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Majnooni MB, Fakhri S, Bahrami G, Naseri M, Farzaei MH, Echeverría J. Alkaloids as Potential Phytochemicals against SARS-CoV-2: Approaches to the Associated Pivotal Mechanisms. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2021; 2021:6632623. [PMID: 34104202 PMCID: PMC8159655 DOI: 10.1155/2021/6632623] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 05/03/2021] [Indexed: 12/19/2022]
Abstract
Since its inception, the coronavirus disease 2019 (COVID-19) pandemic has infected millions of people around the world. Therefore, it is necessary to find effective treatments against Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), as it is the viral source of COVID-19. Alkaloids are one of the most widespread plant-derived natural compounds with prominent antiviral effects. Accordingly, these phytochemicals have been promising candidates towards discovering effective treatments for COVID-19. Alkaloids have shown potential anti-SARS-CoV activities via inhibiting pathogenesis-associated targets of the Coronaviridae family that are required for the virus life cycle. In the current study, the chemistry, plant sources, and antiviral effects of alkaloids, as well as their anti-SARS-CoV-2 effect with related mechanisms, are reviewed towards discovering an effective treatment against COVID-19.
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Affiliation(s)
| | - Sajad Fakhri
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Gholamreza Bahrami
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Maryam Naseri
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohammad Hosein Farzaei
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Javier Echeverría
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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Agrawal N, Goyal A. Potential Candidates against COVID-19 Targeting RNA-Dependent RNA Polymerase: A Comprehensive Review. Curr Pharm Biotechnol 2021; 23:396-419. [PMID: 33882805 DOI: 10.2174/1389201022666210421102513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/26/2021] [Accepted: 03/11/2021] [Indexed: 11/22/2022]
Abstract
Due to the extremely contagious nature of SARS-COV-2, it presents a significant threat to humans worldwide. A plethora of studies are going on all over the world to discover the drug to fight SARS-COV-2. One of the most promising targets is RNA-dependent RNA polymerase (RdRp), responsible for viral RNA replication in host cells. Since RdRp is a viral enzyme with no host cell homologs, it allows the development of selective SARS-COV-2 RdRp inhibitors. A variety of studies used in silico approaches for virtual screening, molecular docking, and repurposing of already existing drugs and phytochemicals against SARS-COV-2 RdRp. This review focuses on collating compounds possessing the potential to inhibit SARS-COV-2 RdRp based on in silico studies to give medicinal chemists food for thought so that the existing drugs can be repurposed for the control and treatment of ongoing COVID-19 pandemic after performing in vitro and in vivo experiments.
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Affiliation(s)
- Neetu Agrawal
- Institute of Pharmaceutical Research, GLA University, Mathura-281406 (U.P.), India
| | - Ahsas Goyal
- Institute of Pharmaceutical Research, GLA University, Mathura-281406 (U.P.), India
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Quimque MT, Notarte KI, Letada A, Fernandez RA, Pilapil DY, Pueblos KR, Agbay JC, Dahse HM, Wenzel-Storjohann A, Tasdemir D, Khan A, Wei DQ, Gose Macabeo AP. Potential Cancer- and Alzheimer's Disease-Targeting Phosphodiesterase Inhibitors from Uvaria alba: Insights from In Vitro and Consensus Virtual Screening. ACS OMEGA 2021; 6:8403-8417. [PMID: 33817501 PMCID: PMC8015132 DOI: 10.1021/acsomega.1c00137] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/03/2021] [Indexed: 05/06/2023]
Abstract
Inhibition of the major cyclic adenosine monophosphate-metabolizing enzyme PDE4 has shown potential for the discovery of drugs for cancer, inflammation, and neurodegenerative disorders such as Alzheimer's disease. As a springboard to explore new anti-cancer and anti-Alzheimer's chemical prototypes from rare Annonaceae species, the present study evaluated anti-PDE4B along with antiproliferative and anti-cholinesterase activities of the extracts of the Philippine endemic species Uvaria alba using in vitro assays and framed the resulting biological significance through computational binding and reactivity-based experiments. Thus, the PDE4 B2B-inhibiting dichloromethane sub-extract (UaD) of U. alba elicited antiproliferative activity against chronic myelogenous leukemia (K-562) and cytostatic effects against human cervical cancer (HeLa). The extract also profoundly inhibited acetylcholinesterase (AChE), an enzyme involved in the progression of neurodegenerative diseases. Chemical profiling analysis of the bioactive extract identified 18 putative secondary metabolites. Molecular docking and molecular dynamics simulations showed strong free energy binding mechanisms and dynamic stability at 50-ns simulations in the catalytic domains of PDE4 B2B, ubiquitin-specific peptidase 14, and Kelch-like ECH-associated protein 1 (KEAP-1 Kelch domain) for the benzylated dihydroflavone dichamanetin (16), and of an AChE and KEAP-1 BTB domain for 3-(3,4-dihydroxybenzyl)-3',4',6-trihydroxy-2,4-dimethoxychalcone (8) and grandifloracin (15), respectively. Density functional theory calculations to demonstrate Michael addition reaction of the most electrophilic metabolite and kinetically stable grandifloracin (15) with Cys151 of the KEAP-1 BTB domain illustrated favorable formation of a β-addition adduct. The top-ranked compounds also conferred favorable in silico pharmacokinetic properties.
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Affiliation(s)
- Mark Tristan Quimque
- Laboratory
of Organic Reactivity, Discovery & Synthesis (LORDS), Research
Center for Natural & Applied Sciences, University of Santo Tomas, España Blvd., 1015 Manila, Philippines
- The
Graduate School, University of Santo Tomas, España Blvd., 1015 Manila, Philippines
- Department
of Chemistry, College of Science and Mathematics, Mindanao State University-Iligan Institute of Technology, Tibanga, 9200 Iligan
City, Philippines
| | - Kin Israel Notarte
- Laboratory
of Organic Reactivity, Discovery & Synthesis (LORDS), Research
Center for Natural & Applied Sciences, University of Santo Tomas, España Blvd., 1015 Manila, Philippines
- Faculty
of Medicine & Surgery, University of
Santo Tomas, España Blvd., 1015 Manila, Philippines
| | - Arianne Letada
- Laboratory
of Organic Reactivity, Discovery & Synthesis (LORDS), Research
Center for Natural & Applied Sciences, University of Santo Tomas, España Blvd., 1015 Manila, Philippines
- The
Graduate School, University of Santo Tomas, España Blvd., 1015 Manila, Philippines
| | - Rey Arturo Fernandez
- Laboratory
of Organic Reactivity, Discovery & Synthesis (LORDS), Research
Center for Natural & Applied Sciences, University of Santo Tomas, España Blvd., 1015 Manila, Philippines
| | - Delfin Yñigo Pilapil
- Laboratory
of Organic Reactivity, Discovery & Synthesis (LORDS), Research
Center for Natural & Applied Sciences, University of Santo Tomas, España Blvd., 1015 Manila, Philippines
- Department
of Biological Sciences, College of Science, University of Santo Tomas, España Blvd., 1015 Manila, Philippines
| | - Kirstin Rhys Pueblos
- Laboratory
of Organic Reactivity, Discovery & Synthesis (LORDS), Research
Center for Natural & Applied Sciences, University of Santo Tomas, España Blvd., 1015 Manila, Philippines
- The
Graduate School, University of Santo Tomas, España Blvd., 1015 Manila, Philippines
- Department
of Chemistry, College of Science and Mathematics, Mindanao State University-Iligan Institute of Technology, Tibanga, 9200 Iligan
City, Philippines
| | - Jay Carl Agbay
- Department
of Chemistry, College of Science and Mathematics, Mindanao State University-Iligan Institute of Technology, Tibanga, 9200 Iligan
City, Philippines
- Philippine
Science High School—Central Mindanao Campus, 9217 Balo-i, Lanao del Norte, Philippines
| | - Hans-Martin Dahse
- Leibniz-Institute
for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), D-07745 Jena, Germany
| | - Arlette Wenzel-Storjohann
- GEOMAR
Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit, Marine
Natural Products Chemistry, GEOMAR Helmholtz
Centre for Ocean Research Kiel, Am Kiel-Kanal, Kiel 24106, Germany
| | - Deniz Tasdemir
- GEOMAR
Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit, Marine
Natural Products Chemistry, GEOMAR Helmholtz
Centre for Ocean Research Kiel, Am Kiel-Kanal, Kiel 24106, Germany
- Faculty
of Mathematics and Natural Sciences, Kiel
University, Christian-Albrechts-Platz
4, Kiel 24118, Germany
| | - Abbas Khan
- Department
of Bioinformatics and Biostatistics, State Key Laboratory of Microbial
Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
| | - Dong-Qing Wei
- Department
of Bioinformatics and Biostatistics, State Key Laboratory of Microbial
Metabolism, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen 518055, Guangdong, P.R. China
| | - Allan Patrick Gose Macabeo
- Laboratory
of Organic Reactivity, Discovery & Synthesis (LORDS), Research
Center for Natural & Applied Sciences, University of Santo Tomas, España Blvd., 1015 Manila, Philippines
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Abstract
The recent outbreak of the highly contagious coronavirus disease 2019 (COVID-19) caused by the novel coronavirus SARS-CoV-2 has created a global health crisis with socioeconomic impacts. Although, recently, vaccines have been approved for the prevention of COVID-19, there is still an urgent need for the discovery of more efficacious and safer drugs especially from natural sources. In this study, a number of quinoline and quinazoline alkaloids with antiviral and/or antimalarial activity were virtually screened against three potential targets for the development of drugs against COVID-19. Among seventy-one tested compounds, twenty-three were selected for molecular docking based on their pharmacokinetic and toxicity profiles. The results identified a number of potential inhibitors. Three of them, namely, norquinadoline A, deoxytryptoquivaline, and deoxynortryptoquivaline, showed strong binding to the three targets, SARS-CoV-2 main protease, spike glycoprotein, and human angiotensin-converting enzyme 2. These alkaloids therefore have promise for being further investigated as possible multitarget drugs against COVID-19.
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Structure-based inhibitor screening of natural products against NSP15 of SARS-CoV-2 revealed thymopentin and oleuropein as potent inhibitors. ACTA ACUST UNITED AC 2021; 12:71-80. [PMID: 33776343 PMCID: PMC7985738 DOI: 10.1007/s42485-021-00059-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/26/2021] [Accepted: 03/09/2021] [Indexed: 12/26/2022]
Abstract
Coronaviruses are enveloped, non-segmented positive-sense RNA viruses with the largest genome among RNA viruses. Their genome contains a large replicase ORF which encodes nonstructural proteins (NSPs), structural, and accessory genes. NSP15 is a nidoviral RNA uridylate-specific endoribonuclease (NendoU) with C-terminal catalytic domain. The endoribonuclease activity of NSP15 interferes with the innate immune response of the host. Here, we screened Selleckchem Natural product database of the compounds against NSP15, and we found that thymopentin and oleuropein displayed highest binding energies. The binding of these molecules was further validated by molecular dynamic simulations that revealed them as very stable complexes. These drugs might serve as effective counter molecules in the reduction of virulence of this virus; may be more effective if treated in combination with replicase inhibitors. Future validation of both these inhibitors is worth the consideration for patients being treated for COVID-19.
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Petit L, Vernès L, Cadoret JP. Docking and in silico toxicity assessment of Arthrospira compounds as potential antiviral agents against SARS-CoV-2. JOURNAL OF APPLIED PHYCOLOGY 2021; 33:1579-1602. [PMID: 33776210 DOI: 10.21203/rs.3.rs-40890/v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 01/03/2021] [Accepted: 01/03/2021] [Indexed: 05/23/2023]
Abstract
UNLABELLED A race is currently being launched as a result of the international health situation. This race aims to find, by various means, weapons to counter the Covid-19 pandemic now widespread on all continents. The aquatic world and in particular that of photosynthetic organisms is regularly highlighted but paradoxically little exploited in view of the tremendous possibilities it offers. Computational tools allow not only to clear the existence and activity of many molecules but also to model their relationships with receptors identified in potential hosts. On a routine basis, our laboratory carries out a research activity on functionalities of molecules derived from algae using in silico tools. We have implemented our skills in algae biology and in modeling, as tests in order to identify molecules expressed by the genus Arthrospira showing an antiviral potential and more particularly anti-SARS-CoV-2. Using consensus docking and redocking with Autodock Vina and SwissDock, we were able to identify several promising molecules from Arthrospira: phycocyanobilin, phycoerythrobilin, phycourobilin, and folic acid. These four compounds showed reliable binding energies comprised between - 6.95 and - 7.45 kcal.mol-1 in Autodock Vina and between - 9.285 and - 10.35 kcal.mol-1 with SwissDock. Toxicity prediction as well as current regulations provided promising arguments for the inclusion of these compounds in further studies to assess their ability to compete with the SARS-CoV-2/ACE2 complex both in vitro and in vivo. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10811-021-02372-9.
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Affiliation(s)
- Léna Petit
- Algama, 81 rue Réaumur, 75002 Paris, France
| | - Léa Vernès
- Algama, 81 rue Réaumur, 75002 Paris, France
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Kathiravan MK, Radhakrishnan S, Namasivayam V, Palaniappan S. An Overview of Spike Surface Glycoprotein in Severe Acute Respiratory Syndrome-Coronavirus. Front Mol Biosci 2021; 8:637550. [PMID: 33898518 PMCID: PMC8058706 DOI: 10.3389/fmolb.2021.637550] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/22/2021] [Indexed: 12/28/2022] Open
Abstract
The novel coronavirus originated in December 2019 in Hubei, China. This contagious disease named as COVID-19 resulted in a massive expansion within 6 months by spreading to more than 213 countries. Despite the availability of antiviral drugs for the treatment of various viral infections, it was concluded by the WHO that there is no medicine to treat novel CoV, SARS-CoV-2. It has been confirmed that SARS-COV-2 is the most highly virulent human coronavirus and occupies the third position following SARS and MERS with the highest mortality rate. The genetic assembly of SARS-CoV-2 is segmented into structural and non-structural proteins, of which two-thirds of the viral genome encodes non-structural proteins and the remaining genome encodes structural proteins. The most predominant structural proteins that make up SARS-CoV-2 include spike surface glycoproteins (S), membrane proteins (M), envelope proteins (E), and nucleocapsid proteins (N). This review will focus on one of the four major structural proteins in the CoV assembly, the spike, which is involved in host cell recognition and the fusion process. The monomer disintegrates into S1 and S2 subunits with the S1 domain necessitating binding of the virus to its host cell receptor and the S2 domain mediating the viral fusion. On viral infection by the host, the S protein is further cleaved by the protease enzyme to two major subdomains S1/S2. Spike is proven to be an interesting target for developing vaccines and in particular, the RBD-single chain dimer has shown initial success. The availability of small molecules and peptidic inhibitors for host cell receptors is briefly discussed. The development of new molecules and therapeutic druggable targets for SARS-CoV-2 is of global importance. Attacking the virus employing multiple targets and strategies is the best way to inhibit the virus. This article will appeal to researchers in understanding the structural and biological aspects of the S protein in the field of drug design and discovery.
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Affiliation(s)
- Muthu Kumaradoss Kathiravan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRMIST, Tamil Nadu, India
- Dr. APJ Abdul Kalam Research Lab, SRM College of Pharmacy, SRMIST, Tamil Nadu, India
| | - Srimathi Radhakrishnan
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRMIST, Tamil Nadu, India
- Dr. APJ Abdul Kalam Research Lab, SRM College of Pharmacy, SRMIST, Tamil Nadu, India
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Abdallah HM, El-Halawany AM, Sirwi A, El-Araby AM, Mohamed GA, Ibrahim SRM, Koshak AE, Asfour HZ, Awan ZA, A. Elfaky M. Repurposing of Some Natural Product Isolates as SARS-COV-2 Main Protease Inhibitors via In Vitro Cell Free and Cell-Based Antiviral Assessments and Molecular Modeling Approaches. Pharmaceuticals (Basel) 2021; 14:213. [PMID: 33806331 PMCID: PMC8001104 DOI: 10.3390/ph14030213] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 02/26/2021] [Accepted: 02/28/2021] [Indexed: 12/18/2022] Open
Abstract
The emergence of the SARS-CoV-2 pandemic has prompted scientists to search for an efficient antiviral medicine to overcome the rapid spread and the marked increase in the number of patients worldwide. In this regard natural products could be a potential source of substances active against coronavirus infections. A systematic computer-aided virtual screening approach was carried out using commercially available natural products found on the Zinc Database in addition to an in-house compound library to identify potential natural product inhibitors of SARS-CoV-2 main protease (MPRO). The top eighteen hits from the screening were selected for in vitro evaluation on the viral protease (SARS-CoV-2 MPRO). Five compounds (naringenin, 2,3',4,5',6-pentahydroxybenzophenone, apigenin-7-O-glucoside, sennoside B, and acetoside) displayed high activity against the viral protein. Acteoside showed similar activity to the positive control GC376. The most potent compounds were tested in vitro on SARS-CoV-2 Egyptian strain where only naringenin showed moderate anti-SARS-CoV-2 activity at non-cytotoxic micromolar concentrations in vitro with a significant selectivity index (CC50/IC50 = 178.748/28.347 = 6.3). Moreover; a common feature pharmacophore model was generated to explain the requirements for enzyme inhibition by this diverse group of active ligands. These results pave a path for future repurposing and development of natural products to aid in the battle against COVID-19.
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Affiliation(s)
- Hossam M. Abdallah
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.S.); (G.A.M.); (A.E.K.); (M.A.E.)
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt;
| | - Ali M. El-Halawany
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt;
| | - Alaa Sirwi
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.S.); (G.A.M.); (A.E.K.); (M.A.E.)
| | - Amr M. El-Araby
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams Universit, Cairo 11566, Egypt;
| | - Gamal A. Mohamed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.S.); (G.A.M.); (A.E.K.); (M.A.E.)
- Department of Pharmacognosy, Faculty of Pharmacy, Al-Azhar University, Assiut Branch, Assiut 71524, Egypt
| | - Sabrin R. M. Ibrahim
- Batterjee Medical College, P.O. Box 6231, North Obhur, Prince Abdullah Al-Faisal Street, Jeddah 21442, Saudi Arabia;
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Abdulrahman E. Koshak
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.S.); (G.A.M.); (A.E.K.); (M.A.E.)
| | - Hani Z. Asfour
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Zuhier A. Awan
- Department of Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Mahmoud A. Elfaky
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (A.S.); (G.A.M.); (A.E.K.); (M.A.E.)
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Magpantay HD, Malaluan IN, Manzano JAH, Quimque MT, Pueblos KR, Moor N, Budde S, Bangcaya PS, Lim-Valle D, Dahse HM, Khan A, Wei DQ, Alejandro GJD, Macabeo APG. Antibacterial and COX-2 Inhibitory Tetrahydrobisbenzylisoquinoline Alkaloids from the Philippine Medicinal Plant Phaeanthus ophthalmicus. PLANTS (BASEL, SWITZERLAND) 2021; 10:462. [PMID: 33804446 PMCID: PMC7999448 DOI: 10.3390/plants10030462] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 12/21/2022]
Abstract
Phaeanthus ophthalmicus (Roxb. ex G.Don) J.Sinclair (previously known as P. ebracteolatus (Presl) Merr) is a Philippine medicinal plant occurring as evergreen shrub in the lowland forests of Luzon islands. It is used traditionally by Filipinos to treat bacterial conjunctivitis, ulcer and wound infections. Based on previous investigations where cyclooxygenase-2 (COX-2) functions as immune-linked factor in infectious sensitivities to bacterial pathogens by triggering pro-inflammatory immune-associated reactions, we investigated the antimicrobial and COX inhibitory activities of the extracts and tetrahydrobisbenzylisoquinoline alkaloids of P. ophthalmicus in vitro and in silico to validate its ethnomedicinal uses. Thus, the dichloromethane-methanol (DCM-MeOH) crude extract and alkaloid extracts exhibiting antibacterial activities against drug-resistant bacterial strains such as methicillin-resistance Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE), Klebsiella pneumoniae + CRE and Pseudomonas aeruginosa + MBL afforded (+)-tetrandrine (1) and (+)-limacusine (2) as the major biologically active tetrahydrobisbenzylisoquinoline alkaloidal constituents after purification. Both tetrahydrobisbenzylisoquinoline alkaloids 1 and 2 showed broad spectrum antibacterial activity with strongest inhibition against the Gram-negative bacteria MβL-Pseudomonas aeruginosa Klebsiella pneumoniae + CRE. Interestingly, the alkaloid limacusine (2) showed selective inhibition against ovine COX-2 in vitro. These results were ascertained by molecular docking and molecular dynamics simulation experiments where alkaloid 2 showed strong affinity in the catalytic sites of Gram-negative bacterial enzymes P. aeruginosa elastase and K. pneumoniae KPC-2 carbapenemase (enzymes involved in infectivity mechanisms), and of ovine COX-2. Overall, our study provides credence on the ethnomedicinal use of the Philippine medicinal plant P. ophthalmicus as traditional plant-based adjuvant to treat bacterial conjunctivitis and other related infections. The antibacterial activities and selective COX-2 inhibition observed for limacusine (2) point to its role as the biologically active constituent of P. ophthalmicus. A limited number of drugs with COX-2 inhibitory properties like celecoxib also confer antibacterial activity. Thus, tetrahydrobisbenzyl alkaloids, especially 2, are promising pharmaceutical inspirations for developing treatments of bacterial/inflammation-related infections.
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Affiliation(s)
- Hilbert D. Magpantay
- Chemistry Department, De La Salle University, 2401 Taft Avenue, Manila 0922, Philippines;
| | - Ivane N. Malaluan
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd., Manila 1015, Philippines; (I.N.M.); (J.A.H.M.); (M.T.Q.); (K.R.P.)
- Chemistry Department, College of Science, Bicol University, Rizal St., Legazpi City 4500, Philippines
| | - Joe Anthony H. Manzano
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd., Manila 1015, Philippines; (I.N.M.); (J.A.H.M.); (M.T.Q.); (K.R.P.)
- Department of Biological Sciences, College of Science, University of Santo Tomas, España Blvd., Manila 1015, Philippines
| | - Mark Tristan Quimque
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd., Manila 1015, Philippines; (I.N.M.); (J.A.H.M.); (M.T.Q.); (K.R.P.)
- Chemistry Department, College of Science, MSU-Iligan State University, Iligan City 9200, Philippines
| | - Kirstin Rhys Pueblos
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd., Manila 1015, Philippines; (I.N.M.); (J.A.H.M.); (M.T.Q.); (K.R.P.)
- Chemistry Department, College of Science, MSU-Iligan State University, Iligan City 9200, Philippines
| | - Natalija Moor
- Institut für Organische Chemie, Universität Regensburg, Universitätstrasse 31, D-93053 Regensburg, Germany; (N.M.); (S.B.)
| | - Simon Budde
- Institut für Organische Chemie, Universität Regensburg, Universitätstrasse 31, D-93053 Regensburg, Germany; (N.M.); (S.B.)
| | - Porferio S. Bangcaya
- Biological Science Department, College of Teacher Education—University of Antique, Tario-Lim Memorial Campus, Tibiao, Antique 5707, Philippines;
| | - Demi Lim-Valle
- Clinical Microbiology Laboratory, Department of Pathology and Laboratories, Makati Medical Center, Amorsolo St., Legaspi Village, Makati City 1229, Philippines;
| | - Hans-Martin Dahse
- Leibniz-Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute (HKI), D-07745 Jena, Germany;
| | - Abbas Khan
- Department of Bioinformatics and Biostatistics, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (D.-Q.W.)
| | - Dong-Qing Wei
- Department of Bioinformatics and Biostatistics, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (D.-Q.W.)
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Bldg. 8, Xili St., Nashan District, Shenzhen 518055, China
| | - Grecebio Jonathan D. Alejandro
- Plant Sciences Laboratory, Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd., Manila 1015, Philippines;
| | - Allan Patrick G. Macabeo
- Laboratory for Organic Reactivity, Discovery and Synthesis (LORDS), Research Center for the Natural and Applied Sciences, University of Santo Tomas, España Blvd., Manila 1015, Philippines; (I.N.M.); (J.A.H.M.); (M.T.Q.); (K.R.P.)
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Hajbabaie R, Harper MT, Rahman T. Establishing an Analogue Based In Silico Pipeline in the Pursuit of Novel Inhibitory Scaffolds against the SARS Coronavirus 2 Papain-Like Protease. Molecules 2021; 26:1134. [PMID: 33672721 PMCID: PMC7924369 DOI: 10.3390/molecules26041134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 01/18/2023] Open
Abstract
The ongoing coronavirus pandemic has been a burden on the worldwide population, with mass fatalities and devastating socioeconomic consequences. It has particularly drawn attention to the lack of approved small-molecule drugs to inhibit SARS coronaviruses. Importantly, lessons learned from the SARS outbreak of 2002-2004, caused by severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), can be applied to current drug discovery ventures. SARS-CoV-1 and SARS-CoV-2 both possess two cysteine proteases, the main protease (Mpro) and the papain-like protease (PLpro), which play a significant role in facilitating viral replication, and are important drug targets. The non-covalent inhibitor, GRL-0617, which was found to inhibit replication of SARS-CoV-1, and more recently SARS-CoV-2, is the only PLpro inhibitor co-crystallised with the recently solved SARS-CoV-2 PLpro crystal structure. Therefore, the GRL-0617 structural template and pharmacophore features are instrumental in the design and development of more potent PLpro inhibitors. In this work, we conducted scaffold hopping using GRL-0617 as a reference to screen over 339,000 ligands in the chemical space using the ChemDiv, MayBridge, and Enamine screening libraries. Twenty-four distinct scaffolds with structural and electrostatic similarity to GRL-0617 were obtained. These proceeded to molecular docking against PLpro using the AutoDock tools. Of two compounds that showed the most favourable predicted binding affinities to the target site, as well as comparable protein-ligand interactions to GRL-0617, one was chosen for further analogue-based work. Twenty-seven analogues of this compound were further docked against the PLpro, which resulted in two additional hits with promising docking profiles. Our in silico pipeline consisted of an integrative four-step approach: (1) ligand-based virtual screening (scaffold-hopping), (2) molecular docking, (3) an analogue search, and, (4) evaluation of scaffold drug-likeness, to identify promising scaffolds and eliminate those with undesirable properties. Overall, we present four novel, and lipophilic, scaffolds obtained from an exhaustive search of diverse and uncharted regions of chemical space, which may be further explored in vitro through structure-activity relationship (SAR) studies in the search for more potent inhibitors. Furthermore, these scaffolds were predicted to have fewer off-target interactions than GRL-0617. Lastly, to our knowledge, this work contains the largest ligand-based virtual screen performed against GRL-0617.
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Affiliation(s)
| | | | - Taufiq Rahman
- Department of Pharmacology, Cambridge University, Tennis Court Road, Cambridge CB2 1PD, UK; (R.H.); (M.T.H.)
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Fu J, Wei C, He J, Zhang L, Zhou J, Balaji KS, Shen S, Peng J, Sharma A, Fu J. Evaluation and characterization of HSPA5 (GRP78) expression profiles in normal individuals and cancer patients with COVID-19. Int J Biol Sci 2021; 17:897-910. [PMID: 33767597 PMCID: PMC7975696 DOI: 10.7150/ijbs.54055] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 02/05/2021] [Indexed: 12/15/2022] Open
Abstract
HSPA5 (BiP, GRP78) has been reported as a potential host-cell receptor for SARS-Cov-2, but its expression profiles on different tissues including tumors, its susceptibility to SARS-Cov-2 virus and severity of its adverse effects on malignant patients are unclear. In the current study, HSPA5 has been found to be expressed ubiquitously in normal tissues and significantly increased in 14 of 31 types of cancer tissues. In lung cancer, mRNA levels of HSPA5 were 253-fold increase than that of ACE2. Meanwhile, in both malignant tumors and matched normal samples across almost all cancer types, mRNA levels of HSPA5 were much higher than those of ACE2. Higher expression of HSPA5 significantly decreased patient overall survival (OS) in 7 types of cancers. Moreover, systematic analyses found that 7.15% of 5,068 COVID-19 cases have malignant cancer coincidental situations, and the rate of severe events of COVID-19 patients with cancers present a higher trend than that for all COVID-19 patients, showing a significant difference (33.33% vs 16.09%, p<0.01). Collectively, these data imply that the tissues with high HSPA5 expression, not low ACE2 expression, are susceptible to be invaded by SARS-CoV-2. Taken together, this study not only indicates the clinical significance of HSPA5 in COVID-19 disease and cancers, but also provides potential clues for further medical treatments and managements of COVID-19 patients.
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Affiliation(s)
- Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Chunli Wei
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Jiayue He
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Lianmei Zhang
- Department of Pathology, the Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an 223300, Jiangsu, China
| | - Ju Zhou
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
| | | | - Shiyi Shen
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Jiangzhou Peng
- Department of Thoracic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510000, China
| | - Amrish Sharma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston 77030, Texas, USA
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
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Vivarelli S, Falzone L, Torino F, Scandurra G, Russo G, Bordonaro R, Pappalardo F, Spandidos DA, Raciti G, Libra M. Immune-checkpoint inhibitors from cancer to COVID‑19: A promising avenue for the treatment of patients with COVID‑19 (Review). Int J Oncol 2021; 58:145-157. [PMID: 33491759 PMCID: PMC7864014 DOI: 10.3892/ijo.2020.5159] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023] Open
Abstract
The severe acute respiratory syndrome associated coronavirus‑2 (SARS‑CoV‑2) poses a threat to human life worldwide. Since early March, 2020, coronavirus disease 2019 (COVID‑19), characterized by an acute and often severe form of pneumonia, has been declared a pandemic. This has led to a boom in biomedical research studies at all stages of the pipeline, from the in vitro to the clinical phase. In line with this global effort, known drugs, currently used for the treatment of other pathologies, including antivirals, immunomodulating compounds and antibodies, are currently used off‑label for the treatment of COVID‑19, in association with the supportive standard care. Yet, no effective treatments have been identified. A new hope stems from medical oncology and relies on the use of immune‑checkpoint inhibitors (ICIs). In particular, amongst the ICIs, antibodies able to block the programmed death‑1 (PD‑1)/PD ligand-1 (PD‑L1) pathway have revealed a hidden potential. In fact, patients with severe and critical COVID‑19, even prior to the appearance of acute respiratory distress syndrome, exhibit lymphocytopenia and suffer from T‑cell exhaustion, which may lead to viral sepsis and an increased mortality rate. It has been observed that cancer patients, who usually are immunocompromised, may restore their anti‑tumoral immune response when treated with ICIs. Moreover, viral-infected mice and humans, exhibit a T‑cell exhaustion, which is also observed following SARS‑CoV‑2 infection. Importantly, when treated with anti‑PD‑1 and anti‑PD‑L1 antibodies, they restore their T‑cell competence and efficiently counteract the viral infection. Based on these observations, four clinical trials are currently open, to examine the efficacy of anti‑PD‑1 antibody administration to both cancer and non‑cancer individuals affected by COVID‑19. The results may prove the hypothesis that restoring exhausted T‑cells may be a winning strategy to beat SARS‑CoV‑2 infection.
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Affiliation(s)
- Silvia Vivarelli
- Section of General Pathology, Clinics and Oncology, Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania
| | - Luca Falzone
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori 'Fondazione G. Pascale', I-80131 Naples
| | - Francesco Torino
- Department of Systems Medicine, Medical Oncology, University of Rome Tor Vergata, I-00133 Rome
| | | | - Giulia Russo
- Department of Drug Sciences, University of Catania, I-95123 Catania
| | | | - Francesco Pappalardo
- Department of Drug Sciences, University of Catania, I-95123 Catania
- Research Center for Prevention, Diagnosis and Treatment of Tumors, University of Catania, I-95123 Catania, Italy
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Greece
| | | | - Massimo Libra
- Section of General Pathology, Clinics and Oncology, Department of Biomedical and Biotechnological Sciences, University of Catania, I-95123 Catania
- Research Center for Prevention, Diagnosis and Treatment of Tumors, University of Catania, I-95123 Catania, Italy
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Romeo I, Mesiti F, Lupia A, Alcaro S. Current Updates on Naturally Occurring Compounds Recognizing SARS-CoV-2 Druggable Targets. Molecules 2021; 26:632. [PMID: 33530467 PMCID: PMC7865633 DOI: 10.3390/molecules26030632] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 02/06/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified in China as the etiologic agent of the recent COVID-19 pandemic outbreak. Due to its high transmissibility, this virus quickly spread throughout the world, causing considerable health issues. The scientific community exerted noteworthy efforts to obtain therapeutic solutions for COVID-19, and new scientific networks were constituted. No certified drugs to efficiently inhibit the virus were identified, and the development of de-novo medicines requires approximately ten years of research. Therefore, the repurposing of natural products could be an effective strategy to handle SARS-CoV-2 infection. This review aims to update on current status of the natural occurring compounds recognizing SARS-CoV-2 druggable targets. Among the clinical trials actually recruited, some natural compounds are ongoing to examine their potential role to prevent and to treat the COVID-19 infection. Many natural scaffolds, including alkaloids, terpenes, flavonoids, and benzoquinones, were investigated by in-silico, in-vitro, and in-vivo approaches. Despite the large data set obtained by a computational approach, experimental evidences in most cases are not available. To fill this gap, further efforts to validate these results are required. We believe that an accurate investigation of naturally occurring compounds may provide insights for the potential treatment of COVID-19 patients.
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Affiliation(s)
- Isabella Romeo
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy;
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (F.M.); (A.L.)
| | - Francesco Mesiti
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (F.M.); (A.L.)
| | - Antonio Lupia
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (F.M.); (A.L.)
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy;
- Net4Science Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (F.M.); (A.L.)
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Vougogiannopoulou K, Corona A, Tramontano E, Alexis MN, Skaltsounis AL. Natural and Nature-Derived Products Targeting Human Coronaviruses. Molecules 2021; 26:448. [PMID: 33467029 PMCID: PMC7831024 DOI: 10.3390/molecules26020448] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 01/18/2023] Open
Abstract
The ongoing pandemic of severe acute respiratory syndrome (SARS), caused by the SARS-CoV-2 human coronavirus (HCoV), has brought the international scientific community before a state of emergency that needs to be addressed with intensive research for the discovery of pharmacological agents with antiviral activity. Potential antiviral natural products (NPs) have been discovered from plants of the global biodiversity, including extracts, compounds and categories of compounds with activity against several viruses of the respiratory tract such as HCoVs. However, the scarcity of natural products (NPs) and small-molecules (SMs) used as antiviral agents, especially for HCoVs, is notable. This is a review of 203 publications, which were selected using PubMed/MEDLINE, Web of Science, Scopus, and Google Scholar, evaluates the available literature since the discovery of the first human coronavirus in the 1960s; it summarizes important aspects of structure, function, and therapeutic targeting of HCoVs as well as NPs (19 total plant extracts and 204 isolated or semi-synthesized pure compounds) with anti-HCoV activity targeting viral and non-viral proteins, while focusing on the advances on the discovery of NPs with anti-SARS-CoV-2 activity, and providing a critical perspective.
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Affiliation(s)
- Konstantina Vougogiannopoulou
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece;
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Biomedical Section, Laboratory of Molecular Virology, E block, Cittadella Universitaria di Monserrato, SS55409042 Monserrato, Italy; (A.C.); (E.T.)
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Biomedical Section, Laboratory of Molecular Virology, E block, Cittadella Universitaria di Monserrato, SS55409042 Monserrato, Italy; (A.C.); (E.T.)
| | - Michael N. Alexis
- Molecular Endocrinology Team, Inst of Chemical Biology, National Hellenic Research Foundation (NHRF), 48 Vassileos Constantinou Ave., 11635 Athens, Greece;
| | - Alexios-Leandros Skaltsounis
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece;
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Sakshi C, Harikrishnan A, Jayaraman S, Choudhury AR, Veena V. Predictive medicinal metabolites from Momordica dioica against comorbidity related proteins of SARS-CoV-2 infections. J Biomol Struct Dyn 2021; 40:5175-5188. [PMID: 33427588 PMCID: PMC7814569 DOI: 10.1080/07391102.2020.1868340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Momordica dioica have proven medicinal potential of antidiabetic, antiviral and immune stimulating properties. Flavonoids and triterpenoids from M. dioica were more extensively investigated for antiviral, antidiabetic and immunomodulatory activities. In this present study, we have predicted the reported bioactive flavonoids and triterpenoids of the plant against the SARS-CoV-2 main protease, RNA-dependent RNA polymerase (RdRp), spike protein, angiotensin converting enzyme (ACE-2) receptor and dipeptidyl peptidase (DPP4) receptor through molecular docking and in silico ADME predictions methods. According to the binding affinities, the two triterpenoids, hederagenin and oleanolic acid exhibited the best docking scores with these proteins than the catechin and quercetin with compared to standard remdesivir, favipiravir and hydroxychloroquine. The in vitro protein-drug studies have also showed significant interaction of catechin and quercetin compounds than standard drugs. The in silico binding studies correlated with the in silico binding studies. Further, M. dioica being used as antidiabetic and its metabolite had significant interaction with DDP4, a comorbidity protein involved in aiding the viral entry. Out of all the natural ligands, quercetin was reported relatively good and safe for humans with high gastrointestinal tract permeability and poor blood brain barrier crossing abilities. Hence, M. dioica phytocompounds reflects promising therapeutic properties against SARS-CoV-2 infections under comorbid conditions such as diabetes, cardiovascular disease and kidney disorders. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Chavan Sakshi
- Department of Bioanalytical Sciences, Ramnarain Ruia Autonomous College, Mumbai, Maharashtra, India
| | - A Harikrishnan
- Department of Chemistry, School of Arts and Sciences, Vinayaka Mission Research Foundation-Aarupadai Veedu (VMRF-AV) Campus, Chennai, Tamil Nadu, India
| | | | - Ahana Roy Choudhury
- Centre for Bioinformatics, School of Life Science, Pondicherry University, Puducherry, India
| | - V Veena
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru, Karnataka, India
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Petit L, Vernès L, Cadoret JP. Docking and in silico toxicity assessment of Arthrospira compounds as potential antiviral agents against SARS-CoV-2. JOURNAL OF APPLIED PHYCOLOGY 2021; 33:1579-1602. [PMID: 33776210 PMCID: PMC7979453 DOI: 10.1007/s10811-021-02372-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 01/03/2021] [Accepted: 01/03/2021] [Indexed: 05/07/2023]
Abstract
UNLABELLED A race is currently being launched as a result of the international health situation. This race aims to find, by various means, weapons to counter the Covid-19 pandemic now widespread on all continents. The aquatic world and in particular that of photosynthetic organisms is regularly highlighted but paradoxically little exploited in view of the tremendous possibilities it offers. Computational tools allow not only to clear the existence and activity of many molecules but also to model their relationships with receptors identified in potential hosts. On a routine basis, our laboratory carries out a research activity on functionalities of molecules derived from algae using in silico tools. We have implemented our skills in algae biology and in modeling, as tests in order to identify molecules expressed by the genus Arthrospira showing an antiviral potential and more particularly anti-SARS-CoV-2. Using consensus docking and redocking with Autodock Vina and SwissDock, we were able to identify several promising molecules from Arthrospira: phycocyanobilin, phycoerythrobilin, phycourobilin, and folic acid. These four compounds showed reliable binding energies comprised between - 6.95 and - 7.45 kcal.mol-1 in Autodock Vina and between - 9.285 and - 10.35 kcal.mol-1 with SwissDock. Toxicity prediction as well as current regulations provided promising arguments for the inclusion of these compounds in further studies to assess their ability to compete with the SARS-CoV-2/ACE2 complex both in vitro and in vivo. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10811-021-02372-9.
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Affiliation(s)
- Léna Petit
- Algama, 81 rue Réaumur, 75002 Paris, France
| | - Léa Vernès
- Algama, 81 rue Réaumur, 75002 Paris, France
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Identification of Persuasive Antiviral Natural Compounds for COVID-19 by Targeting Endoribonuclease NSP15: A Structural-Bioinformatics Approach. Molecules 2020; 25:molecules25235657. [PMID: 33271751 PMCID: PMC7729992 DOI: 10.3390/molecules25235657] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 is a positive-stranded RNA virus that bundles its genomic material as messenger-sense RNA in infectious virions and replicates these genomes through RNA intermediates. Several virus-encoded nonstructural proteins play a key role during the viral life cycle. Endoribonuclease NSP15 is vital for the replication and life cycle of the virus, and is thus considered a compelling druggable target. Here, we performed a combination of multiscoring virtual screening and molecular docking of a library of 1624 natural compounds (Nuclei of Bioassays, Ecophysiology and Biosynthesis of Natural Products (NuBBE) database) on the active sites of NSP15 (PDB:6VWW). After sequential high-throughput screening by LibDock and GOLD, docking optimization by CDOCKER, and final scoring by calculating binding energies, top-ranked compounds NuBBE-1970 and NuBBE-242 were further investigated via an indepth molecular-docking and molecular-dynamics simulation of 60 ns, which revealed that the binding of these two compounds with active site residues of NSP15 was sufficiently strong and stable. The findings strongly suggest that further optimization and clinical investigations of these potent compounds may lead to effective SARS-CoV-2 treatment.
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Delre P, Caporuscio F, Saviano M, Mangiatordi GF. Repurposing Known Drugs as Covalent and Non-covalent Inhibitors of the SARS-CoV-2 Papain-Like Protease. Front Chem 2020; 8:594009. [PMID: 33304884 PMCID: PMC7701290 DOI: 10.3389/fchem.2020.594009] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022] Open
Abstract
In the absence of an approved vaccine, developing effective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antivirals is essential to tackle the current pandemic health crisis due to the coronavirus disease 2019 (COVID-19) spread. As any traditional drug discovery program is a time-consuming and costly process requiring more than one decade to be completed, in silico repurposing of existing drugs is the preferred way for rapidly selecting promising clinical candidates. We present a virtual screening campaign to identify covalent and non-covalent inhibitors of the SARS-CoV-2 papain-like protease (PLpro) showing potential multitarget activities (i.e., a desirable polypharmacology profile) for the COVID-19 treatment. A dataset including 688 phase III and 1,702 phase IV clinical trial drugs was downloaded from ChEMBL (version 27.1) and docked to the recently released crystal structure of PLpro in complex with a covalently bound peptide inhibitor. The obtained results were analyzed by combining protein-ligand interaction fingerprint similarities, conventional docking scores, and MM-GBSA-binding free energies and allowed the identification of some interesting candidates for further in vitro testing. To the best of our knowledge, this study represents the first attempt to repurpose drugs for a covalent inhibition of PLpro and could pave the way for new therapeutic strategies against COVID-19.
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Affiliation(s)
- Pietro Delre
- Department of Chemistry, University of Bari “Aldo Moro”, Bari, Italy
- National Research Council (CNR) – Institute of Crystallography, Bari, Italy
| | - Fabiana Caporuscio
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Michele Saviano
- National Research Council (CNR) – Institute of Crystallography, Bari, Italy
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An in-silico study on selected organosulfur compounds as potential drugs for SARS-CoV-2 infection via binding multiple drug targets. Chem Phys Lett 2020; 763:138193. [PMID: 33223560 PMCID: PMC7666712 DOI: 10.1016/j.cplett.2020.138193] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/18/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023]
Abstract
Lurasidone and Lurasidone exo inhibit SARS-CoV-2 via ‘one drug multiple targets’ strategy. MD simulation revealed their strong binding affinity against multiple targets of SARS-CoV-2. Both the drugs exhibit favourable pharmacokinetic properties as predicted by ADMET parameters. Their unique multitargeting feature warrants further in-vitro and in-vivo experiments.
The emerging paradigm shift from ‘one molecule, one target, for one disease’ towards ‘multi-targeted small molecules’ has paved an ingenious pathway in drug discovery in recent years. We extracted this idea for the investigation of drugs for COVID-19. Perceiving the importance of organosulfur compounds, seventy-six known organosulfur compounds were screened and studied for the interaction with multiple SARS-CoV-2 target proteins by molecular dynamics simulation. Lurasidone and its derivatives displayed substantial binding affinity against five proteins (Mpro, PLpro, Spro, helicase and RdRp). The pharmacokinetics, ADMET properties and target prediction studies performed in this work further potentiates the effectiveness against SARS-CoV-2.
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Rathod SB, Prajapati PB, Punjabi LB, Prajapati KN, Chauhan N, Mansuri MF. Peptide modelling and screening against human ACE2 and spike glycoprotein RBD of SARS-CoV-2. In Silico Pharmacol 2020; 8:3. [PMID: 33184600 PMCID: PMC7649901 DOI: 10.1007/s40203-020-00055-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/28/2020] [Indexed: 02/06/2023] Open
Abstract
Outbreak of Coronavirus Disease 2019 (COVID-19) has become a great challenge for scientific community globally. Virus enters cell through spike glycoprotein fusion with ACE2 (Angiotensin-Converting Enzyme 2) human receptor. Hence, spike glycoprotein of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a potential target for diagnostics, vaccines, and antibodies. Also, virus entry can be prevented by blocking ACE2 thus, ACE2 can be considered potential target for therapeutics. As being highly specific, safe and efficacious, peptides hold their place in therapeutics. In present study, we retrieved sequence of 70 peptides from Antiviral Peptide Database (AVPdb), modelled them using 3D structure predicting web tool and docked them with receptor binding domain (RBD) of spike protein and human host receptor ACE2 using peptide-protein docking. It was observed that peptides have more affinity towards ACE2 in comparison with spike RBD. Interestingly it was noticed that most of the peptides bind to RBM (residue binding motif) which is responsible for ACE2 binding at the interface of RBD while, for ACE2, peptides prefer to bind the core cavity rather than RBD binding interface. To further investigate how peptides at the interface of RBD or ACE2 alter the binding between RBD and ACE2, protein-protein docking of RBD and ACE2 with and without peptides was performed. Peptides, AVP0671 at RBD and AVP1244 at ACE2 interfaces significantly reduce the binding affinity and change the orientation of RBD and ACE2 binding. This finding suggests that peptides can be used as a drug to inhibit virus entry in cells to stop COVID-19 pandemic in the future after experimental evidences.
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Affiliation(s)
- Shravan B. Rathod
- Department of Chemistry, Smt. S. M. Panchal Science College, Talod, Gujarat India
| | | | - Lata B. Punjabi
- Department of Chemistry, School of Sciences, Gujarat University, Ahmedabad, Gujarat India
| | | | - Neha Chauhan
- Department of Biosciences and Biotechnology, Banasthali Vidhyapith, Banasthali, Rajasthan India
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Petushkova AI, Zamyatnin AA. Papain-Like Proteases as Coronaviral Drug Targets: Current Inhibitors, Opportunities, and Limitations. Pharmaceuticals (Basel) 2020; 13:E277. [PMID: 32998368 PMCID: PMC7601131 DOI: 10.3390/ph13100277] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/26/2020] [Accepted: 09/26/2020] [Indexed: 12/23/2022] Open
Abstract
Papain-like proteases (PLpro) of coronaviruses (CoVs) support viral reproduction and suppress the immune response of the host, which makes CoV PLpro perspective pharmaceutical targets. Their inhibition could both prevent viral replication and boost the immune system of the host, leading to the speedy recovery of the patient. Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the third CoV outbreak in the last 20 years. Frequent mutations of the viral genome likely lead to the emergence of more CoVs. Inhibitors for CoV PLpro can be broad-spectrum and can diminish present and prevent future CoV outbreaks as PLpro from different CoVs have conservative structures. Several inhibitors have been developed to withstand SARS-CoV and Middle East respiratory syndrome CoV (MERS-CoV). This review summarizes the structural features of CoV PLpro, the inhibitors that have been identified over the last 20 years, and the compounds that have the potential to become novel effective therapeutics against CoVs in the near future.
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Affiliation(s)
- Anastasiia I. Petushkova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
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Tan DX, Hardeland R. Targeting Host Defense System and Rescuing Compromised Mitochondria to Increase Tolerance against Pathogens by Melatonin May Impact Outcome of Deadly Virus Infection Pertinent to COVID-19. Molecules 2020; 25:molecules25194410. [PMID: 32992875 PMCID: PMC7582936 DOI: 10.3390/molecules25194410] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/19/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023] Open
Abstract
Fighting infectious diseases, particularly viral infections, is a demanding task for human health. Targeting the pathogens or targeting the host are different strategies, but with an identical purpose, i.e., to curb the pathogen's spreading and cure the illness. It appears that targeting a host to increase tolerance against pathogens can be of substantial advantage and is a strategy used in evolution. Practically, it has a broader protective spectrum than that of only targeting the specific pathogens, which differ in terms of susceptibility. Methods for host targeting applied in one pandemic can even be effective for upcoming pandemics with different pathogens. This is even more urgent if we consider the possible concomitance of two respiratory diseases with potential multi-organ afflictions such as Coronavirus disease 2019 (COVID-19) and seasonal flu. Melatonin is a molecule that can enhance the host's tolerance against pathogen invasions. Due to its antioxidant, anti-inflammatory, and immunoregulatory activities, melatonin has the capacity to reduce the severity and mortality of deadly virus infections including COVID-19. Melatonin is synthesized and functions in mitochondria, which play a critical role in viral infections. Not surprisingly, melatonin synthesis can become a target of viral strategies that manipulate the mitochondrial status. For example, a viral infection can switch energy metabolism from respiration to widely anaerobic glycolysis even if plenty of oxygen is available (the Warburg effect) when the host cell cannot generate acetyl-coenzyme A, a metabolite required for melatonin biosynthesis. Under some conditions, including aging, gender, predisposed health conditions, already compromised mitochondria, when exposed to further viral challenges, lose their capacity for producing sufficient amounts of melatonin. This leads to a reduced support of mitochondrial functions and makes these individuals more vulnerable to infectious diseases. Thus, the maintenance of mitochondrial function by melatonin supplementation can be expected to generate beneficial effects on the outcome of viral infectious diseases, particularly COVID-19.
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Affiliation(s)
- Dun-Xian Tan
- S.T. Bio-Life, San Antonio, TX 78240, USA
- Correspondence: ; Tel.: +1-215-672-550
| | - Ruediger Hardeland
- Johann Friedrich Blumenbach Institute of Zoology and Anthropology, University of Göttingen, 37073 Göttingen, Germany;
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Mukherjee S, Dasgupta S, Adhikary T, Adhikari U, Panja SS. Structural insight to hydroxychloroquine-3C-like proteinase complexation from SARS-CoV-2: inhibitor modelling study through molecular docking and MD-simulation study. J Biomol Struct Dyn 2020; 39:7322-7334. [PMID: 32772895 PMCID: PMC7484585 DOI: 10.1080/07391102.2020.1804458] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The spread of novel coronavirus strain, Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) causes Coronavirus disease (COVID-19) has now spread worldwide and effecting the entire human race. The viral genetic material is transcripted and replicated by 3 C-like protease, as a result, it is an important drug target for COVID-19. Hydroxychloroquine (HCQ) report promising results against this drug target so, we perform molecular docking followed by MD-simulation studies of HCQ and modelled some ligand (Mod-I and Mod-II) molecules with SARS-CoV-2-main protease which reveals the structural organization of the active site residues and presence of a conserve water-mediated catalytic triad that helps in the recognition of Mod-I/II ligand molecules. The study may be helpful to gain a detailed structural insight on the presence of water-mediated catalytic triad which could be useful for inhibitor modelling. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Soumita Mukherjee
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, West Bengal, India
| | - Subrata Dasgupta
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, West Bengal, India
| | - Tapasendra Adhikary
- Department of Metallurgical & Materials Engineering, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Utpal Adhikari
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, West Bengal, India
| | - Sujit Sankar Panja
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, West Bengal, India
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74
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Computational search for potential COVID-19 drugs from FDAapproved drugs and small molecules of natural origin identifies several anti-virals and plant products. J Biosci 2020. [PMID: 32713863 PMCID: PMC7366452 DOI: 10.1007/s12038-020-00069-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The world is currently facing the COVID-19 pandemic, for which mild symptoms include fever and dry cough. In severe cases, it could lead to pneumonia and ultimately death in some instances. Moreover, the causative pathogen is highly contagious and there are no drugs or vaccines for it yet. The pathogen, SARS-CoV-2, is one of the human coronaviruses which was identified to infect humans first in December 2019. SARS-CoV-2 shares evolutionary relationship to other highly pathogenic viruses such as Severe Acute Respiratory Syndrome (SARS) and Middle East respiratory syndrome (MERS). We have exploited this similarity to model a target non-structural protein, NSP1, since it is implicated in the regulation of host gene expression by the virus and hijacking of host machinery. We next interrogated the capacity to repurpose around 2300 FDA-approved drugs and more than 3,00,000 small molecules of natural origin towards drug identification through virtual screening and molecular dynamics. Interestingly, we observed simple molecules like lactose, previously known anti-virals and few secondary metabolites of plants as promising hits. These herbal plants are already practiced in Ayurveda over centuries to treat respiratory problems and inflammation. Disclaimer: we would not like to recommend uptake of these small molecules for suspect COVID patients until it is approved by competent national or international authorities.
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75
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Sen Gupta PS, Biswal S, Singha D, Rana MK. Binding insight of clinically oriented drug famotidine with the identified potential target of SARS-CoV-2. J Biomol Struct Dyn 2020; 39:5327-5333. [DOI: 10.1080/07391102.2020.1784795] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Parth Sarthi Sen Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Ganjam, Odisha, India
| | - Satyaranjan Biswal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Ganjam, Odisha, India
| | - Dipankar Singha
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Ganjam, Odisha, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Ganjam, Odisha, India
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76
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Sharma A, Tiwari V, Sowdhamini R. Computational search for potential COVID-19 drugs from FDAapproved drugs and small molecules of natural origin identifies several anti-virals and plant products. J Biosci 2020; 45:100. [PMID: 32713863 PMCID: PMC7366452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/23/2020] [Indexed: 08/23/2024]
Abstract
The world is currently facing the COVID-19 pandemic, for which mild symptoms include fever and dry cough. In severe cases, it could lead to pneumonia and ultimately death in some instances. Moreover, the causative pathogen is highly contagious and there are no drugs or vaccines for it yet. The pathogen, SARS-CoV-2, is one of the human coronaviruses which was identified to infect humans first in December 2019. SARS-CoV-2 shares evolutionary relationship to other highly pathogenic viruses such as Severe Acute Respiratory Syndrome (SARS) and Middle East respiratory syndrome (MERS). We have exploited this similarity to model a target non-structural protein, NSP1, since it is implicated in the regulation of host gene expression by the virus and hijacking of host machinery. We next interrogated the capacity to repurpose around 2300 FDA-approved drugs and more than 3,00,000 small molecules of natural origin towards drug identification through virtual screening and molecular dynamics. Interestingly, we observed simple molecules like lactose, previously known anti-virals and few secondary metabolites of plants as promising hits. These herbal plants are already practiced in Ayurveda over centuries to treat respiratory problems and inflammation. Disclaimer: we would not like to recommend uptake of these small molecules for suspect COVID patients until it is approved by competent national or international authorities.
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Affiliation(s)
- Abhishek Sharma
- National Centre for Biological Sciences, GKVK Campus, Bengaluru, 560 065 India
| | - Vikas Tiwari
- National Centre for Biological Sciences, GKVK Campus, Bengaluru, 560 065 India
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