon turned their heads towards glycosylated flavonoids. Glycosyl flavonoids, widespread in the plant kingdom, have received a lot of attention due to their widely recognized antioxidant, anti-inflammatory, neuroprotective, anticarcinogenic, antidiabetic, antimicrobial, and antiviral properties together with their capacity to modulate key cellular functions. The wide range of biological activities displayed by glycosyl flavonoids, along with their low toxicity, make them ideal candidates for drug development. In this review, we examine and discuss the up-to-date developments on glycosyl flavonoids as evidence-based natural sources of antivirals against coronaviruses and their potential role in the management of COVID-19.
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Affiliation(s)
- Patrícia I. C. Godinho
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Raquel G. Soengas
- Department of Organic and Inorganic Chemistry, University of Oviedo, Julián Clavería 7, 33006 Oviedo, Spain
| | - Vera L. M. Silva
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal;
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17
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Jaskolski M, Dauter Z, Shabalin IG, Gilski M, Brzezinski D, Kowiel M, Rupp B, Wlodawer A. Crystallographic models of SARS-CoV-2 3CL pro: in-depth assessment of structure quality and validation. IUCRJ 2021; 8:238-256. [PMID: 33708401 PMCID: PMC7924243 DOI: 10.1107/s2052252521001159] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/01/2021] [Indexed: 05/26/2023]
Abstract
The appearance at the end of 2019 of the new SARS-CoV-2 coronavirus led to an unprecedented response by the structural biology community, resulting in the rapid determination of many hundreds of structures of proteins encoded by the virus. As part of an effort to analyze and, if necessary, remediate these structures as deposited in the Protein Data Bank (PDB), this work presents a detailed analysis of 81 crystal structures of the main protease 3CLpro, an important target for the design of drugs against COVID-19. The structures of the unliganded enzyme and its complexes with a number of inhibitors were determined by multiple research groups using different experimental approaches and conditions; the resulting structures span 13 different polymorphs representing seven space groups. The structures of the enzyme itself, all determined by molecular replacement, are highly similar, with the exception of one polymorph with a different inter-domain orientation. However, a number of complexes with bound inhibitors were found to pose significant problems. Some of these could be traced to faulty definitions of geometrical restraints for ligands and to the general problem of a lack of such information in the PDB depositions. Several problems with ligand definition in the PDB itself were also noted. In several cases extensive corrections to the models were necessary to adhere to the evidence of the electron-density maps. Taken together, this analysis of a large number of structures of a single, medically important protein, all determined within less than a year using modern experimental tools, should be useful in future studies of other systems of high interest to the biomedical community.
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Affiliation(s)
- Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Zbigniew Dauter
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Ivan G. Shabalin
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Miroslaw Gilski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Dariusz Brzezinski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Marcin Kowiel
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Bernhard Rupp
- k.-k Hofkristallamt, San Diego, CA 92084, USA
- Institute of Genetic Epidemiology, Medical University Innsbruck, A-6020 Innsbruck, Austria
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
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