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Mochamad L, Malarvili S, Jasmine K, Lim V. In vitro analysis of quercetin-like compounds from mistletoe Dendrophthoe pentandra (L.) Miq as a potential antiviral agent for Newcastle disease. F1000Res 2024; 12:1214. [PMID: 38962299 PMCID: PMC11220444 DOI: 10.12688/f1000research.133489.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/10/2024] [Indexed: 07/05/2024] Open
Abstract
Background Recent evidence suggests that some flavonoid compounds obtained from crude methanol extract of mistletoe leaves ( Dendrophthoe pentandra L. Miq), also known as Benalu Duku (BD), have antimicrobial effects. Thus, the plant has the potential to eliminate viruses that may cause outbreaks in chicken farms. This study aimed to prove the in vitro ability of flavonoid compounds, namely quercetin-like compounds (QLCs), to eliminate field viruses, specifically the Newcastle disease virus (NDV). Methods This research was performed in two stages. An in vitro test was used with a post-test of the control groups designed at a significance of 0.05. BD leaves (5 kg) were extracted using a maceration method with methanol and then separated into hexane, chloroform, ethyl acetate, and methanol fractions. The final extracted products were separated using semi-preparative high-performance liquid chromatography (HPLC) to obtain QLCs. The QLCs were identified and compared with quercetin using HPLC, proton and carbon nuclear magnetic resonance spectrometry, Fourier transform infrared spectrophotometry and ultra-performance liquid chromatography-mass spectrometry. The activity of QLCs was tested in vitro against the NDV at a virulence titter of 10 -5 Tissue Culture Infectious Dose 50% (TCID50) in chicken kidney cell culture. Results Solutions of 0.05% (w/v) QLCs were discovered to have antiviral activity against NDVs, with an average cytopathogenic effect antigenicity at a 10 -5 dilution (p<0.05). Conclusions QLCs from flavonoids from the leaves of BD have in vitro antiviral bioactivity against NDV at a virulence titter of 10-5 Tissue Culture Infectious Dose 50% (TCID50) in chicken kidney cell culture. QLCs may have the potential to be developed as medicinal compounds for the treatment of other human or animal viral infections.
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Affiliation(s)
- Lazuardi Mochamad
- Sub-division Veterinary Pharmacy Science, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, East Java, 60115, Indonesia
| | - Selvaraja Malarvili
- Faculty of Pharmaceutical Sciences, UCSI University, No.1, Jalan Menara Gading, Taman Connaught, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | - Khairat Jasmine
- Institute of Biological Science, Faculty of Science, University Malaya, Kuala Lumpur, 50603, Malaysia
| | - Vuanghao Lim
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam 13200 Kepala Batas, Penang, Penang, 13200, Malaysia
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2
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Zagórska A, Czopek A, Fryc M, Jończyk J. Inhibitors of SARS-CoV-2 Main Protease (Mpro) as Anti-Coronavirus Agents. Biomolecules 2024; 14:797. [PMID: 39062511 PMCID: PMC11275247 DOI: 10.3390/biom14070797] [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: 05/31/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
The main protease (Mpro) of SARS-CoV-2 is an essential enzyme that plays a critical part in the virus's life cycle, making it a significant target for developing antiviral drugs. The inhibition of SARS-CoV-2 Mpro has emerged as a promising approach for developing therapeutic agents to treat COVID-19. This review explores the structure of the Mpro protein and analyzes the progress made in understanding protein-ligand interactions of Mpro inhibitors. It focuses on binding kinetics, origin, and the chemical structure of these inhibitors. The review provides an in-depth analysis of recent clinical trials involving covalent and non-covalent inhibitors and emerging dual inhibitors targeting SARS-CoV-2 Mpro. By integrating findings from the literature and ongoing clinical trials, this review captures the current state of research into Mpro inhibitors, offering a comprehensive understanding of challenges and directions in their future development as anti-coronavirus agents. This information provides new insights and inspiration for medicinal chemists, paving the way for developing more effective Mpro inhibitors as novel COVID-19 therapies.
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Affiliation(s)
- Agnieszka Zagórska
- Department of Medicinal Chemistry, Jagiellonian University Medical College, Medyczna 9, 30-688 Kraków, Poland; (A.C.); (M.F.); (J.J.)
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Li H, Sun M, Lei F, Liu J, Chen X, Li Y, Wang Y, Lu J, Yu D, Gao Y, Xu J, Chen H, Li M, Yi Z, He X, Chen L. Methyl rosmarinate is an allosteric inhibitor of SARS-CoV-2 3 CL protease as a potential candidate against SARS-cov-2 infection. Antiviral Res 2024; 224:105841. [PMID: 38408645 DOI: 10.1016/j.antiviral.2024.105841] [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: 11/10/2023] [Revised: 02/09/2024] [Accepted: 02/24/2024] [Indexed: 02/28/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been ongoing for more than three years and urgently needs to be addressed. Traditional Chinese medicine (TCM) prescriptions have played an important role in the clinical treatment of patients with COVID-19 in China. However, it is difficult to uncover the potential molecular mechanisms of the active ingredients in these TCM prescriptions. In this paper, we developed a new approach by integrating the experimental assay, virtual screening, and the experimental verification, exploring the rapid discovery of active ingredients from TCM prescriptions. To achieve this goal, 4 TCM prescriptions in clinical use for different indications were selected to find the antiviral active ingredients in TCMs. The 3-chymotrypsin-like protease (3CLpro), an important target for fighting COVID-19, was utilized to determine the inhibitory activity of the TCM prescriptions and single herb. It was found that 10 single herbs had better inhibitory activity than other herbs by using a fluorescence resonance energy transfer (FRET) - based enzymatic assay of SARS-CoV-2 3CLpro. The ingredients contained in 10 herbs were thus virtually screened and the predicted active ingredients were experimentally validated. Thus, such a research strategy firstly removed many single herbs with no inhibitory activity against SARS-CoV-2 3CLpro at the very beginning by FRET-based assay, making our subsequent virtual screening more effective. Finally, 4 active components were found to have stronger inhibitory effects on SARS-CoV-2 3CLpro, and their inhibitory mechanism was subsequently investigated. Among of them, methyl rosmarinate as an allosteric inhibitor of SARS-CoV-2 3CLpro was confirmed and its ability to inhibit viral replication was demonstrated by the SARS-CoV-2 replicon system. To validate the binding mode via docking, the mutation experiment, circular dichroism (CD), enzymatic inhibition and surface plasmon resonance (SPR) assay were performed, demonstrating that methyl rosmarinate bound to the allosteric site of SARS-CoV-2 3CLpro. In conclusion, this paper provides the new ideas for the rapid discovery of active ingredients in TCM prescriptions based on a specific target, and methyl rosmarinate has the potential to be developed as an antiviral therapeutic candidate against SARS-CoV-2 infection.
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Affiliation(s)
- Hongtao Li
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Meng Sun
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Fuzhi Lei
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 210009, China; Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Xixiang Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yaqi Li
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China; Peptide and small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China; DP Technology, Beijing, China
| | - Ying Wang
- The National and Local Joint Engineering Laboratory of Animal Peptide Drug Development, College of Life Sciences, Hunan Normal University, Changsha 410081, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha 410081, China; Peptide and small Molecule Drug R&D Plateform, Furong Laboratory, Hunan Normal University, Changsha 410081, Hunan, China
| | - Jiani Lu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Danmei Yu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yueqiu Gao
- Department of Hepatopathy, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China; Laboratory of Cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China; Institute of Infectious Diseases of Integrated Traditional Chinese and Western Medicine, China
| | - Jianrong Xu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Man Li
- Laboratory of Cellular Immunity, Shuguang Hospital, Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.
| | - Zhigang Yi
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China; Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai, 200062, China.
| | - Lili Chen
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China; Longhua Hospital Shanghai University of Traditional Chinese Medicine, 725 South Wanping Road, Shanghai, 200032, China.
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Pennisi R, Gentile D, Rescifina A, Napoli E, Trischitta P, Piperno A, Sciortino MT. An Integrated In Silico and In Vitro Approach for the Identification of Natural Products Active against SARS-CoV-2. Biomolecules 2023; 14:43. [PMID: 38254643 PMCID: PMC10813393 DOI: 10.3390/biom14010043] [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: 11/30/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has provoked a global health crisis due to the absence of a specific therapeutic agent. 3CLpro (also known as the main protease or Mpro) and PLpro are chymotrypsin-like proteases encoded by the SARS-CoV-2 genome, and play essential roles during the virus lifecycle. Therefore, they are recognized as a prospective therapeutic target in drug discovery against SARS-CoV-2 infection. Thus, this work aims to collectively present potential natural 3CLpro and PLpro inhibitors by in silico simulations and in vitro entry pseudotype-entry models. We screened luteolin-7-O-glucuronide (L7OG), cynarin (CY), folic acid (FA), and rosmarinic acid (RA) molecules against PLpro and 3CLpro through a luminogenic substrate assay. We only reported moderate inhibitory activity on the recombinant 3CLpro and PLpro by L7OG and FA. Afterward, the entry inhibitory activity of L7OG and FA was tested in cell lines transduced with the two different SARS-CoV-2 pseudotypes harboring alpha (α) and omicron (o) spike (S) protein. The results showed that both compounds have a consistent inhibitory activity on the entry for both variants. However, L7OG showed a greater degree of entry inhibition against α-SARS-CoV-2. Molecular modeling studies were used to determine the inhibitory mechanism of the candidate molecules by focusing on their interactions with residues recognized by the protease active site and receptor-binding domain (RBD) of spike SARS-CoV-2. This work allowed us to identify the binding sites of FA and L7OG within the RBD domain in the alpha and omicron variants, demonstrating how FA is active in both variants. We have confidence that future in vivo studies testing the safety and effectiveness of these natural compounds are warranted, given that they are effective against a variant of concerns.
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Affiliation(s)
- Rosamaria Pennisi
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
| | - Davide Gentile
- Department of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, Via Mancinelli 7, 20131 Milano, Italy
| | - Antonio Rescifina
- Department of Drug and Health Sciences, University of Catania, V.le A. Doria 6, 95125 Catania, Italy;
| | - Edoardo Napoli
- Istituto di Chimica Biomolecolare—Consiglio Nazionale delle Ricerche, 95126 Catania, Italy;
| | - Paola Trischitta
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
| | - Maria Teresa Sciortino
- Department of Chemical, Biological, Pharmaceutical and Environmental Science, University of Messina, Viale Ferdinando Stagno d’Alcontres 31, 98166 Messina, Italy; (P.T.); (A.P.); (M.T.S.)
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Rieder GS, Nogara PA, Omage FB, Duarte T, Dalla Corte CL, da Rocha JBT. Computational analysis of the interactions between Ebselen and derivatives with the active site of the main protease from SARS-CoV-2. Comput Biol Chem 2023; 107:107956. [PMID: 37748316 DOI: 10.1016/j.compbiolchem.2023.107956] [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: 05/18/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/27/2023]
Abstract
The main protease (Mpro) of the novel coronavirus SARS-CoV-2 is a key target for developing antiviral drugs. Ebselen (EbSe) is a selenium-containing compound that has been shown to inhibit Mpro in vitro by forming a covalent bond with the cysteine (Cys) residue in the active site of the enzyme. However, EbSe can also bind to other proteins, like albumin, and low molecular weight compounds that have free thiol groups, such as Cys and glutathione (GSH), which may affect its availability and activity. In this study, we analyzed the Mpro interaction with EbSe, its analogues, and its metabolites with Cys, GSH, and albumin by molecular docking. We also simulated the electronic structure of the generated molecules by density functional theory (DFT) and explored the stability of EbSe and one of its best derivatives, EbSe-2,5-MeClPh, in the catalytic pocket of Mpro through covalent docking and molecular dynamics. Our results show that EbSe and its analogues bound to GSH/albumin have larger distance between the selenium atom of the ligands and the sulfur atom of Cys145 of Mpro than the other compounds. This suggests that EbSe and its GSH/albumin-analogues may have less affinity for the active site of Mpro. EbSe-2,5-MeClPh was found one of the best molecules, and in molecular dynamics simulations, it showed to undergo more conformational changes in the active site of Mpro, in relation to EbSe, which remained stable in the catalytic pocket. Moreover, this study also reveals that all compounds have the potential to interact closely with the active site of Mpro, providing us with a concept of which derivatives may be promising for in vitro analysis in the future. We propose that these compounds are potential covalent inhibitors of Mpro and that organoselenium compounds are molecules that should be studied for their antiviral properties.
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Affiliation(s)
- Guilherme Schmitt Rieder
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - Pablo Andrei Nogara
- Federal Institute of Education, Science and Technology Sul-rio-grandense (IFSul), Bagé 96418-400, RS, Brazil
| | - Folorunsho Bright Omage
- Biological Chemistry Laboratory, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil; Computational Biology Research Group, Embrapa Agricultural Informatics, Campinas, São Paulo, Brazil
| | - Tâmie Duarte
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - Cristiane Lenz Dalla Corte
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, 97105-900 Santa Maria, RS, Brazil
| | - João Batista Teixeira da Rocha
- Postgraduate Program in Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, 97105-900 Santa Maria, RS, Brazil; Department of Biochemistry, Institute of Basic Health Science, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil, 90035-003.
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Shafiq N, Mehroze A, Sarwar W, Arshad U, Parveen S, Rashid M, Farooq A, Rafiq N, Wondmie GF, Bin Jardan YA, Brogi S, Bourhia M. Exploration of phenolic acid derivatives as inhibitors of SARS-CoV-2 main protease and receptor binding domain: potential candidates for anti-SARS-CoV-2 therapy. Front Chem 2023; 11:1251529. [PMID: 37822772 PMCID: PMC10562575 DOI: 10.3389/fchem.2023.1251529] [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: 07/01/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023] Open
Abstract
Severe acute respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is the etiological virus of Coronavirus Disease 2019 (COVID-19) which has been a public health concern due to its high morbidity and high mortality. Hence, the search for drugs that incapacitate the virus via inhibition of vital proteins in its life cycle is ongoing due to the paucity of drugs in clinical use against the virus. Consequently, this study was aimed at evaluating the potentials of natural phenolics against the Main protease (Mpro) and the receptor binding domain (RBD) using molecular modeling techniques including molecular docking, molecular dynamics (MD) simulation, and density functional theory (DFT) calculations. To this end, thirty-five naturally occurring phenolics were identified and subjected to molecular docking simulation against the proteins. The results showed the compounds including rosmarinic acid, cynarine, and chlorogenic acid among many others possessed high binding affinities for both proteins as evident from their docking scores, with some possessing lower docking scores compared to the standard compound (Remdesivir). Further subjection of the hit compounds to drug-likeness, pharmacokinetics, and toxicity profiling revealed chlorogenic acid, rosmarinic acid, and chicoric acid as the compounds with desirable profiles and toxicity properties, while the study of their electronic properties via density functional theory calculations revealed rosmarinic acid as the most reactive and least stable among the sets of lead compounds that were identified in the study. Molecular dynamics simulation of the complexes formed after docking revealed the stability of the complexes. Ultimately, further experimental procedures are needed to validate the findings of this study.
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Affiliation(s)
- Nusrat Shafiq
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Aiman Mehroze
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Warda Sarwar
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Uzma Arshad
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Shagufta Parveen
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Maryam Rashid
- Synthetic and Natural Products Discovery (SNPD) Laboratory, Department of Chemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | - Ariba Farooq
- Department of Chemistry, University of Lahore, Lahore, Pakistan
| | - Naila Rafiq
- Department of Biochemistry, Government College Women University Faisalabad, Faisalabad, Pakistan
| | | | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Simone Brogi
- Department of Pharmacy, Pisa University, Pisa, Italy
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune, Morocco
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7
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Maltarollo VG, da Silva EB, Kronenberger T, Sena Andrade MM, de Lima Marques GV, Cândido Oliveira NJ, Santos LH, Oliveira Rezende Júnior CD, Cassiano Martinho AC, Skinner D, Fajtová P, M Fernandes TH, Silveira Dos Santos ED, Rodrigues Gazolla PA, Martins de Souza AP, da Silva ML, Dos Santos FS, Lavorato SN, Oliveira Bretas AC, Carvalho DT, Franco LL, Luedtke S, Giardini MA, Poso A, Dias LC, Podust LM, Alves RJ, McKerrow J, Andrade SF, Teixeira RR, Siqueira-Neto JL, O'Donoghue A, de Oliveira RB, Ferreira RS. Structure-based discovery of thiosemicarbazones as SARS-CoV-2 main protease inhibitors. Future Med Chem 2023; 15:959-985. [PMID: 37435731 DOI: 10.4155/fmc-2023-0034] [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] [Indexed: 07/13/2023] Open
Abstract
Aim: Discovery of novel SARS-CoV-2 main protease (Mpro) inhibitors using a structure-based drug discovery strategy. Materials & methods: Virtual screening employing covalent and noncovalent docking was performed to discover Mpro inhibitors, which were subsequently evaluated in biochemical and cellular assays. Results: 91 virtual hits were selected for biochemical assays, and four were confirmed as reversible inhibitors of SARS CoV-2 Mpro with IC50 values of 0.4-3 μM. They were also shown to inhibit SARS-CoV-1 Mpro and human cathepsin L. Molecular dynamics simulations indicated the stability of the Mpro inhibitor complexes and the interaction of ligands at the subsites. Conclusion: This approach led to the discovery of novel thiosemicarbazones as potent SARS-CoV-2 Mpro inhibitors.
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Affiliation(s)
- Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Thales Kronenberger
- Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided & Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, 72076, Germany
- Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, Tübingen, 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Marina Mol Sena Andrade
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Gabriel V de Lima Marques
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Nereu J Cândido Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Lucianna H Santos
- Department of Biochemistry & Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Celso de Oliveira Rezende Júnior
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, 38400-902, Brazil
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Ana C Cassiano Martinho
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, 38400-902, Brazil
| | - Danielle Skinner
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Pavla Fajtová
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
- Institute of Organic Chemistry & Biochemistry, Academy of Sciences of the Czech Republic, Prague, 16610, Czech Republic
| | - Thaís H M Fernandes
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
- Pharmaceutical Synthesis Group (PHARSG), Departamento de Produção de Matéria-Prima, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
| | - Eduardo da Silveira Dos Santos
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
- Pharmaceutical Synthesis Group (PHARSG), Departamento de Produção de Matéria-Prima, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
| | - Poliana A Rodrigues Gazolla
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Ana P Martins de Souza
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Milene Lopes da Silva
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Fabíola S Dos Santos
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Stefânia N Lavorato
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
- Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Barreiras, Bahia, 47810-047, Brazil
| | - Ana C Oliveira Bretas
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Diogo Teixeira Carvalho
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Lucas Lopardi Franco
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Stephanie Luedtke
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Miriam A Giardini
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Antti Poso
- Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Tübingen 72076, Germany
- Cluster of Excellence iFIT (EXC 2180) 'Image-Guided & Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, 72076, Germany
- Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, Tübingen, 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Luiz C Dias
- Instituto de Química, Universidade Estadual de Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Larissa M Podust
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Ricardo J Alves
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - James McKerrow
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Saulo F Andrade
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
- Pharmaceutical Synthesis Group (PHARSG), Departamento de Produção de Matéria-Prima, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90160-093, Brazil
| | - Róbson R Teixeira
- Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Departamento de Química, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Jair L Siqueira-Neto
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Anthony O'Donoghue
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0657, USA
| | - Renata B de Oliveira
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, 31270-901, Brazil
| | - Rafaela S Ferreira
- Department of Biochemistry & Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
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