1
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Rafiq A, Jabeen T, Aslam S, Ahmad M, Ashfaq UA, Mohsin NUA, Zaki MEA, Al-Hussain SA. A Comprehensive Update of Various Attempts by Medicinal Chemists to Combat COVID-19 through Natural Products. Molecules 2023; 28:4860. [PMID: 37375415 PMCID: PMC10305344 DOI: 10.3390/molecules28124860] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The ongoing COVID-19 pandemic has resulted in a global panic because of its continual evolution and recurring spikes. This serious malignancy is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the outbreak, millions of people have been affected from December 2019 till now, which has led to a great surge in finding treatments. Despite trying to handle the pandemic with the repurposing of some drugs, such as chloroquine, hydroxychloroquine, remdesivir, lopinavir, ivermectin, etc., against COVID-19, the SARS-CoV-2 virus continues its out-of-control spread. There is a dire need to identify a new regimen of natural products to combat the deadly viral disease. This article deals with the literature reports to date of natural products showing inhibitory activity towards SARS-CoV-2 through different approaches, such as in vivo, in vitro, and in silico studies. Natural compounds targeting the proteins of SARS-CoV-2-the main protease (Mpro), papain-like protease (PLpro), spike proteins, RNA-dependent RNA polymerase (RdRp), endoribonuclease, exoribonuclease, helicase, nucleocapsid, methyltransferase, adeno diphosphate (ADP) phosphatase, other nonstructural proteins, and envelope proteins-were extracted mainly from plants, and some were isolated from bacteria, algae, fungi, and a few marine organisms.
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Affiliation(s)
- Ayesha Rafiq
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Tooba Jabeen
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Sana Aslam
- Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
| | - Noor ul Amin Mohsin
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Magdi E. A. Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Sami A. Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
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2
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Barazorda-Ccahuana HL, Goyzueta-Mamani LD, Candia Puma MA, Simões de Freitas C, de Sousa Vieria Tavares G, Pagliara Lage D, Ferraz Coelho EA, Chávez-Fumagalli MA. Computer-aided drug design approaches applied to screen natural product's structural analogs targeting arginase in Leishmania spp. F1000Res 2023; 12:93. [PMID: 37424744 PMCID: PMC10323282 DOI: 10.12688/f1000research.129943.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/12/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction: Leishmaniasis is a disease with high mortality rates and approximately 1.5 million new cases each year. Despite the new approaches and advances to fight the disease, there are no effective therapies. Methods: Hence, this study aims to screen for natural products' structural analogs as new drug candidates against leishmaniasis. We applied Computer-aided drug design (CADD) approaches, such as virtual screening, molecular docking, molecular dynamics simulation, molecular mechanics-generalized Born surface area (MM-GBSA) binding free estimation, and free energy perturbation (FEP) aiming to select structural analogs from natural products that have shown anti-leishmanial and anti-arginase activities and that could bind selectively against the Leishmania arginase enzyme. Results: The compounds 2H-1-benzopyran, 3,4-dihydro-2-(2-methylphenyl)-(9CI), echioidinin, and malvidin showed good results against arginase targets from three parasite species and negative results for potential toxicities. The echioidinin and malvidin ligands generated interactions in the active center at pH 2.0 conditions by MM-GBSA and FEP methods. Conclusions: This work suggests the potential anti-leishmanial activity of the compounds and thus can be further in vitro and in vivo experimentally validated.
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Affiliation(s)
- Haruna Luz Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Catolica de Santa Maria de Arequipa, Arequipa, Peru
| | - Luis Daniel Goyzueta-Mamani
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Catolica de Santa Maria de Arequipa, Arequipa, Peru
- Sustainable Innovative Biomaterials Department, Le Qara Research Center, Arequipa, Peru
| | - Mayron Antonio Candia Puma
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Catolica de Santa Maria de Arequipa, Arequipa, Peru
- Universidad Católica de Santa María, Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Arequipa, Peru
| | - Camila Simões de Freitas
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Belo Horizonte, Minas Gerais, Brazil
| | - Grasiele de Sousa Vieria Tavares
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Belo Horizonte, Minas Gerais, Brazil
| | - Daniela Pagliara Lage
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Belo Horizonte, Minas Gerais, Brazil
| | - Eduardo Antonio Ferraz Coelho
- Universidade Federal de Minas Gerais, Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Belo Horizonte, Minas Gerais, Brazil
- Universidade Federal de Minas Gerais, Departamento de Patologia Clínica, COLTEC, Belo Horizonte, Minas Gerais, Brazil
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Catolica de Santa Maria de Arequipa, Arequipa, Peru
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3
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Barazorda-Ccahuana HL, Ranilla LG, Candia-Puma MA, Cárcamo-Rodriguez EG, Centeno-Lopez AE, Davila-Del-Carpio G, Medina-Franco JL, Chávez-Fumagalli MA. PeruNPDB: the Peruvian Natural Products Database for in silico drug screening. Sci Rep 2023; 13:7577. [PMID: 37165197 PMCID: PMC10170056 DOI: 10.1038/s41598-023-34729-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/06/2023] [Indexed: 05/12/2023] Open
Abstract
Since the number of drugs based on natural products (NPs) represents a large source of novel pharmacological entities, NPs have acquired significance in drug discovery. Peru is considered a megadiverse country with many endemic species of plants, terrestrial, and marine animals, and microorganisms. NPs databases have a major impact on drug discovery development. For this reason, several countries such as Mexico, Brazil, India, and China have initiatives to assemble and maintain NPs databases that are representative of their diversity and ethnopharmacological usage. We describe the assembly, curation, and chemoinformatic evaluation of the content and coverage in chemical space, as well as the physicochemical attributes and chemical diversity of the initial version of the Peruvian Natural Products Database (PeruNPDB), which contains 280 natural products. Access to PeruNPDB is available for free ( https://perunpdb.com.pe/ ). The PeruNPDB's collection is intended to be used in a variety of tasks, such as virtual screening campaigns against various disease targets or biological endpoints. This emphasizes the significance of biodiversity protection both directly and indirectly on human health.
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Affiliation(s)
- Haruna L Barazorda-Ccahuana
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Lena Gálvez Ranilla
- Laboratory of Research in Food Science, Universidad Catolica de Santa Maria, 04000, Arequipa, Peru
- Escuela Profesional de Ingeniería de Industria Alimentaria, Facultad de Ciencias e Ingenierías Biológicas y Químicas, Universidad Catolica de Santa Maria, 04000, Arequipa, Peru
| | - Mayron Antonio Candia-Puma
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Eymi Gladys Cárcamo-Rodriguez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Angela Emperatriz Centeno-Lopez
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - Gonzalo Davila-Del-Carpio
- Facultad de Ciencias Farmacéuticas, Bioquímicas y Biotecnológicas, Universidad Católica de Santa María, 04000, Arequipa, Peru
| | - José L Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Miguel Angel Chávez-Fumagalli
- Computational Biology and Chemistry Research Group, Vicerrectorado de Investigación, Universidad Católica de Santa María, 04000, Arequipa, Peru.
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4
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Peralta-Moreno MN, Anton-Muñoz V, Ortega-Alarcon D, Jimenez-Alesanco A, Vega S, Abian O, Velazquez-Campoy A, Thomson TM, Granadino-Roldán JM, Machicado C, Rubio-Martinez J. Autochthonous Peruvian Natural Plants as Potential SARS-CoV-2 M pro Main Protease Inhibitors. Pharmaceuticals (Basel) 2023; 16:ph16040585. [PMID: 37111342 PMCID: PMC10146424 DOI: 10.3390/ph16040585] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Over 750 million cases of COVID-19, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), have been reported since the onset of the global outbreak. The need for effective treatments has spurred intensive research for therapeutic agents based on pharmaceutical repositioning or natural products. In light of prior studies asserting the bioactivity of natural compounds of the autochthonous Peruvian flora, the present study focuses on the identification SARS-CoV-2 Mpro main protease dimer inhibitors. To this end, a target-based virtual screening was performed over a representative set of Peruvian flora-derived natural compounds. The best poses obtained from the ensemble molecular docking process were selected. These structures were subjected to extensive molecular dynamics steps for the computation of binding free energies along the trajectory and evaluation of the stability of the complexes. The compounds exhibiting the best free energy behaviors were selected for in vitro testing, confirming the inhibitory activity of Hyperoside against Mpro, with a Ki value lower than 20 µM, presumably through allosteric modulation.
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Affiliation(s)
- Maria Nuria Peralta-Moreno
- Department of Materials Science and Physical Chemistry, University of Barcelona, and the Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), 08028 Barcelona, Spain
| | - Vanessa Anton-Muñoz
- Facultad de Farmacia y Bioquímica, Universidad Nacional Mayor de San Marcos, Jr. Puno 1002, Lima 15001, Peru
| | - David Ortega-Alarcon
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ana Jimenez-Alesanco
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria de Aragón (IIS Aragon), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Timothy M Thomson
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas Digestivas (CIBERehd), 28029 Madrid, Spain
- Institute of Molecular Biology of Barcelona (IBMB-CSIC), 08028 Barcelona, Spain
- Laboratorio de Investigación Traslacional y Biología Computacional, Facultad de Ciencias y Filosofía-LID, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, Lima 15102, Peru
| | - José Manuel Granadino-Roldán
- Departamento de Química Física y Analítica, Facultad de Ciencias Experimentales, Universidad de Jaén, Campus "Las Lagunillas" s/n, 23071 Jaén, Spain
| | - Claudia Machicado
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Laboratorio de Investigación Traslacional y Biología Computacional, Facultad de Ciencias y Filosofía-LID, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, Lima 15102, Peru
| | - Jaime Rubio-Martinez
- Department of Materials Science and Physical Chemistry, University of Barcelona, and the Institut de Recerca en Quimica Teorica i Computacional (IQTCUB), 08028 Barcelona, Spain
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5
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Jantan I, Arshad L, Septama AW, Haque MA, Mohamed-Hussein ZA, Govender NT. Antiviral effects of phytochemicals against severe acute respiratory syndrome coronavirus 2 and their mechanisms of action: A review. Phytother Res 2023; 37:1036-1056. [PMID: 36343627 PMCID: PMC9878073 DOI: 10.1002/ptr.7671] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022]
Abstract
The worldwide spreading of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a serious threat to health, economic, environmental, and social aspects of human lives. Currently, there are no approved treatments that can effectively block the virus although several existing antimalarial and antiviral agents have been repurposed and allowed use during the pandemic under the emergency use authorization (EUA) status. This review gives an updated overview of the antiviral effects of phytochemicals including alkaloids, flavonoids, and terpenoids against the COVID-19 virus and their mechanisms of action. Search for natural lead molecules against SARS-CoV-2 has been focusing on virtual screening and in vitro studies on phytochemicals that have shown great promise against other coronaviruses such as SARS-CoV. Until now, there is limited data on in vivo investigations to examine the antiviral activity of plants in SARS-CoV-2-infected animal models and the studies were performed using crude extracts. Further experimental and preclinical investigations on the in vivo effects of phytochemicals have to be performed to provide sufficient efficacy and safety data before clinical studies can be performed to develop them into COVID-19 drugs. Phytochemicals are potential sources of new chemical leads for the development of safe and potent anti-SARS-CoV-2 agents.
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Affiliation(s)
- Ibrahim Jantan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Laiba Arshad
- Department of Pharmacy, Forman Christian College (A Chartered University), Lahore, Pakistan
| | - Abdi Wira Septama
- Research Center for Pharmaceutical Ingredient and Traditional Medicine, National Research and Innovation Agency (BRIN), Cibinong Science Center, West Java, Indonesia
| | - Md Areeful Haque
- Department of Symptom Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia.,Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
| | - Nisha T Govender
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Selangor, Malaysia
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6
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Patil SM, Phanindra B, Shirahatti PS, Martiz RM, Sajal H, Babakr AT, Ramu R. Computational approaches to define poncirin from Magnolia champaka leaves as a novel multi-target inhibitor of SARS-CoV-2. J Biomol Struct Dyn 2023; 41:13078-13097. [PMID: 36695109 DOI: 10.1080/07391102.2023.2171137] [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: 11/10/2022] [Accepted: 01/13/2023] [Indexed: 01/26/2023]
Abstract
Phytochemical-based drug discovery against the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been the focus of the current scenario. In this context, we aimed to perform the phytochemical profiling of Magnolia champaka, an evergreen tree from the Magnoliaceae family, in order to perform a virtual screening of its phytoconstituents against different biological targets of SARS-CoV-2. The phytochemicals identified from the ethanol extract of M. champaka leaves using liquid chromatography-mass spectroscopy (LC-MS) technique were screened against SARS-CoV-2 spike glycoprotein (PDB ID: 6M0J), main protease/Mpro (PDB ID: 6LU7), and papain-like protease/PLpro (PDB ID: 7CMD) through computational tools. The experimentation design included molecular docking simulation, molecular dynamics simulation, and binding free energy calculations. Through molecular docking simulation, we identified poncirin as a common potential inhibitor of all the above-mentioned target proteins. In addition, molecular dynamics simulations, binding free energy calculations, and PCA analysis also supported the outcomes of the virtual screening. By the virtue of all the in silico results obtained, poncirin could be taken for in vitro and in vivo studies in near future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shashank M Patil
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysore, Karnataka, India
| | - Bhaskar Phanindra
- Department of Pharmacology, JSS Medical College, JSS Academy of Higher Education and Research, Mysore, Karnataka, India
| | | | - Reshma Mary Martiz
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysore, Karnataka, India
| | - Harshit Sajal
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysore, Karnataka, India
| | - Abdullatif Taha Babakr
- Department of Medical Biochemistry - College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ramith Ramu
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysore, Karnataka, India
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7
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Srinivasan V, Brognaro H, Prabhu PR, de Souza EE, Günther S, Reinke PYA, Lane TJ, Ginn H, Han H, Ewert W, Sprenger J, Koua FHM, Falke S, Werner N, Andaleeb H, Ullah N, Franca BA, Wang M, Barra ALC, Perbandt M, Schwinzer M, Schmidt C, Brings L, Lorenzen K, Schubert R, Machado RRG, Candido ED, Oliveira DBL, Durigon EL, Niebling S, Garcia AS, Yefanov O, Lieske J, Gelisio L, Domaracky M, Middendorf P, Groessler M, Trost F, Galchenkova M, Mashhour AR, Saouane S, Hakanpää J, Wolf M, Alai MG, Turk D, Pearson AR, Chapman HN, Hinrichs W, Wrenger C, Meents A, Betzel C. Antiviral activity of natural phenolic compounds in complex at an allosteric site of SARS-CoV-2 papain-like protease. Commun Biol 2022; 5:805. [PMID: 35953531 PMCID: PMC9366811 DOI: 10.1038/s42003-022-03737-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/18/2022] [Indexed: 11/09/2022] Open
Abstract
SARS-CoV-2 papain-like protease (PLpro) covers multiple functions. Beside the cysteine-protease activity, facilitating cleavage of the viral polypeptide chain, PLpro has the additional and vital function of removing ubiquitin and ISG15 (Interferon-stimulated gene 15) from host-cell proteins to support coronaviruses in evading the host's innate immune responses. We identified three phenolic compounds bound to PLpro, preventing essential molecular interactions to ISG15 by screening a natural compound library. The compounds identified by X-ray screening and complexed to PLpro demonstrate clear inhibition of PLpro in a deISGylation activity assay. Two compounds exhibit distinct antiviral activity in Vero cell line assays and one inhibited a cytopathic effect in non-cytotoxic concentration ranges. In the context of increasing PLpro mutations in the evolving new variants of SARS-CoV-2, the natural compounds we identified may also reinstate the antiviral immune response processes of the host that are down-regulated in COVID-19 infections.
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Affiliation(s)
- Vasundara Srinivasan
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.
| | - Hévila Brognaro
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Prince R Prabhu
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Edmarcia Elisa de Souza
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Sebastian Günther
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Patrick Y A Reinke
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Thomas J Lane
- Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Helen Ginn
- Diamond Light Source Ltd. Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Huijong Han
- European XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany
| | - Wiebke Ewert
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Janina Sprenger
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Faisal H M Koua
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Sven Falke
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Nadine Werner
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Hina Andaleeb
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Department of Biochemistry, Bahauddin Zakariya University Multan-, 60800, Punjab, Pakistan
| | - Najeeb Ullah
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Department of Biochemistry, Bahauddin Zakariya University Multan-, 60800, Punjab, Pakistan
| | - Bruno Alves Franca
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Mengying Wang
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Angélica Luana C Barra
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany.,Pólo TerRa, São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil
| | - Markus Perbandt
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | - Martin Schwinzer
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany
| | | | - Lea Brings
- European XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Robin Schubert
- European XFEL GmbH. Holzkoppel 4, 22869, Schenefeld, Germany
| | | | - Erika Donizette Candido
- Department of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Danielle Bruna Leal Oliveira
- Department of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.,Clinical Laboratory, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Edison Luiz Durigon
- Department of Microbiology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil.,Scientific Platform Pasteur USP, São Paulo, Brazil
| | - Stephan Niebling
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Angelica Struve Garcia
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Julia Lieske
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Luca Gelisio
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Martin Domaracky
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Philipp Middendorf
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Michael Groessler
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Fabian Trost
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Marina Galchenkova
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Aida Rahmani Mashhour
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Sofiane Saouane
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany
| | - Johanna Hakanpää
- Photon Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607, Hamburg, Germany
| | - Markus Wolf
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Schnackenburgallee114, 22525, Hamburg, Germany
| | - Maria Garcia Alai
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Dusan Turk
- Department of Biochemistry & Molecular & Structural Biology, Jozef Stefan Institute, Jamova 39, 1 000, Ljubljana, Slovenia.,Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKEBIP), Jamova 39, 1 000, Ljubljana, Slovenia
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Institut für Nanostruktur- und Festkörperphysik, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Henry N Chapman
- Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.,Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany.,Department of Physics, Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Winfried Hinrichs
- Institute of Biochemistry, Universität Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Carsten Wrenger
- Department of Parasitology, Institute of Biomedical Sciences at the University of São Paulo, São Paulo, Brazil
| | - Alke Meents
- Center for Free-Electron Laser Science, CFEL, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Christian Betzel
- Department of Chemistry, Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, Universität Hamburg, Build. 22a, c/o DESY, 22607, Hamburg, Germany. .,Hamburg Centre for Ultrafast Imaging (CUI), Universität Hamburg, Luruper Chaussee 149, 22761, Hamburg, Germany.
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8
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Jiang H, Yang P, Zhang J. Potential Inhibitors Targeting Papain-Like Protease of SARS-CoV-2: Two Birds With One Stone. Front Chem 2022; 10:822785. [PMID: 35281561 PMCID: PMC8905519 DOI: 10.3389/fchem.2022.822785] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/28/2022] [Indexed: 12/23/2022] Open
Abstract
Severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2), the pathogen of the Coronavirus disease-19 (COVID-19), is still devastating the world causing significant chaos to the international community and posing a significant threat to global health. Since the first outbreak in late 2019, several lines of intervention have been developed to prevent the spread of this virus. Nowadays, some vaccines have been approved and extensively administered. However, the fact that SARS-CoV-2 rapidly mutates makes the efficacy and safety of this approach constantly under debate. Therefore, antivirals are still needed to combat the infection of SARS-CoV-2. Papain-like protease (PLpro) of SARS-CoV-2 supports viral reproduction and suppresses the innate immune response of the host, which makes PLpro an attractive pharmaceutical target. Inhibition of PLpro could not only prevent viral replication but also restore the antiviral immunity of the host, resulting in the speedy recovery of the patient. In this review, we describe structural and functional features on PLpro of SARS-CoV-2 and the latest development in searching for PLpro inhibitors. Currently available inhibitors targeting PLpro as well as their structural basis are also summarized.
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Affiliation(s)
- Haihai Jiang
- School of Basic Medical Sciences, Nanchang University, Nanchang, China
- *Correspondence: Haihai Jiang, ; Jin Zhang,
| | - Peiyao Yang
- Queen Mary School, Nanchang University, Nanchang, China
| | - Jin Zhang
- School of Basic Medical Sciences, Nanchang University, Nanchang, China
- *Correspondence: Haihai Jiang, ; Jin Zhang,
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9
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Goyzueta-Mamani LD, Barazorda-Ccahuana HL, Chávez-Fumagalli MA, F. Alvarez KL, Aguilar-Pineda JA, Vera-Lopez KJ, Lino Cardenas CL. In Silico Analysis of Metabolites from Peruvian Native Plants as Potential Therapeutics against Alzheimer's Disease. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030918. [PMID: 35164183 PMCID: PMC8838509 DOI: 10.3390/molecules27030918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 12/19/2022]
Abstract
Background: Despite research on the molecular bases of Alzheimer’s disease (AD), effective therapies against its progression are still needed. Recent studies have shown direct links between AD progression and neurovascular dysfunction, highlighting it as a potential target for new therapeutics development. In this work, we screened and evaluated the inhibitory effect of natural compounds from native Peruvian plants against tau protein, amyloid beta, and angiotensin II type 1 receptor (AT1R) pathologic AD markers. Methods: We applied in silico analysis, such as virtual screening, molecular docking, molecular dynamics simulation (MD), and MM/GBSA estimation, to identify metabolites from Peruvian plants with inhibitory properties, and compared them to nicotinamide, telmisartan, and grapeseed extract drugs in clinical trials. Results: Our results demonstrated the increased bioactivity of three plants’ metabolites against tau protein, amyloid beta, and AT1R. The MD simulations indicated the stability of the AT1R:floribundic acid, amyloid beta:rutin, and tau:brassicasterol systems. A polypharmaceutical potential was observed for rutin due to its high affinity to AT1R, amyloid beta, and tau. The metabolite floribundic acid showed bioactivity against the AT1R and tau, and the metabolite brassicasterol showed bioactivity against the amyloid beta and tau. Conclusions: This study has identified molecules from native Peruvian plants that have the potential to bind three pathologic markers of AD.
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Affiliation(s)
- Luis Daniel Goyzueta-Mamani
- Laboratory of Genomics and Neurovascular Diseases, Universidad Católica de Santa María, Urb. San José s/n—Umacollo, Arequipa 04000, Peru; (M.A.C.-F.); (K.L.F.A.); (J.A.A.-P.); (K.J.V.-L.)
- Correspondence: (L.D.G.-M.); (C.L.L.C.)
| | - Haruna Luz Barazorda-Ccahuana
- Vicerrectorado de Investigación, Universidad Católica de Santa María, Urb. San José s/n—Umacollo, Arequipa 04000, Peru;
| | - Miguel Angel Chávez-Fumagalli
- Laboratory of Genomics and Neurovascular Diseases, Universidad Católica de Santa María, Urb. San José s/n—Umacollo, Arequipa 04000, Peru; (M.A.C.-F.); (K.L.F.A.); (J.A.A.-P.); (K.J.V.-L.)
| | - Karla Lucia F. Alvarez
- Laboratory of Genomics and Neurovascular Diseases, Universidad Católica de Santa María, Urb. San José s/n—Umacollo, Arequipa 04000, Peru; (M.A.C.-F.); (K.L.F.A.); (J.A.A.-P.); (K.J.V.-L.)
| | - Jorge Alberto Aguilar-Pineda
- Laboratory of Genomics and Neurovascular Diseases, Universidad Católica de Santa María, Urb. San José s/n—Umacollo, Arequipa 04000, Peru; (M.A.C.-F.); (K.L.F.A.); (J.A.A.-P.); (K.J.V.-L.)
| | - Karin Jannet Vera-Lopez
- Laboratory of Genomics and Neurovascular Diseases, Universidad Católica de Santa María, Urb. San José s/n—Umacollo, Arequipa 04000, Peru; (M.A.C.-F.); (K.L.F.A.); (J.A.A.-P.); (K.J.V.-L.)
| | - Christian Lacks Lino Cardenas
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Correspondence: (L.D.G.-M.); (C.L.L.C.)
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10
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Pizzorno J. Are Antiviral Flavonoids Part of the Solution to the COVID-19 Pandemic? Integr Med (Encinitas) 2021; 20:8-13. [PMID: 35250397 PMCID: PMC8887228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The relentless continuation of the COVID-19 (coronavirus disease 2019) pandemic clearly indicates the need to broaden our approach to this serious, worldwide problem. An important factor that has received little attention is the protective role of dietary antiviral flavonoids. Many flavonoids have been shown through molecular docking assays, as well as in silico studies, and in vitro and in vivo studies to inhibit virtually every mechanism needed by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) to penetrate cells and hijack molecular processes. These inhibitory effects have shown clinical benefit in a few preliminary studies. In this editorial I present research which makes the case for dietary flavonoids as part of the solution to the COVID-19 pandemic.
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11
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Barazorda-Ccahuana HL, Nedyalkova M, Mas F, Madurga S. Unveiling the Effect of Low pH on the SARS-CoV-2 Main Protease by Molecular Dynamics Simulations. Polymers (Basel) 2021; 13:3823. [PMID: 34771379 PMCID: PMC8587287 DOI: 10.3390/polym13213823] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 12/19/2022] Open
Abstract
(1) Background: Main Protease (Mpro) is an attractive therapeutic target that acts in the replication and transcription of the SARS-CoV-2 coronavirus. Mpro is rich in residues exposed to protonation/deprotonation changes which could affect its enzymatic function. This work aimed to explore the effect of the protonation/deprotonation states of Mpro at different pHs using computational techniques. (2) Methods: The different distribution charges were obtained in all the evaluated pHs by the Semi-Grand Canonical Monte Carlo (SGCMC) method. A set of Molecular Dynamics (MD) simulations was performed to consider the different protonation/deprotonation during 250 ns, verifying the structural stability of Mpro at different pHs. (3) Results: The present findings demonstrate that active site residues and residues that allow Mpro dimerisation was not affected by pH changes. However, Mpro substrate-binding residues were altered at low pHs, allowing the increased pocket volume. Additionally, the results of the solvent distribution around Sγ, Hγ, Nδ1 and Hδ1 atoms of the catalytic residues Cys145 and His41 showed a low and high-water affinity at acidic pH, respectively. It which could be crucial in the catalytic mechanism of SARS-CoV-2 Mpro at low pHs. Moreover, we analysed the docking interactions of PF-00835231 from Pfizer in the preclinical phase, which shows excellent affinity with the Mpro at different pHs. (4) Conclusion: Overall, these findings indicate that SARS-CoV-2 Mpro is highly stable at acidic pH conditions, and this inhibitor could have a desirable function at this condition.
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Affiliation(s)
- Haruna Luz Barazorda-Ccahuana
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08028 Barcelona, Spain;
- Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
| | - Miroslava Nedyalkova
- Department of Inorganic Chemistry, University of Sofia “St. Kl. Okhridski”, 1164 Sofia, Bulgaria;
| | - Francesc Mas
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08028 Barcelona, Spain;
| | - Sergio Madurga
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08028 Barcelona, Spain;
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