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Liang JJ, Pitsillou E, Hung A, Karagiannis TC. A repository of COVID-19 related molecular dynamics simulations and utilisation in the context of nsp10-nsp16 antivirals. J Mol Graph Model 2024; 126:108666. [PMID: 37976980 DOI: 10.1016/j.jmgm.2023.108666] [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: 09/14/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of establishing systems and infrastructure to develop vaccines, antiviral drugs, and therapeutic antibodies against emerging pathogens. Typical drug discovery processes involve targeting suitable proteins to effect pathogen replication or to attenuate host responses, by examining either large chemical databases or protein-protein interactions. Following initial screens, molecular dynamics (MD) simulations are critical for gaining further insight into molecular interactions. During the COVID-19 pandemic, many research groups made their simulations widely available, as highlighted by the comprehensive D.E. Shaw Research trajectory database. To investigate protein target sites and evaluate potential lead compounds, we performed over 300 MD simulations relating to COVID-19. We organised our simulations into a repository, which is publicly available at https://epimedlab.org/trajectories/. The trajectories cover a large part of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteome, and the majority of our MD simulations focused on the identification of potential antivirals. For example, we focused on the S-adenosyl-l-methionine binding site of the nsp10-nsp16 complex, a critical component of viral replication, revealing verbascoside as a potential lead. Moreover, we utilised MD trajectories to explore the interface between the spike protein receptor binding domain and human angiotensin-converting enzyme 2 receptor, with the ultimate aim being investigation of new variants in real-time. Overall, MD simulations are a critical component of the in silico drug discovery process and as highlighted throughout the pandemic, data sharing enables accelerated progress. We have organised our extensive collection of COVID-19 related MD trajectories into an easily accessible repository.
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Affiliation(s)
- Julia J Liang
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia; Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia; School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, VIC, 3001, Australia
| | - Tom C Karagiannis
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC, 3004, Australia; Epigenomic Medicine Laboratory at prospED Training, Carlton, VIC, 3053, Australia; Department of Clinical Pathology, The University of Melbourne, Parkville, VIC, 3010, Australia; Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Ijinu TP, De Lellis LF, Shanmugarama S, Pérez-Gregorio R, Sasikumar P, Ullah H, Buccato DG, Di Minno A, Baldi A, Daglia M. Anthocyanins as Immunomodulatory Dietary Supplements: A Nutraceutical Perspective and Micro-/Nano-Strategies for Enhanced Bioavailability. Nutrients 2023; 15:4152. [PMID: 37836436 PMCID: PMC10574533 DOI: 10.3390/nu15194152] [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: 09/07/2023] [Revised: 09/21/2023] [Accepted: 09/24/2023] [Indexed: 10/15/2023] Open
Abstract
Anthocyanins (ACNs) have attracted considerable attention for their potential to modulate the immune system. Research has revealed their antioxidant and anti-inflammatory properties, which play a crucial role in immune regulation by influencing key immune cells, such as lymphocytes, macrophages, and dendritic cells. Moreover, ACNs contribute towards maintaining a balance between proinflammatory and anti-inflammatory cytokines, thus promoting immune health. Beyond their direct effects on immune cells, ACNs significantly impact gut health and the microbiota, essential factors in immune regulation. Emerging evidence suggests that they positively influence the composition of the gut microbiome, enhancing their immunomodulatory effects. Furthermore, these compounds synergize with other bioactive substances, such as vitamins and minerals, further enhancing their potential as immune-supporting dietary supplements. However, detailed clinical studies must fully validate these findings and determine safe dosages across varied populations. Incorporating these natural compounds into functional foods or supplements could revolutionize the management of immune-related conditions. Personalized nutrition and healthcare strategies may be developed to enhance overall well-being and immune resilience by fully understanding the mechanisms underlying the actions of their components. Recent advancements in delivery methods have focused on improving the bioavailability and effectiveness of ACNs, providing promising avenues for future applications.
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Affiliation(s)
- Thadiyan Parambil Ijinu
- Naturæ Scientific, Kerala University-Business Innovation and Incubation Centre, Kariavattom Campus, University of Kerala, Thiruvananthapuram 695581, India;
- The National Society of Ethnopharmacology, VRA-179, Mannamoola, Peroorkada P.O., Thiruvananthapuram 695005, India
| | - Lorenza Francesca De Lellis
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Naples, Italy; (L.F.D.L.); (D.G.B.); (A.D.M.); (A.B.)
| | - Santny Shanmugarama
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Rosa Pérez-Gregorio
- Food and Health Omics Group, Institute of Agroecology and Food, Faculty of Sciences, University of Vigo, 32004 Ourense, Spain;
- LAQV-REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
- Department of Analytical and Food Chemistry, Galicia Sur Health Research Institute (IISGS), SERGAS-UVIGO, 32002 Ourense, Spain
| | | | - Hammad Ullah
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Naples, Italy; (L.F.D.L.); (D.G.B.); (A.D.M.); (A.B.)
| | - Daniele Giuseppe Buccato
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Naples, Italy; (L.F.D.L.); (D.G.B.); (A.D.M.); (A.B.)
| | - Alessandro Di Minno
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Naples, Italy; (L.F.D.L.); (D.G.B.); (A.D.M.); (A.B.)
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore 486, 80145 Naples, Italy
| | - Alessandra Baldi
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Naples, Italy; (L.F.D.L.); (D.G.B.); (A.D.M.); (A.B.)
| | - Maria Daglia
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Naples, Italy; (L.F.D.L.); (D.G.B.); (A.D.M.); (A.B.)
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
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Ershov PV, Yablokov EO, Mezentsev YV, Chuev GN, Fedotova MV, Kruchinin SE, Ivanov AS. SARS-COV-2 Coronavirus Papain-like Protease PLpro as an Antiviral Target for Inhibitors of Active Site and Protein-Protein Interactions. Biophysics (Nagoya-shi) 2023; 67:902-912. [PMID: 36883182 PMCID: PMC9984130 DOI: 10.1134/s0006350922060082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 03/06/2023] Open
Abstract
The papain-like protease PLpro of the SARS-CoV-2 coronavirus is a multifunctional enzyme that catalyzes the proteolytic processing of two viral polyproteins, pp1a and pp1ab. PLpro also cleaves peptide bonds between host cell proteins and ubiquitin (or ubiquitin-like proteins), which is associated with a violation of immune processes. Nine structures of the most effective inhibitors of the PLpro active center were prioritized according to the parameters of biochemical (IC 50) and cellular tests to assess the suppression of viral replication (EC 50) and cytotoxicity (CC 50). A literature search has shown that PLpro can interact with at least 60 potential protein partners in cells, 23 of which are targets for other viral proteins (human papillomavirus and Epstein-Barr virus). The analysis of protein-protein interactions showed that the proteins USP3, UBE2J1, RCHY1, and FAF2 involved in deubiquitinylation and ubiquitinylation processes contain the largest number of bonds with other proteins; the interaction of viral proteins with them can affect the architecture of the entire network of protein-protein interactions. Using the example of a spatial model of the PLpro/ubiquitin complex and a set of 154 naturally occurring compounds with known antiviral activity, 13 compounds (molecular masses in the range of 454-954 Da) were predicted as potential PLpro inhibitors. These compounds bind to the "hot" amino acid residues of the protease at the positions Gly163, Asp164, Arg166, Glu167, and Tyr264 involved in the interaction with ubiquitin. Thus, pharmacological effects on peripheral PLpro sites, which play important roles in binding protein substrates, may be an additional target-oriented antiviral strategy.
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Affiliation(s)
- P. V. Ershov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - E. O. Yablokov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | | | - G. N. Chuev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow oblast Russia
| | - M. V. Fedotova
- Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - S. E. Kruchinin
- Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - A. S. Ivanov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
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Dinda B, Dinda S, Dinda M. Therapeutic potential of green tea catechin, (-)-epigallocatechin-3- O-gallate (EGCG) in SARS-CoV-2 infection: Major interactions with host/virus proteases. PHYTOMEDICINE PLUS : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 3:100402. [PMID: 36597465 PMCID: PMC9800022 DOI: 10.1016/j.phyplu.2022.100402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND The current COVID-19 pandemic from the human pathogenic virus SARS-CoV-2 has resulted in a major health hazard globally. The morbidity and transmission modality of this disease are severe and uncontrollable. As no effective clinical drugs are available for treatment of COVID-19 infection till to date and only vaccination is used as prophylaxis and its efficacy is restricted due to emergent of new variants of SARS-CoV-2, there is an urgent need for effective drugs for its treatment. PURPOSE The aim of this review was to provide a detailed analysis of anti-SARS-CoV-2 efficacy of (-)-epigallocatechin-3-O-gallate (EGCG), a major catechin constituent of green tea (Camellia sinensis (L.) Kuntze) beverage to highlight the scope of EGCG in clinical medicine as both prophylaxis and treatment of present COVID-19 infection. In addition, the factors related to poor oral bioavailabilty of EGCG was also analysed for a suggestion for future research in this direction. STUDY DESIGN We collected the published articles related to anti-SARS-CoV-2 activity of EGCG against the original strain (Wuhan type) and its newly emerged variants of SARS-CoV-2 virus. METHODS A systematic search on the published literature was conducted in various databases including Google Scholar, PubMed, Science Direct and Scopus to collect the relevant literature. RESULTS The findings of this search demonstrate that EGCG shows potent antiviral activity against SARS-CoV-2 virus by preventing viral entry and replication in host cells in vitro models. The studies on the molecular mechanisms of EGCG in inhibition of SARS-CoV-2 infection in host cells reveal that EGCG blocks the entry of the virus particles by interaction with the receptor binding domain (RBD) of viral spike (S) protein to host cell surface receptor protease angiotensin-converting enzyme 2 (ACE2) as well as suppression of the expressions of host proteases, ACE2, TMPRSS2 and GRP78, required for viral entry, by Nrf2 activation in host cells. Moreover, EGCG inhibits the activities of SARS-CoV-2 main protease (Mpro), papain-like protease (PLpro), endoribonuclease Nsp15 in vitro models and of RNA-dependent RNA polymerase (RdRp) in molecular docking model for suppression of viral replication. In addition, EGCG significantly inhibits viral inflammatory cytokine production by stimulating Nrf2- dependent host immune response in virus-infected cells. EGCG significantly reduces the elevated levels of HMGB1, a biomarker of sepsis, lung fibrosis and thrombotic complications in viral infections. EGCG potentially inhibits the infection of original (Wuhan type) strain of SARS-CoV-2 and other newly emerged variants as well as the infections of SARS-CoV-2 virus spike-protein of WT and its mutants-mediated pseudotyped viruses . EGCG shows maximum inhibitory effect against SARS-CoV-2 infection when the host cells are pre-incubated with the drug prior to viral infection. A sorbitol/lecithin-based throat spray containing concentrated green tea extract rich in EGCG content significantly reduces SARS-CoV-2 infectivity in oral mucosa. Several factors including degradation in gastrointestinal environment, low absorption in small intestine and extensive metabolism of EGCG are responsible for its poor bioavailability in humans. Pharmacokinetic and metabolism studies of EGCG in humans reveal poor bioavailability of EGCG in human plasma and EGCG-4"-sulfate is its major metabolite. The concentration of EGCG-4"-sulfate in human plasma is almost equivalent to that of free EGCG (Cmax 177.9 vs 233.5 nmol/L). These findings suggest that inhibition of sulfation of EGCG is a crucial factor for improvement of its bioavailability. In vitro study on the mechanism of EGCG sulfonation indicates that sulfotransferases, SULT1A1 and SULT1A3 are responsible for sulfonation in human liver and small intestine, respectively. Some attempts including structural modifications, and nanoformulations of EGCG and addition of nutrients with EGCG have been made to improve the bioavailability of EGCG. CONCLUSIONS The findings of this study suggest that EGCG has strong antiviral activity against SARS-CoV-2 infection independent of viral strains (Wuhan type (WT), other variants) by inhibition of viral entry and replication in host cells in vitro models. EGCG may be useful in reduction of this viral load in salivary glands of COVID-19 patients, if it is applied in mouth and throat wash formulations in optimal concentrations. EGCG could be a promising candidate in the development of effective vaccine for prevention of the infections of newly emergent strains of SARS-CoV-2 virus. EGCG might be useful also as a clinical medicine for treatment of COVID-19 patients if its bioavailability in human plasma is enhanced.
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Affiliation(s)
- Biswanath Dinda
- Department of Chemistry, Tripura University, Suryamaninagar, Agartala, Tripura, 799 022, India
| | - Subhajit Dinda
- Department of Chemistry, Kamalpur Govt Degree College, Dhalai,Tripura, 799 285, India
| | - Manikarna Dinda
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, 1300 Jefferson Park Ave, VA, 22908, United States of America
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Helman DS. Case Report: Psychiatric Symptoms Associated With the Moderna mRNA COVID-19 Vaccine Administration and Their Resolution. CLINICAL MEDICINE INSIGHTS-CASE REPORTS 2023; 16:11795476231166626. [PMID: 37065637 PMCID: PMC10099908 DOI: 10.1177/11795476231166626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/13/2023] [Indexed: 04/18/2023]
Abstract
This case report describes the sudden presentation and successful cessation of psychiatric symptoms following the first administration of the Moderna mRNA vaccine against the SARS-CoV-2 virus during early 2021. The process of discovery of symptoms is described, along with an empirical procedure which identified St. John's wort as the mediating agent. Implications for self-medication of mild depression are discussed. Hypericin, a constituent agent in St. John's wort, interacts with the SARS-CoV-2 spike protein. Sensitization to hypericin following vaccine administration is consistent with the observed symptoms.
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Affiliation(s)
- Daniel S Helman
- Daniel S Helman, Education Division, College of
Micronesia-FSM, Yap Campus, PO Box 286, Yap 96943, Federated States of Micronesia. Emails:
;
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Lei S, Chen X, Wu J, Duan X, Men K. Small molecules in the treatment of COVID-19. Signal Transduct Target Ther 2022; 7:387. [PMID: 36464706 PMCID: PMC9719906 DOI: 10.1038/s41392-022-01249-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 12/11/2022] Open
Abstract
The outbreak of COVID-19 has become a global crisis, and brought severe disruptions to societies and economies. Until now, effective therapeutics against COVID-19 are in high demand. Along with our improved understanding of the structure, function, and pathogenic process of SARS-CoV-2, many small molecules with potential anti-COVID-19 effects have been developed. So far, several antiviral strategies were explored. Besides directly inhibition of viral proteins such as RdRp and Mpro, interference of host enzymes including ACE2 and proteases, and blocking relevant immunoregulatory pathways represented by JAK/STAT, BTK, NF-κB, and NLRP3 pathways, are regarded feasible in drug development. The development of small molecules to treat COVID-19 has been achieved by several strategies, including computer-aided lead compound design and screening, natural product discovery, drug repurposing, and combination therapy. Several small molecules representative by remdesivir and paxlovid have been proved or authorized emergency use in many countries. And many candidates have entered clinical-trial stage. Nevertheless, due to the epidemiological features and variability issues of SARS-CoV-2, it is necessary to continue exploring novel strategies against COVID-19. This review discusses the current findings in the development of small molecules for COVID-19 treatment. Moreover, their detailed mechanism of action, chemical structures, and preclinical and clinical efficacies are discussed.
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Affiliation(s)
- Sibei Lei
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Xiaohua Chen
- grid.54549.390000 0004 0369 4060Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072 China
| | - Jieping Wu
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
| | - Xingmei Duan
- grid.54549.390000 0004 0369 4060Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072 China
| | - Ke Men
- grid.412901.f0000 0004 1770 1022State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041 People’s Republic of China
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Novel Drug Design for Treatment of COVID-19: A Systematic Review of Preclinical Studies. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:2044282. [PMID: 36199815 PMCID: PMC9527439 DOI: 10.1155/2022/2044282] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/23/2022] [Accepted: 08/03/2022] [Indexed: 11/27/2022]
Abstract
Background Since the beginning of the novel coronavirus (SARS-CoV-2) disease outbreak, there has been an increasing interest in discovering potential therapeutic agents for this disease. In this regard, we conducted a systematic review through an overview of drug development (in silico, in vitro, and in vivo) for treating COVID-19. Methods A systematic search was carried out in major databases including PubMed, Web of Science, Scopus, EMBASE, and Google Scholar from December 2019 to March 2021. A combination of the following terms was used: coronavirus, COVID-19, SARS-CoV-2, drug design, drug development, In silico, In vitro, and In vivo. A narrative synthesis was performed as a qualitative method for the data synthesis of each outcome measure. Results A total of 2168 articles were identified through searching databases. Finally, 315 studies (266 in silico, 34 in vitro, and 15 in vivo) were included. In studies with in silico approach, 98 article study repurposed drug and 91 studies evaluated herbal medicine on COVID-19. Among 260 drugs repurposed by the computational method, the best results were observed with saquinavir (n = 9), ritonavir (n = 8), and lopinavir (n = 6). Main protease (n = 154) following spike glycoprotein (n = 62) and other nonstructural protein of virus (n = 45) was among the most studied targets. Doxycycline, chlorpromazine, azithromycin, heparin, bepridil, and glycyrrhizic acid showed both in silico and in vitro inhibitory effects against SARS-CoV-2. Conclusion The preclinical studies of novel drug design for COVID-19 focused on main protease and spike glycoprotein as targets for antiviral development. From evaluated structures, saquinavir, ritonavir, eucalyptus, Tinospora cordifolia, aloe, green tea, curcumin, pyrazole, and triazole derivatives in in silico studies and doxycycline, chlorpromazine, and heparin from in vitro and human monoclonal antibodies from in vivo studies showed promised results regarding efficacy. It seems that due to the nature of COVID-19 disease, finding some drugs with multitarget antiviral actions and anti-inflammatory potential is valuable and some herbal medicines have this potential.
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Ruchawapol C, Fu WW, Xu HX. A review on computational approaches that support the researches on traditional Chinese medicines (TCM) against COVID-19. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 104:154324. [PMID: 35841663 PMCID: PMC9259013 DOI: 10.1016/j.phymed.2022.154324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/23/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND COVID-19 highly caused contagious infections and massive deaths worldwide as well as unprecedentedly disrupting global economies and societies, and the urgent development of new antiviral medications are required. Medicinal herbs are promising resources for the discovery of prophylactic candidate against COVID-19. Considerable amounts of experimental efforts have been made on vaccines and direct-acting antiviral agents (DAAs), but neither of them was fast and fully developed. PURPOSE This study examined the computational approaches that have played a significant role in drug discovery and development against COVID-19, and these computational methods and tools will be helpful for the discovery of lead compounds from phytochemicals and understanding the molecular mechanism of action of TCM in the prevention and control of the other diseases. METHODS A search conducting in scientific databases (PubMed, Science Direct, ResearchGate, Google Scholar, and Web of Science) found a total of 2172 articles, which were retrieved via web interface of the following websites. After applying some inclusion and exclusion criteria and full-text screening, only 292 articles were collected as eligible articles. RESULTS In this review, we highlight three main categories of computational approaches including structure-based, knowledge-mining (artificial intelligence) and network-based approaches. The most commonly used database, molecular docking tool, and MD simulation software include TCMSP, AutoDock Vina, and GROMACS, respectively. Network-based approaches were mainly provided to help readers understanding the complex mechanisms of multiple TCM ingredients, targets, diseases, and networks. CONCLUSION Computational approaches have been broadly applied to the research of phytochemicals and TCM against COVID-19, and played a significant role in drug discovery and development in terms of the financial and time saving.
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Affiliation(s)
- Chattarin Ruchawapol
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Cai Lun Lu 1200, Shanghai 201203, China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Cai Lun Lu 1200, Shanghai 201203, China
| | - Wen-Wei Fu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Cai Lun Lu 1200, Shanghai 201203, China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Cai Lun Lu 1200, Shanghai 201203, China.
| | - Hong-Xi Xu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Cai Lun Lu 1200, Shanghai 201203, China; Engineering Research Centre of Shanghai Colleges for TCM New Drug Discovery, Cai Lun Lu 1200, Shanghai 201203, China.
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Peniche-Pavía HA, Guzmán TJ, Magaña-Cerino JM, Gurrola-Díaz CM, Tiessen A. Maize Flavonoid Biosynthesis, Regulation, and Human Health Relevance: A Review. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165166. [PMID: 36014406 PMCID: PMC9413827 DOI: 10.3390/molecules27165166] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/01/2022] [Accepted: 08/10/2022] [Indexed: 11/25/2022]
Abstract
Maize is one of the most important crops for human and animal consumption and contains a chemical arsenal essential for survival: flavonoids. Moreover, flavonoids are well known for their beneficial effects on human health. In this review, we decided to organize the information about maize flavonoids into three sections. In the first section, we include updated information about the enzymatic pathway of maize flavonoids. We describe a total of twenty-one genes for the flavonoid pathway of maize. The first three genes participate in the general phenylpropanoid pathway. Four genes are common biosynthetic early genes for flavonoids, and fourteen are specific genes for the flavonoid subgroups, the anthocyanins, and flavone C-glycosides. The second section explains the tissue accumulation and regulation of flavonoids by environmental factors affecting the expression of the MYB-bHLH-WD40 (MBW) transcriptional complex. The study of transcription factors of the MBW complex is fundamental for understanding how the flavonoid profiles generate a palette of colors in the plant tissues. Finally, we also include an update of the biological activities of C3G, the major maize anthocyanin, including anticancer, antidiabetic, and antioxidant effects, among others. This review intends to disclose and integrate the existing knowledge regarding maize flavonoid pigmentation and its relevance in the human health sector.
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Affiliation(s)
- Héctor A. Peniche-Pavía
- Departamento de Bioquímica y Biotecnología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Libramiento Norte Km. 9.6, Irapuato 36824, Guanajuato, Mexico
| | - Tereso J. Guzmán
- Department of Pharmacology, Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstraße 48, 48149 Münster, Germany
| | - Jesús M. Magaña-Cerino
- División Académica de Ciencias de la Salud, Centro de Investigación y Posgrado, Universidad Juárez Autónoma de Tabasco, Av. Gregorio Méndez Magaña 2838-A, Col. Tamulté de las Barrancas, Villahermosa 86150, Tabasco, Mexico
| | - Carmen M. Gurrola-Díaz
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Instituto de Investigación en Enfermedades Crónico Degenerativas, Instituto Transdisciplinar de Investigación e Innovación en Salud, Universidad de Guadalajara, C. Sierra Mojada 950. Col. Independencia, Guadalajara 44340, Jalisco, Mexico
- Correspondence: ; Tel.: +52-33-10585200 (ext. 33930)
| | - Axel Tiessen
- Departamento de Bioquímica y Biotecnología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Libramiento Norte Km. 9.6, Irapuato 36824, Guanajuato, Mexico
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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11
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Sogukomerogullari HG. Molecular docking-assisted investigation of Pd(II) complexes carrying "SNS" pincer-type pyridine-thioether ligand as potential drug candidates against COVID-19. Comput Biol Med 2022; 145:105512. [PMID: 35429834 PMCID: PMC8994705 DOI: 10.1016/j.compbiomed.2022.105512] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 01/18/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has posed a threat to public health throughout the world since the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was discovered in late 2019. Since the beginning of the pandemic, scientists have done a tremendous amount of work in this area. However, among these studies, the investigation of the effect of newly synthesized compounds against coronavirus is rather weak. Examining the newly synthesized compounds with a computer-assisted molecular docking study provides quite an advantage in terms of the estimation and analysis of the biochemical activity and binding affinity of existing synthesized compounds against a biological target in a labor, time, and cost-saving way. In this study, the SNS pincer type 2,6-bis[[(4-methylphenyl)thio]methyl]pyridine ligand(L) (1) and its novel Pd(II) complexes ([Pd(κ2-L)(OAc)2]·3H2O (2) and [Pd(κ2-L)Cl2]·3H2O (3)) were synthesized and characterized by using FT-IR, UV-Vis, NMR, mass and elemental analysis techniques. The synthesized Pd complexes exhibited a square planar structure. The compounds were found to have non-electrolytic behavior. In the meantime, in silico investigations have defined and justified interaction processes between these molecules and Pd(II) at the atomic level. Furthermore, using molecular docking against target proteins of SARS-CoV-2, the efficiency of the SNS pincer type ligand and its Pd (II) complexes produced was studied and discussed for the first time. The experimental data has been supported and illuminated using computational visual methods and molecular docking, and the findings produced indicate compatibility. The binding energy values of the relevant compounds on the four protein model structures of SARS-CoV-2 (Main Protease, Papain-like protease, RdRp without RNA, and RdRp with RNA) are represented. Compound 2 ([Pd(κ2-L)(OAc)2]·3H2O) is the structure that exhibits the highest biochemical activity. According to all of the docking studies, Papain-like protease is the SARS-CoV-2 protein with which the three compounds exhibit mutual interaction. The compound 2 structure, in particular, is the most effective in terms of structural and interaction with the targets, as well as binding orientations.
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Affiliation(s)
- Hatice Gamze Sogukomerogullari
- Medical Services and Techniques Department, Health Services Vocational School, Gaziantep University, 27310, Gaziantep, Turkey
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12
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Brewitz L, Kamps JJAG, Lukacik P, Strain‐Damerell C, Zhao Y, Tumber A, Malla TR, Orville AM, Walsh MA, Schofield CJ. Mass Spectrometric Assays Reveal Discrepancies in Inhibition Profiles for the SARS-CoV-2 Papain-Like Protease. ChemMedChem 2022; 17:e202200016. [PMID: 35085423 PMCID: PMC9015526 DOI: 10.1002/cmdc.202200016] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/26/2022] [Indexed: 11/20/2022]
Abstract
The two SARS-CoV-2 proteases, i. e. the main protease (Mpro ) and the papain-like protease (PLpro ), which hydrolyze the viral polypeptide chain giving functional non-structural proteins, are essential for viral replication and are medicinal chemistry targets. We report a high-throughput mass spectrometry (MS)-based assay which directly monitors PLpro catalysis in vitro. The assay was applied to investigate the effect of reported small-molecule PLpro inhibitors and selected Mpro inhibitors on PLpro catalysis. The results reveal that some, but not all, PLpro inhibitor potencies differ substantially from those obtained using fluorescence-based assays. Some substrate-competing Mpro inhibitors, notably PF-07321332 (nirmatrelvir) which is in clinical development, do not inhibit PLpro . Less selective Mpro inhibitors, e. g. auranofin, inhibit PLpro , highlighting the potential for dual PLpro /Mpro inhibition. MS-based PLpro assays, which are orthogonal to widely employed fluorescence-based assays, are of utility in validating inhibitor potencies, especially for inhibitors operating by non-covalent mechanisms.
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Affiliation(s)
- Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOX1 3TAOxfordUK
| | - Jos J. A. G. Kamps
- Diamond Light Source Ltd.Harwell Science and Innovation CampusOX11 0DEDidcotUK
- Research Complex at HarwellHarwell Science and Innovation CampusOX11 0FADidcotUK
| | - Petra Lukacik
- Diamond Light Source Ltd.Harwell Science and Innovation CampusOX11 0DEDidcotUK
- Research Complex at HarwellHarwell Science and Innovation CampusOX11 0FADidcotUK
| | - Claire Strain‐Damerell
- Diamond Light Source Ltd.Harwell Science and Innovation CampusOX11 0DEDidcotUK
- Research Complex at HarwellHarwell Science and Innovation CampusOX11 0FADidcotUK
| | - Yilin Zhao
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOX1 3TAOxfordUK
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOX1 3TAOxfordUK
| | - Tika R. Malla
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOX1 3TAOxfordUK
| | - Allen M. Orville
- Diamond Light Source Ltd.Harwell Science and Innovation CampusOX11 0DEDidcotUK
- Research Complex at HarwellHarwell Science and Innovation CampusOX11 0FADidcotUK
| | - Martin A. Walsh
- Diamond Light Source Ltd.Harwell Science and Innovation CampusOX11 0DEDidcotUK
- Research Complex at HarwellHarwell Science and Innovation CampusOX11 0FADidcotUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of Oxford12 Mansfield RoadOX1 3TAOxfordUK
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13
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Matos ADR, Caetano BC, de Almeida Filho JL, Martins JSCDC, de Oliveira MGP, Sousa TDC, Horta MAP, Siqueira MM, Fernandez JH. Identification of Hypericin as a Candidate Repurposed Therapeutic Agent for COVID-19 and Its Potential Anti-SARS-CoV-2 Activity. Front Microbiol 2022; 13:828984. [PMID: 35222340 PMCID: PMC8866965 DOI: 10.3389/fmicb.2022.828984] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic has had an unprecedented impact on the global economy and public health. Its etiologic agent, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly transmissible, pathogenic and has a rapid global spread. Currently, the increase in the number of new confirmed cases has been slowed down due to the increase of vaccination in some regions of the world. Still, the rise of new variants has influenced the detection of additional waves of rising cases that some countries have experienced. Since the virus replication cycle is composed of many distinct stages, some viral proteins related to them, as the main-protease (Mpro) and RNA dependent RNA polymerase (RdRp), constitute individual potential antiviral targets. In this study, we challenged the mentioned enzymes against compounds pre-approved by health regulatory agencies in a virtual screening and later in Molecular Mechanics/Poisson–Bolzmann Surface Area (MM/PBSA) analysis. Our results showed that, among the identified potential drugs with anti-SARS-CoV-2 properties, Hypericin, an important component of the Hypericum perforatum that presents antiviral and antitumoral properties, binds with high affinity to viral Mpro and RdRp. Furthermore, we evaluated the activity of Hypericin anti-SARS-CoV-2 replication in an in vitro model of Vero-E6 infected cells. Therefore, we show that Hypericin inhibited viral replication in a dose dependent manner. Moreover, the cytotoxicity of the compound, in cultured cells, was evaluated, but no significant activity was found. Thus, the results observed in this study indicate that Hypericin is an excellent candidate for repurposing for the treatment of COVID-19, with possible inhibition of two important phases of virus maturation.
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Affiliation(s)
- Aline da Rocha Matos
- Laboratório de Virus Respiratórios e do Sarampo, Insituto Oswaldo Cruz, Fundação Oswaldo Cruz (LVRS-IOC-Fiocruz), Rio de Janeiro, Brazil
| | - Braulia Costa Caetano
- Laboratório de Virus Respiratórios e do Sarampo, Insituto Oswaldo Cruz, Fundação Oswaldo Cruz (LVRS-IOC-Fiocruz), Rio de Janeiro, Brazil
| | - João Luiz de Almeida Filho
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense (LQFPP-CBB-UENF), Campos dos Goytacazes, Brazil
| | | | | | - Thiago das Chagas Sousa
- Laboratório de Virus Respiratórios e do Sarampo, Insituto Oswaldo Cruz, Fundação Oswaldo Cruz (LVRS-IOC-Fiocruz), Rio de Janeiro, Brazil
| | - Marco Aurélio Pereira Horta
- Plataforma de Laboratórios de Biossegurança Nível 3, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (NB3-IOC-Fiocruz), Rio de Janeiro, Brazil
| | - Marilda Mendonça Siqueira
- Laboratório de Virus Respiratórios e do Sarampo, Insituto Oswaldo Cruz, Fundação Oswaldo Cruz (LVRS-IOC-Fiocruz), Rio de Janeiro, Brazil
| | - Jorge Hernandez Fernandez
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense (LQFPP-CBB-UENF), Campos dos Goytacazes, Brazil
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14
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Bakour M, Laaroussi H, Ousaaid D, El Ghouizi A, Es-safi I, Mechchate H, Lyoussi B. New Insights into Potential Beneficial Effects of Bioactive Compounds of Bee Products in Boosting Immunity to Fight COVID-19 Pandemic: Focus on Zinc and Polyphenols. Nutrients 2022; 14:nu14050942. [PMID: 35267917 PMCID: PMC8912813 DOI: 10.3390/nu14050942] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/16/2022] [Accepted: 02/20/2022] [Indexed: 02/01/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) is an epidemic caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). Populations at risk as well as those who can develop serious complications are people with chronic diseases such as diabetes, hypertension, and the elderly. Severe symptoms of SARS-CoV-2 infection are associated with immune failure and dysfunction. The approach of strengthening immunity may be the right choice in order to save lives. This review aimed to provide an overview of current information revealing the importance of bee products in strengthening the immune system against COVID-19. We highlighted the immunomodulatory and the antiviral effects of zinc and polyphenols, which may actively contribute to improving symptoms and preventing complications caused by COVID-19 and can counteract viral infections. Thus, this review will pave the way for conducting advanced experimental research to evaluate zinc and polyphenols-rich bee products to prevent and reduce the severity of COVID-19 symptoms.
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Affiliation(s)
- Meryem Bakour
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health, and Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdellah, Fez 30000, Morocco; (M.B.); (H.L.); (D.O.); (A.E.G.); (B.L.)
| | - Hassan Laaroussi
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health, and Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdellah, Fez 30000, Morocco; (M.B.); (H.L.); (D.O.); (A.E.G.); (B.L.)
| | - Driss Ousaaid
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health, and Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdellah, Fez 30000, Morocco; (M.B.); (H.L.); (D.O.); (A.E.G.); (B.L.)
| | - Asmae El Ghouizi
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health, and Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdellah, Fez 30000, Morocco; (M.B.); (H.L.); (D.O.); (A.E.G.); (B.L.)
| | - Imane Es-safi
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland;
| | - Hamza Mechchate
- Laboratory of Inorganic Chemistry, Department of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland;
- Correspondence:
| | - Badiaa Lyoussi
- Laboratory of Natural Substances, Pharmacology, Environment, Modeling, Health, and Quality of Life (SNAMOPEQ), Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdellah, Fez 30000, Morocco; (M.B.); (H.L.); (D.O.); (A.E.G.); (B.L.)
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15
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Liang JJ, Pitsillou E, Ververis K, Guallar V, Hung A, Karagiannis TC. Investigation of small molecule inhibitors of the SARS-CoV-2 papain-like protease by all-atom microsecond modelling, PELE Monte Carlo simulations, and in vitro activity inhibition. Chem Phys Lett 2022; 788:139294. [PMID: 34961797 PMCID: PMC8693950 DOI: 10.1016/j.cplett.2021.139294] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/03/2021] [Accepted: 12/15/2021] [Indexed: 12/16/2022]
Abstract
The SARS-CoV-2 papain-like (PLpro) protease is essential for viral replication. We investigated potential antiviral effects of hypericin relative to the well-known noncovalent PLpro inhibitor GRL-0617. Molecular dynamics and PELE Monte Carlo simulations highlight favourable binding of hypericin and GRL-0617 to the naphthalene binding pocket of PLpro. Although not potent as GRL-0617 (45.8 vs 1.6 µM for protease activity, respectively), in vitro fluorogenic enzymatic assays with hypericin show concentration-dependent inhibition of both PLpro protease and deubiquitinating activities. Given its use in supplementations and the FDA conditional approval of a synthetic version, further evaluation of hypericin as a potential SARS-CoV-2 antiviral is warranted.
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Affiliation(s)
- Julia J. Liang
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia,School of Science, STEM College, RMIT University, VIC 3001, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia,School of Science, STEM College, RMIT University, VIC 3001, Australia
| | - Katherine Ververis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Victor Guallar
- Barcelona Supercomputing Center, Jordi Girona 29, E-08034 Barcelona, Spain,ICREA, Passeig Lluís Companys 23, E-08010 Barcelona, Spain
| | - Andrew Hung
- School of Science, STEM College, RMIT University, VIC 3001, Australia
| | - Tom C. Karagiannis
- Epigenomic Medicine, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia,Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3052, Australia,Corresponding author at: Head Epigenomic Medicine Program, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
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16
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Kankariya RA, Chaudhari AB, Dandi ND. Inhibitory efficacy of 2, 4-diacetylphloroglucinol against SARS-COV-2 proteins: in silico study. Biologia (Bratisl) 2022; 77:815-828. [PMID: 35125499 PMCID: PMC8800849 DOI: 10.1007/s11756-021-00979-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Raksha A. Kankariya
- School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon, MS 425001 India
| | - Ambalal B. Chaudhari
- School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon, MS 425001 India
| | - Navin D. Dandi
- School of Life Sciences, Kavayitri Bahinabai Chaudhari North Maharashtra University, Jalgaon, MS 425001 India
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17
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Yu PC, Huang CH, Kuo CJ, Liang PH, Wang LHC, Pan MYC, Chang SY, Chao TL, Ieong SM, Fang JT, Huang HC, Juan HF. Drug Repurposing for the Identification of Compounds with Anti-SARS-CoV-2 Capability via Multiple Targets. Pharmaceutics 2022; 14:176. [PMID: 35057070 PMCID: PMC8779140 DOI: 10.3390/pharmaceutics14010176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/27/2021] [Accepted: 01/07/2022] [Indexed: 02/07/2023] Open
Abstract
Since 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been rapidly spreading worldwide, causing hundreds of millions of infections. Despite the development of vaccines, insufficient protection remains a concern. Therefore, the screening of drugs for the treatment of coronavirus disease 2019 (COVID-19) is reasonable and necessary. This study utilized bioinformatics for the selection of compounds approved by the U.S. Food and Drug Administration with therapeutic potential in this setting. In addition, the inhibitory effect of these compounds on the enzyme activity of transmembrane protease serine 2 (TMPRSS2), papain-like protease (PLpro), and 3C-like protease (3CLpro) was evaluated. Furthermore, the capability of compounds to attach to the spike-receptor-binding domain (RBD) was considered an important factor in the present assessment. Finally, the antiviral potency of compounds was validated using a plaque reduction assay. Our funnel strategy revealed that tamoxifen possesses an anti-SARS-CoV-2 property owing to its inhibitory performance in multiple assays. The proposed time-saving and feasible strategy may accelerate drug screening for COVID-19 and other diseases.
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Affiliation(s)
- Pei-Chen Yu
- Department of Life Science and Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan;
| | - Chen-Hao Huang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan;
| | - Chih-Jung Kuo
- Department of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan;
| | - Po-Huang Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan;
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Lily Hui-Ching Wang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30004, Taiwan; (L.H.-C.W.); (M.Y.-C.P.)
| | - Max Yu-Chen Pan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30004, Taiwan; (L.H.-C.W.); (M.Y.-C.P.)
| | - Sui-Yuan Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 10048, Taiwan; (S.-Y.C.); (T.-L.C.); (S.-M.I.); (J.-T.F.)
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei 10002, Taiwan
| | - Tai-Ling Chao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 10048, Taiwan; (S.-Y.C.); (T.-L.C.); (S.-M.I.); (J.-T.F.)
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Si-Man Ieong
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 10048, Taiwan; (S.-Y.C.); (T.-L.C.); (S.-M.I.); (J.-T.F.)
| | - Jun-Tung Fang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 10048, Taiwan; (S.-Y.C.); (T.-L.C.); (S.-M.I.); (J.-T.F.)
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang Ming Chaio Tung University, Taipei 11230, Taiwan
| | - Hsueh-Fen Juan
- Department of Life Science and Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan;
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan;
- Center for Computational and Systems Biology, National Taiwan University, Taipei 10617, Taiwan
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18
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Wu XM, Guan QY, Han YB, Wang XC, Zhuang WY, Tan RX. Regeneration of Phytochemicals by Structure‐Driven Organization of Microbial Biosynthetic Steps. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202114919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xue Ming Wu
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy Nanjing University of Chinese Medicine No. 138 Xianlin Avenue Nanjing Jiangsu 210023 China
| | - Qiu Yan Guan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy Nanjing University of Chinese Medicine No. 138 Xianlin Avenue Nanjing Jiangsu 210023 China
| | - Yun Bin Han
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy Nanjing University of Chinese Medicine No. 138 Xianlin Avenue Nanjing Jiangsu 210023 China
| | - Xin Cun Wang
- Insitute of Microbiology Chinese Academy of Sciences Beijing 100101 China
| | - Wen Ying Zhuang
- Insitute of Microbiology Chinese Academy of Sciences Beijing 100101 China
| | - Ren Xiang Tan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy School of Pharmacy Nanjing University of Chinese Medicine No. 138 Xianlin Avenue Nanjing Jiangsu 210023 China
- State Key Laboratory of Pharmaceutical Biotechnology Institute of Functional Biomolecules, School of Life Sciences Nanjing University No. 163 Xianlin Avenue Nanjing Jiangsu 210023 China
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19
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Wu XM, Guan QY, Han YB, Wang XC, Zhuang WY, Tan RX. Regeneration of Phytochemicals by Structure-Driven Organization of Microbial Biosynthetic Steps. Angew Chem Int Ed Engl 2021; 61:e202114919. [PMID: 34931419 DOI: 10.1002/anie.202114919] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Indexed: 11/05/2022]
Abstract
Medicinal phytochemicals, such as artemisinin and taxol, have impacted the world, and hypericin might do so if its availability issue could be addressed. Hypericin is the hallmark component of Saint John's wort (Hypericum perforatum L.), an approved depression alleviator documented in the US, European, and British pharmacopoeias with its additional effectiveness against diverse cancers and viruses. However, the academia-to-industry transition of hypericin remain hampered by its low in planta abundance, unfeasible bulk chemical synthesis, and unclear biosynthetic mechanism. Here, we present a strategy consisting of the hypericin-structure-centered modification and reorganization of microbial biosynthetic steps in the repurposed cells that have been tamed to enable the designed consecutive reactions to afford hypericin (43.1 mg L-1 ), without acquiring its biosynthetic knowledge in native plants. The study provides a synthetic biology route to hypericin and establishes a platform for biosustainable access to medicinal phytochemicals.
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Affiliation(s)
- Xue Ming Wu
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, No. 138 Xianlin Avenue, Nanjing, Jiangsu, 210023, China
| | - Qiu Yan Guan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, No. 138 Xianlin Avenue, Nanjing, Jiangsu, 210023, China
| | - Yun Bin Han
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, No. 138 Xianlin Avenue, Nanjing, Jiangsu, 210023, China
| | - Xin Cun Wang
- Insitute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wen Ying Zhuang
- Insitute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ren Xiang Tan
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, No. 138 Xianlin Avenue, Nanjing, Jiangsu, 210023, China.,State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, No. 163 Xianlin Avenue, Nanjing, Jiangsu, 210023, China
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Agrawal PK, Agrawal C, Blunden G. Naringenin as a Possible Candidate Against SARS-CoV-2 Infection and in the Pathogenesis of COVID-19. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211066723] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Naringenin, widely distributed in fruits and vegetables, is endowed with antiviral and other health beneficial activities, such as immune-stimulating and anti-inflammatory actions that could play a role in contributing, to some extent, to either preventing or alleviating coronavirus infection. Several computational studies have identified naringenin as one of the prominent flavonoids that can possibly inhibit internalization of the virus, virus-host interactions that trigger the cytokine storm, and replication of the virus. This review highlights the antiviral potential of naringenin in COVID-19 associated risk factors and its predicted therapeutic targets against SARS-CoV-2 infection.
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Affiliation(s)
- Pawan K. Agrawal
- Natural Product Inc., 7963 Anderson Park Lane, Westerville, OH 43081, USA
| | - Chandan Agrawal
- Natural Product Inc., 7963 Anderson Park Lane, Westerville, OH 43081, USA
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21
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Kaul R, Paul P, Kumar S, Büsselberg D, Dwivedi VD, Chaari A. Promising Antiviral Activities of Natural Flavonoids against SARS-CoV-2 Targets: Systematic Review. Int J Mol Sci 2021; 22:11069. [PMID: 34681727 PMCID: PMC8539743 DOI: 10.3390/ijms222011069] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 12/13/2022] Open
Abstract
The ongoing COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became a globally leading public health concern over the past two years. Despite the development and administration of multiple vaccines, the mutation of newer strains and challenges to universal immunity has shifted the focus to the lack of efficacious drugs for therapeutic intervention for the disease. As with SARS-CoV, MERS-CoV, and other non-respiratory viruses, flavonoids present themselves as a promising therapeutic intervention given their success in silico, in vitro, in vivo, and more recently, in clinical studies. This review focuses on data from in vitro studies analyzing the effects of flavonoids on various key SARS-CoV-2 targets and presents an analysis of the structure-activity relationships for the same. From 27 primary papers, over 69 flavonoids were investigated for their activities against various SARS-CoV-2 targets, ranging from the promising 3C-like protease (3CLpro) to the less explored nucleocapsid (N) protein; the most promising were quercetin and myricetin derivatives, baicalein, baicalin, EGCG, and tannic acid. We further review promising in silico studies featuring activities of flavonoids against SARS-CoV-2 and list ongoing clinical studies involving the therapeutic potential of flavonoid-rich extracts in combination with synthetic drugs or other polyphenols and suggest prospects for the future of flavonoids against SARS-CoV-2.
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Affiliation(s)
- Ridhima Kaul
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha 24144, Qatar; (R.K.); (P.P.)
| | - Pradipta Paul
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha 24144, Qatar; (R.K.); (P.P.)
| | - Sanjay Kumar
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida 201308, India; (S.K.); (V.D.D.)
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Dietrich Büsselberg
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha 24144, Qatar;
| | - Vivek Dhar Dwivedi
- Center for Bioinformatics, Computational and Systems Biology, Pathfinder Research and Training Foundation, Greater Noida 201308, India; (S.K.); (V.D.D.)
| | - Ali Chaari
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha 24144, Qatar; (R.K.); (P.P.)
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22
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Small molecule interactions with the SARS-CoV-2 main protease: In silico all-atom microsecond MD simulations, PELE Monte Carlo simulations, and determination of in vitro activity inhibition. J Mol Graph Model 2021; 110:108050. [PMID: 34655918 PMCID: PMC8504156 DOI: 10.1016/j.jmgm.2021.108050] [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] [Received: 06/18/2021] [Revised: 09/16/2021] [Accepted: 10/08/2021] [Indexed: 12/20/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the ongoing COVID-19 pandemic. With some notable exceptions, safe and effective vaccines, which are now being widely distributed globally, have largely begun to stabilise the situation. However, emerging variants of concern and vaccine hesitancy are apparent obstacles to eradication. Therefore, the need for the development of potent antivirals is still of importance. In this context, the SARS-CoV-2 main protease (Mpro) is a critical target and numerous clinical trials, predominantly in the private domain, are currently in progress. Here, our aim was to extend our previous studies, with hypericin and cyanidin-3-O-glucoside, as potential inhibitors of the SARS-CoV-2 Mpro. Firstly, we performed all-atom microsecond molecular dynamics simulations, which highlight the stability of the ligands in the Mpro active site over the duration of the trajectories. We also invoked PELE Monte Carlo simulations which indicate that both hypericin and cyanidin-3-O-glucoside preferentially interact with the Mpro active site and known allosteric sites. For further validation, we performed an in vitro enzymatic activity assay that demonstrated that hypericin and cyanidin-3-O-glucoside inhibit Mpro activity in a dose-dependent manner at biologically relevant (μM) concentrations. However, both ligands are much less potent than the well-known covalent antiviral GC376, which was used as a positive control in our experiments. Nevertheless, the biologically relevant activity of hypericin and cyanidin-3-O-glucoside is encouraging. In particular, a synthetic version of hypericin has FDA orphan drug designation, which could simplify potential clinical evaluation in the context of COVID-19.
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Ali AM, Kunugi H. Propolis, Bee Honey, and Their Components Protect against Coronavirus Disease 2019 (COVID-19): A Review of In Silico, In Vitro, and Clinical Studies. Molecules 2021; 26:1232. [PMID: 33669054 PMCID: PMC7956496 DOI: 10.3390/molecules26051232] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 12/14/2022] Open
Abstract
Despite the virulence and high fatality of coronavirus disease 2019 (COVID-19), no specific antiviral treatment exists until the current moment. Natural agents with immune-promoting potentials such as bee products are being explored as possible treatments. Bee honey and propolis are rich in bioactive compounds that express strong antimicrobial, bactericidal, antiviral, anti-inflammatory, immunomodulatory, and antioxidant activities. This review examined the literature for the anti-COVID-19 effects of bee honey and propolis, with the aim of optimizing the use of these handy products as prophylactic or adjuvant treatments for people infected with severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Molecular simulations show that flavonoids in propolis and honey (e.g., rutin, naringin, caffeic acid phenyl ester, luteolin, and artepillin C) may inhibit viral spike fusion in host cells, viral-host interactions that trigger the cytokine storm, and viral replication. Similar to the potent antiviral drug remdesivir, rutin, propolis ethanolic extract, and propolis liposomes inhibited non-structural proteins of SARS-CoV-2 in vitro, and these compounds along with naringin inhibited SARS-CoV-2 infection in Vero E6 cells. Propolis extracts delivered by nanocarriers exhibit better antiviral effects against SARS-CoV-2 than ethanolic extracts. In line, hospitalized COVID-19 patients receiving green Brazilian propolis or a combination of honey and Nigella sativa exhibited earlier viral clearance, symptom recovery, discharge from the hospital as well as less mortality than counterparts receiving standard care alone. Thus, the use of bee products as an adjuvant treatment for COVID-19 may produce beneficial effects. Implications for treatment outcomes and issues to be considered in future studies are discussed.
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Affiliation(s)
- Amira Mohammed Ali
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-0031, Japan;
- Department of Psychiatric Nursing and Mental Health, Faculty of Nursing, Alexandria University, Alexandria 21527, Egypt
| | - Hiroshi Kunugi
- Department of Mental Disorder Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-0031, Japan;
- Department of Psychiatry, Teikyo University School of Medicine, Tokyo 173-8605, Japan
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