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Sundararajan S, Karunakaran K, Muniyan R. Structure based virtual screening and discovery of novel inhibitors against FabD protein of Mycobacterium tuberculosis. J Biomol Struct Dyn 2024; 42:6280-6291. [PMID: 37424186 DOI: 10.1080/07391102.2023.2233622] [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: 03/03/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
The highly flexible nature of Mycobacterium tuberculosis (Mtb) can be owed to its tough cell wall and multiple gene interaction system which makes it resistant to frontline TB drugs. Mycolic acids are the key components of the unique cell wall that protects the organism from external threats. Proteins of the fatty acid synthesis pathway are evolutionarily conserved that enables cellular survival in harsh conditions and hence have become attractive targets. Malonyl Co-A Acyl carrier protein transacylase (FabD; MCAT, EC2.3.1.39) is an enzyme in the branching point of the unique and vast fatty acid synthase (FAS-I and FAS-II) systems of Mtb. In the present investigation, in-silico structure based drug discovery with the compounds from an open source library (NPASS) is used for target fishing and employed to understand the interaction with the target protein FabD. The potential hit compounds were filtered using exhaustive docking, considering the binding energy, key residue interaction and drug likeness property. Three compounds from the library namely NPC475074 (Hit 1), NPC260631 (Hit 2) and NPC313985 (Hit 3) with binding energies -14.45, -13.29 and -12.37 respectively were taken for molecular dynamic simulation. The results suggested that Hit 3 (NPC313985) has stable interaction with FabD protein. This article further elaborates the interaction of the identified novel compounds Hit 1 and Hit 3 along with the other known compound (Hit 2) against Mtb FabD protein. The hit compounds identified from this study could be further evaluated against mutated FabD protein and considered for in-vitro evaluation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sadhana Sundararajan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Keerthana Karunakaran
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Rajiniraja Muniyan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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2
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Galván-Ojeda HJ, Acosta-Elias J, Saavedra-Alanis VM, Espinosa-Tanguma R, Del Carmen Rodríguez-Aranda M, Hernández-Arteaga AC, Navarro-Contreras HR. Raman spectroscopy study of 7,8-dihydrofolate inhibition on the Wuhan strain SARS-CoV-2 binding to human ACE2 receptor. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 312:124050. [PMID: 38402702 DOI: 10.1016/j.saa.2024.124050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 02/27/2024]
Abstract
Emerging evidence suggests that elevated levels of folic acid in the bloodstream may confer protection against Wuhan-SARS-CoV-2 infection and mitigate its associated symptoms. Notably, two comprehensive studies of COVID-19 patients in Israel and UK uncovered a remarkable trend, wherein individuals with heightened folic acid levels exhibited only mild symptoms and necessitated no ventilatory support. In parallel, research has underscored the potential connection between decreased folic acid levels and the severity of Covid-19 among hospitalized patients. Yet, the underlying mechanisms governing this intriguing inhibition remain elusive. In a quest to elucidate these mechanisms, we conducted a molecular dynamics simulation approach followed by a Raman spectroscopy study to delve into the intricate interplay between the folic acid metabolite, 7,8-dihydrofolate (DHF), and the angiotensin-converting enzyme ACE2 receptor, coupled with its interaction with the receptor-binding domain (RBD) of the Wuhan strain of SARS-CoV-2. Through a meticulous exploration, we scrutinized the transformation of the ACE2 + RBD complex, allowing these reactants to form bonds. This was juxtaposed with a similar investigation where ACE2 was initially permitted to react with DHF, followed by the exposure of the ACE2 + DHF complex to RBD. We find that DHF, when bonded to ACE2, functions as a physical barrier, effectively inhibiting the binding of the Wuhan strain RBD. This physicochemical process offers a cogent explanation for the observed inhibition of host cell infection in subjects receiving supplementary folic acid doses, as epidemiologically substantiated in multiple studies. This study not only sheds light on a potential avenue for mitigating SARS-CoV-2 infection but also underscores the crucial role of folic acid metabolites in host-virus interactions. This research paves the way for novel therapeutic strategies in the battle against COVID-19 and reinforces the significance of investigating the molecular mechanisms underlying the protective effects of folic acid in the context of viral infections.
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Affiliation(s)
- Hiram Joazet Galván-Ojeda
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a, Sección, CP 78210 San Luis Potosí, SLP, Mexico
| | - Jesus Acosta-Elias
- Facultad de Ciencias, Universidad Autónoma de San Luís Potosí, Álvaro Obregón 64, San Luis Potosí, SLP 78000, Mexico
| | - Victor M Saavedra-Alanis
- Facultad de Medicina, Universidad Autónoma de San Luís Potosí, Álvaro Obregón 64, San Luis Potosí, SLP 78000, Mexico
| | - Ricardo Espinosa-Tanguma
- Facultad de Medicina, Universidad Autónoma de San Luís Potosí, Álvaro Obregón 64, San Luis Potosí, SLP 78000, Mexico
| | - Ma Del Carmen Rodríguez-Aranda
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a, Sección, CP 78210 San Luis Potosí, SLP, Mexico
| | - Aida Catalina Hernández-Arteaga
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a, Sección, CP 78210 San Luis Potosí, SLP, Mexico
| | - Hugo Ricardo Navarro-Contreras
- Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona #550, Col. Lomas 2a, Sección, CP 78210 San Luis Potosí, SLP, Mexico.
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3
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Nhau PT, Gamede M, Sibiya N. COVID-19-Induced Diabetes Mellitus: Comprehensive Cellular and Molecular Mechanistic Insights. PATHOPHYSIOLOGY 2024; 31:197-209. [PMID: 38651404 PMCID: PMC11036300 DOI: 10.3390/pathophysiology31020016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/06/2024] [Accepted: 04/07/2024] [Indexed: 04/25/2024] Open
Abstract
Despite evidence demonstrating the risks of developing diabetes mellitus because of SARS-CoV-2, there is, however, insufficient scientific data available to elucidate the relationship between diabetes mellitus and COVID-19. Research indicates that SARS-CoV-2 infection is associated with persistent damage to organ systems due to the systemic inflammatory response. Since COVID-19 is known to induce these conditions, further investigation is necessary to fully understand its long-term effects on human health. Consequently, it is essential to consider the effect of the COVID-19 pandemic when predicting the prevalence of diabetes mellitus in the future, especially since the incidence of diabetes mellitus was already on the rise before the pandemic. Additional research is required to fully comprehend the impact of SARS-CoV-2 infection on glucose tolerance and insulin sensitivity. Therefore, this article delves deeper into the current literature and links the perceived relationship between SARS-CoV-2 and diabetes. In addition, the article highlights the necessity for further research to fully grasp the mechanisms that SARS-CoV-2 utilises to induce new-onset diabetes. Where understanding and consensus are reached, therapeutic interventions to prevent the onset of diabetes could be proposed. Lastly, we propose advocating for the regular screening of diabetes and pre-diabetes, particularly for the high-risk population with a history of COVID-19 infection.
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Affiliation(s)
- Praise Tatenda Nhau
- Pharmacology Division, Faculty of Pharmacy, Rhodes University, Makhanda 6139, South Africa;
| | - Mlindeli Gamede
- Human Physiology Department, University of Pretoria, Pretoria 0028, South Africa;
| | - Ntethelelo Sibiya
- Pharmacology Division, Faculty of Pharmacy, Rhodes University, Makhanda 6139, South Africa;
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Kumar S, Dubey R, Mishra R, Gupta S, Dwivedi VD, Ray S, Jha NK, Verma D, Tsai LW, Dubey NK. Repurposing of SARS-CoV-2 compounds against Marburg Virus using MD simulation, mm/GBSA, PCA analysis, and free energy landscape. J Biomol Struct Dyn 2024:1-20. [PMID: 38450706 DOI: 10.1080/07391102.2024.2323701] [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: 08/16/2023] [Accepted: 01/22/2024] [Indexed: 03/08/2024]
Abstract
The significant mortality rate associated with Marburg virus infection made it the greatest hazard among infectious diseases. Drug repurposing using in silico methods has been crucial in identifying potential compounds that could prevent viral replication by targeting the virus's primary proteins. This study aimed at repurposing the drugs of SARS-CoV-2 for identifying potential candidates against the matrix protein VP40 of the Marburg virus. Virtual screening was performed where the control compound, Nilotinib, showed a binding score of -9.99 kcal/mol. Based on binding scores, hit compounds 9549298, 11960895, 44545852, 51039094, and 89670174 were selected that had a lower binding score than the control. Subsequent molecular dynamics (MD) simulation revealed that compound 9549298 consistently formed a hydrogen bond with the residue Gln290. This was observed both in molecular docking and MD simulation poses, indicating a strong and significant interaction with the protein. 11960895 had the most stable and consistent RMSD pattern exhibited in 100 ns simulation, while 9549298 had the most identical RMSD plot compared to the control molecule. MM/PBSA analysis showed that the binding free energy (ΔG) of 9549298 and 11960895 was lower than the control, with -30.84 and -38.86 kcal/mol, respectively. It was observed by the PCA (principal component analysis) and FEL (free energy landscape) analysis that compounds 9549298 and 11960895 had lesser conformational variation. Overall, this study proposed 9549298 and 11960895 as potential binders of VP40 MARV that can cause its inhibition, however it inherently lacks experimental validation. Furthermore, the study proposes in-vitro experiments as the next step to validate these computational findings, offering a practical approach to further explore these compounds' potential as antiviral agents.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanjay Kumar
- Biological and Bio-computational Lab, Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, UP, India
| | - Rajni Dubey
- Division of Cardiology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei City, Taiwan
| | - Richa Mishra
- Department of Computer Engineering, Parul University, Vadodara, Gujarat, India
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, India
| | - Vivek Dhar Dwivedi
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
- Bioinformatics Research Division, Greater Noida, UP, India
| | - Subhasree Ray
- Department of Life Science, School of Basic Science and Research, Sharda University, Greater Noida, India
| | - Niraj Kumar Jha
- School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, India
- Centre of Research Impact and Outreach, Chitkara University Institute of Engineering and Technology, Chitkara University, Punjab, India
| | - Devvret Verma
- Department of Biotechnology, Graphic Era (Deemed to Be University), Dehradun, Uttarakhand, India
| | - Lung-Wen Tsai
- Department of Medicine Research, Taipei Medical University Hospital, Taipei, Taiwan
- Department of Information Technology Office, Taipei Medical University Hospital, Taipei, Taiwan
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei, Taiwan
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Binoy A, Kothari M, Sahadevan R, Poddar S, Kar P, Sadhukhan S. Protein S-palmitoylation is markedly inhibited by 4″-alkyl ether lipophilic derivatives of EGCG, the major green tea polyphenol: In vitro and in silico studies. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184264. [PMID: 38104647 DOI: 10.1016/j.bbamem.2023.184264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/27/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
S-palmitoylation is a dynamic lipid-based protein post-translational modification facilitated by a family of protein acyltransferases (PATs) commonly known as DHHC-PATs or DHHCs. It is the only lipid modification that is reversible, and this very fact uniquely qualifies it for therapeutic interventions through the development of DHHC inhibitors. Herein, we report that 4″-alkyl ether lipophilic derivatives of EGCG can effectively inhibit protein S-palmitoylation in vitro. With the help of metabolic labeling followed by copper(I)-catalyzed azide-alkyne cycloaddition Click reaction, we demonstrate that 4″-C14 EGCG and 4″-C16 EGCG markedly inhibited S-palmitoylation in various mammalian cells including HEK 293T, HeLa, and MCF-7 using both in gel fluorescence as well as confocal microscopy. Further, these EGCG derivatives were able to attenuate the S-palmitoylation to the basal level in DHHC3-overexpressed cells, suggesting that they are plausibly targeting DHHCs. Confocal microscopy data qualitatively reflected spatial and temporal distribution of S-palmitoylated proteins in different sub-cellular compartments and the inhibitory effects of 4″-C14 EGCG and 4″-C16 EGCG were clearly observed in the native cellular environment. Our findings were further substantiated by in silico analysis which revealed promising binding affinity and interactions of 4″-C14 EGCG and 4″-C16 EGCG with key amino acid residues present in the hydrophobic cleft of the DHHC20 enzyme. We also demonstrated the successful inhibition of S-palmitoylation of GAPDH by 4″-C16 EGCG. Taken together, our in vitro and in silico data strongly suggest that 4″-C14 EGCG and 4″-C16 EGCG can act as potent inhibitors for S-palmitoylation and can be employed as a complementary tool to investigate S-palmitoylation.
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Affiliation(s)
- Anupama Binoy
- Department of Chemistry, Indian Institute of Technology Palakkad, Kerala 678623, India
| | - Manan Kothari
- Department of Chemistry, Indian Institute of Technology Palakkad, Kerala 678623, India
| | - Revathy Sahadevan
- Department of Chemistry, Indian Institute of Technology Palakkad, Kerala 678623, India
| | - Sayan Poddar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Madhya Pradesh 453552, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Madhya Pradesh 453552, India
| | - Sushabhan Sadhukhan
- Department of Chemistry, Indian Institute of Technology Palakkad, Kerala 678623, India; Physical & Chemical Biology Laboratory, Indian Institute of Technology Palakkad, Kerala 678623, India; Department of Biological Sciences & Engineering, Indian Institute of Technology Palakkad, Kerala 678623, India.
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6
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Al-Jamal H, Idriss S, Roufayel R, Abi Khattar Z, Fajloun Z, Sabatier JM. Treating COVID-19 with Medicinal Plants: Is It Even Conceivable? A Comprehensive Review. Viruses 2024; 16:320. [PMID: 38543686 PMCID: PMC10974729 DOI: 10.3390/v16030320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/15/2024] [Accepted: 02/18/2024] [Indexed: 05/23/2024] Open
Abstract
In 2020, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) challenged the world with a global outbreak that led to millions of deaths worldwide. Coronavirus disease 2019 (COVID-19) is the symptomatic manifestation of this virus, which can range from flu-like symptoms to utter clinical complications and even death. Since there was no clear medicine that could tackle this infection or lower its complications with minimal adverse effects on the patients' health, the world health organization (WHO) developed awareness programs to lower the infection rate and limit the fast spread of this virus. Although vaccines have been developed as preventative tools, people still prefer going back to traditional herbal medicine, which provides remarkable health benefits that can either prevent the viral infection or limit the progression of severe symptoms through different mechanistic pathways with relatively insignificant side effects. This comprehensive review provides scientific evidence elucidating the effect of 10 different plants against SARS-CoV-2, paving the way for further studies to reconsider plant-based extracts, rich in bioactive compounds, into more advanced clinical assessments in order to identify their impact on patients suffering from COVID-19.
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Affiliation(s)
- Hadi Al-Jamal
- Faculty of Public Health 3, Lebanese University, Tripoli 1100, Lebanon;
| | - Sara Idriss
- Laboratory of Applied Biotechnology (LBA3B), Azm Center for Research in Biotechnology and Its Applications, EDST, Lebanese University, Tripoli 1300, Lebanon;
| | - Rabih Roufayel
- College of Engineering and Technology, American University of the Middle East, Egaila 54200, Kuwait;
| | - Ziad Abi Khattar
- Faculty of Medicine and Medical Sciences, University of Balamand, Kalhat, Tripoli P.O. Box 100, Lebanon;
| | - Ziad Fajloun
- Laboratory of Applied Biotechnology (LBA3B), Azm Center for Research in Biotechnology and Its Applications, EDST, Lebanese University, Tripoli 1300, Lebanon;
- Department of Biology, Faculty of Sciences 3, Campus Michel Slayman Ras Maska, Lebanese University, Tripoli 1352, Lebanon
| | - Jean-Marc Sabatier
- INP, Inst Neurophysiopathol, Aix-Marseille Université, CNRS, 13385 Marseille, France
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7
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Karunakaran K, Muniyan R. Identification of allosteric inhibitor against AKT1 through structure-based virtual screening. Mol Divers 2023; 27:2803-2822. [PMID: 36522517 DOI: 10.1007/s11030-022-10582-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
AKT (serine/threonine protein kinase) is a potential therapeutic target for many types of cancer as it plays a vital role in cancer progression. Many AKT inhibitors are already in practice under single and combinatorial therapy. However, most of these inhibitors are orthosteric / pan-AKT that are non-selective and non-specific to AKT kinase and their isoforms. Hence, researchers are searching for novel allosteric inhibitors that bind in the interface between pH and kinase domain. In this study, we performed structure-based virtual screening from the afroDB (a diverse natural compounds library) to find the potential inhibitor targeting the AKT1. These compounds were filtered through Lipinski, ADMET properties, combined with a molecular docking approach to obtain the 8 best compounds. Then we performed molecular dynamics simulation for apoprotein, AKT1 with 8 complexes, and AKT1 with the positive control (Miransertib). Molecular docking and simulation analysis revealed that Bianthracene III (hit 1), 10-acetonyl Knipholonecyclooxanthrone (hit 2), Abyssinoflavanone VII (hit 5) and 8-c-p-hydroxybenzyldiosmetin (hit 6) had a better binding affinity, stability, and compactness than the reference compound. Notably, hit 1, hit 2 and hit 5 had molecular features required for allosteric inhibition.
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Affiliation(s)
- Keerthana Karunakaran
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Rajiniraja Muniyan
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India.
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8
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Srivastava S, Sharma S, Deep S, Khare SK. Screening of Multitarget-Directed Natural Compounds as Drug Candidates for Alzheimer's Disease Using In Silico Techniques: Their Extraction and In Vitro Validation. ACS OMEGA 2023; 8:38118-38129. [PMID: 37867692 PMCID: PMC10586450 DOI: 10.1021/acsomega.3c04261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/18/2023] [Indexed: 10/24/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder that impairs neurocognitive function. Acetylcholinesterase (AChE) and β-site APP cleaving enzyme 1 (BACE1) are the two main proteins implicated in AD. Indeed, the major available commercial drugs (donepezil, rivastigmine, and galantamine) against Alzheimer's are AChE inhibitors. However, none of these drugs are known to reverse or reduce the pathophysiological condition of the disease since there are multiple contributing factors to AD. Therefore, there is a need to develop a multitarget-directed ligand approach for its treatment. In the present study, plant bioactive compounds were screened for their AChE and BACE1 inhibition potential by conducting molecular docking studies. Considering their docking score and pharmacokinetic properties, limonin, peimisine, serratanine B, and withanolide A were selected as the lead compounds. Molecular dynamics simulations of these protein-ligand complexes confirmed the conformational and energetically stabilized enzyme-inhibitor complexes. The inhibition potential of the lead compounds was validated by in vitro enzyme assay. Withanolide A inhibited AChE (IC50 value of 107 μM) and showed mixed-type inhibition. At this concentration, it inhibited BACE1 activity by 57.10% and was stated as most effective. Both the compounds, as well as their crude extracts, were found to have no cytotoxic effect on the SH-SY5Y cell line.
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Affiliation(s)
- Sukriti Srivastava
- Enzyme
and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shilpa Sharma
- Biophysical
Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shashank Deep
- Biophysical
Chemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Sunil Kumar Khare
- Enzyme
and Microbial Biochemistry Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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Storozhuk M, Lee S, Lee JI, Park J. Green Tea Consumption and the COVID-19 Omicron Pandemic Era: Pharmacology and Epidemiology. Life (Basel) 2023; 13:life13030852. [PMID: 36984007 PMCID: PMC10054848 DOI: 10.3390/life13030852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
In spite of the development of numerous vaccines for the prevention of COVID-19 and the approval of several drugs for its treatment, there is still a great need for effective and inexpensive therapies against this disease. Previously, we showed that green tea and tea catechins interfere with coronavirus replication as well as coronavirus 3CL protease activity, and also showed lower COVID-19 morbidity and mortality in countries with higher green tea consumption. However, it is not clear whether green tea is still effective against the newer SARS-CoV-2 variants including omicron. It is also not known whether higher green tea consumption continues to contribute to lower COVID-19 morbidity and mortality now that vaccination rates in many countries are high. Here, we attempted to update the information regarding green tea in relation to COVID-19. Using pharmacological and ecological approaches, we found that EGCG as well as green tea inhibit the activity of the omicron variant 3CL protease efficiently, and there continues to be pronounced differences in COVID-19 morbidity and mortality between groups of countries with high and low green tea consumption as of December 6, 2022. These results collectively suggest that green tea continues to be effective against COVID-19 despite the new omicron variants and increased vaccination.
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Affiliation(s)
- Maksim Storozhuk
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, 01024 Kyiv, Ukraine
| | - Siyun Lee
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Jin I Lee
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Junsoo Park
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
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10
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Verma AK, Sharma S, Jayaraj A, Deep S. In silico study of interaction of (ZnO) 12 nanocluster to glucose oxidase-FAD in absence and presence of glucose. J Biomol Struct Dyn 2023; 41:15234-15242. [PMID: 36914234 DOI: 10.1080/07391102.2023.2188431] [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: 02/17/2022] [Accepted: 02/26/2023] [Indexed: 03/14/2023]
Abstract
Diabetes mellitus is one of the foremost global concerns, as it has impacted millions of lives. Therefore, there is an urgent need to develop a technology for continuous glucose monitoring in vivo. In the current study, we employed computational methods such as docking, MD simulations, and MM/GBSA, to obtain molecular insights into the interaction between (ZnO)12 nanocluster and glucose oxidase (GOx) that cannot be obtained through experiments alone. For this, theoretical modeling of the 3D cage-like (ZnO)12 nanocluster in ground state configuration was performed. Further docking of (ZnO)12 nanocluster with GOx molecule was carried out to find the nano-bio-interaction of (ZnO)12-GOx complex. To understand the whole interaction and dynamics of (ZnO)12-GOx-FAD-with and without glucose, we performed MD simulation and MM/GBSA analysis of (ZnO)12-GOx-FAD complex and glucose-(ZnO)12-GOx-FAD complex separately. The interaction was found to be stable, and the binding energy of (ZnO)12 to GOx-FAD increases in the presence of glucose by 6 kcal mol-1. This may be helpful in nano probing of the interaction of GOx with glucose. It can help in making a device like fluorescence resonance energy transfer (FRET) based nano-biosensor to monitor the glucose level in pre and post diabetic patient.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Awadhesh Kumar Verma
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Delhi, India
| | - Shilpa Sharma
- Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Abhilash Jayaraj
- Department of Chemistry, Indian Institute of Technology, Delhi, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, India
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11
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Gandhi Y, Mishra SK, Rawat H, Grewal J, Kumar R, Shakya SK, Jain VK, Babu G, Singh A, Singh R, Acharya R, Kumar V. Phytomedicines explored under in vitro and in silico studies against coronavirus: An opportunity to develop traditional medicines. SOUTH AFRICAN JOURNAL OF BOTANY : OFFICIAL JOURNAL OF THE SOUTH AFRICAN ASSOCIATION OF BOTANISTS = SUID-AFRIKAANSE TYDSKRIF VIR PLANTKUNDE : AMPTELIKE TYDSKRIF VAN DIE SUID-AFRIKAANSE GENOOTSKAP VAN PLANTKUNDIGES 2022; 151:451-483. [PMID: 35530267 PMCID: PMC9057940 DOI: 10.1016/j.sajb.2022.04.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 04/07/2022] [Accepted: 04/29/2022] [Indexed: 05/21/2023]
Abstract
The widespread COVID-19 pandemic, caused by novel coronavirus SARS-CoV-2, has emanated as one of the most life-threatening transmissible diseases. Currently, the repurposed drugs such as remdesivir, azithromycine, chloroquine, and hydroxychloroquine are being employed in the management of COVID-19 but their adverse effects are a matter of concern. In this regard, alternative treatment options i.e., traditional medicine, medicinal plants, and their phytochemicals, which exhibit significant therapeutic efficacy and show a low toxicity profile, are being explored. The current review aims at unraveling the promising medicinal plants, phytochemicals, and traditional medicines against SARS-CoV-2 to discover phytomedicines for the management of COVID-19 on the basis of their potent antiviral activities against coronaviruses, as demonstrated in various biochemical and computational chemical biology studies. The review consists of integrative and updated information on the potential traditional medicines against COVID-19 and will facilitate researchers to develop traditional medicines for the management of COVID-19.
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Affiliation(s)
- Yashika Gandhi
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Sujeet K Mishra
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Hemant Rawat
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Jyotika Grewal
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Ravi Kumar
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Santosh K Shakya
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Vipin Kumar Jain
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - G Babu
- Department of Ayurveda, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
| | - Arjun Singh
- Central Council for Research in Ayurvedic Sciences, New Delhi, 110058, India
| | - Ravindra Singh
- Central Council for Research in Ayurvedic Sciences, New Delhi, 110058, India
| | - Rabinarayan Acharya
- Central Council for Research in Ayurvedic Sciences, New Delhi, 110058, India
| | - Vijay Kumar
- Department of Chemistry, Central Ayurveda Research Institute Jhansi, Uttar Pradesh, 284003, India
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12
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Shahanshah MFH, Anvitha D, Gupta V. In-silico screening to delineate novel antagonists to SARS-CoV-2 nucleocapsid protein. PHYSICS AND CHEMISTRY OF THE EARTH (2002) 2022; 127:103188. [PMID: 35757560 PMCID: PMC9212792 DOI: 10.1016/j.pce.2022.103188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 06/07/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Since its inception, SARS-CoV-2 has crossed all borders and continues rampaging around the globe, causing profound economic damage and heavy burden on the scientific community and the healthcare fraternity and facilities. With the emergence of new variants, the global pandemic has prolonged and raised concerns regarding the existing therapies. Most of the identified mutants have the potential to exacerbate the already existing crisis. In line with the urgent need for promising antivirals against the novel coronavirus, we conducted an in-silico drug docking study using SeeSAR and other bioinformatics tools and identified prospective molecules that target the nucleocapsid protein of SARS-CoV-2. The highly conserved N protein plays a crucial role in viral assembly and pathogenicity by interacting with the host ribosomal subunits and suppressing nonsense mediated decay (NMD) of viral mRNA by the host cell. In the current study, FDA approved drugs were docked into pockets created within the N protein including the crucial conserved residues and analyzed for their affinity. The docked compounds give us novel plausible models that can be inspected further and paves way for the development of potent therapeutics against SARS-CoV-2.
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Affiliation(s)
| | - D Anvitha
- Ram Lal Anand College, University of Delhi, New Delhi, India
| | - Vandana Gupta
- Ram Lal Anand College, University of Delhi, New Delhi, India
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13
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Calvo-Alvarez E, Dolci M, Perego F, Signorini L, Parapini S, D’Alessandro S, Denti L, Basilico N, Taramelli D, Ferrante P, Delbue S. Antiparasitic Drugs against SARS-CoV-2: A Comprehensive Literature Survey. Microorganisms 2022; 10:microorganisms10071284. [PMID: 35889004 PMCID: PMC9320270 DOI: 10.3390/microorganisms10071284] [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: 05/05/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 01/09/2023] Open
Abstract
More than two years have passed since the viral outbreak that led to the novel infectious respiratory disease COVID-19, caused by the SARS-CoV-2 coronavirus. Since then, the urgency for effective treatments resulted in unprecedented efforts to develop new vaccines and to accelerate the drug discovery pipeline, mainly through the repurposing of well-known compounds with broad antiviral effects. In particular, antiparasitic drugs historically used against human infections due to protozoa or helminth parasites have entered the main stage as a miracle cure in the fight against SARS-CoV-2. Despite having demonstrated promising anti-SARS-CoV-2 activities in vitro, conflicting results have made their translation into clinical practice more difficult than expected. Since many studies involving antiparasitic drugs are currently under investigation, the window of opportunity might be not closed yet. Here, we will review the (controversial) journey of these old antiparasitic drugs to combat the human infection caused by the novel coronavirus SARS-CoV-2.
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Affiliation(s)
- Estefanía Calvo-Alvarez
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
- Correspondence:
| | - Maria Dolci
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Federica Perego
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Lucia Signorini
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Silvia Parapini
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy;
| | - Sarah D’Alessandro
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy; (S.D.); (D.T.)
| | - Luca Denti
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Nicoletta Basilico
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Donatella Taramelli
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy; (S.D.); (D.T.)
| | - Pasquale Ferrante
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
| | - Serena Delbue
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy; (M.D.); (F.P.); (L.S.); (L.D.); (N.B.); (P.F.); (S.D.)
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14
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Agrawal PK, Agrawal C, Blunden G. Artemisia Extracts and Artemisinin-Based Antimalarials for COVID-19 Management: Could These Be Effective Antivirals for COVID-19 Treatment? Molecules 2022; 27:3828. [PMID: 35744958 PMCID: PMC9231170 DOI: 10.3390/molecules27123828] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/03/2022] [Accepted: 06/05/2022] [Indexed: 12/23/2022] Open
Abstract
As the world desperately searches for ways to treat the coronavirus disease 2019 (COVID-19) pandemic, a growing number of people are turning to herbal remedies. The Artemisia species, such as A. annua and A. afra, in particular, exhibit positive effects against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and COVID-19 related symptoms. A. annua is a source of artemisinin, which is active against malaria, and also exhibits potential for other diseases. This has increased interest in artemisinin's potential for drug repurposing. Artemisinin-based combination therapies, so-called ACTs, have already been recognized as first-line treatments against malaria. Artemisia extract, as well as ACTs, have demonstrated inhibition of SARS-CoV-2. Artemisinin and its derivatives have also shown anti-inflammatory effects, including inhibition of interleukin-6 (IL-6) that plays a key role in the development of severe COVID-19. There is now sufficient evidence in the literature to suggest the effectiveness of Artemisia, its constituents and/or artemisinin derivatives, to fight against the SARS-CoV-2 infection by inhibiting its invasion, and replication, as well as reducing oxidative stress and inflammation, and mitigating lung damage.
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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;
| | - Gerald Blunden
- School of Pharmacy and Biomedical Science, University of Portsmouth, Portsmouth PO1 2DT, UK;
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15
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L-amino-acids as immunity booster against COVID-19: DFT, molecular docking and MD simulations. J Mol Struct 2022; 1250:131924. [PMID: 34803185 PMCID: PMC8590830 DOI: 10.1016/j.molstruc.2021.131924] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 12/23/2022]
Abstract
There is great interest to explore the importance of different amino-acids on immunity of human. Immunity helps to protect us from the pathogenic infections. The amino-acids are being use to give energy and is also used as an important basic molecule for the making of cells, protecting cell and others. Still, a little information is known for their importance in the inhibition of main protease of SARS-CoV-2. As known, tens of billions of humans are infected due to the SARS-CoV-2 and about a million of deaths are reported due to it or COVID. As of now, no promising drug is available in the market to cure the patients from this infection. Even, the medicines beings used for the partial cure may have some side effects. Therefore, the focus is to explore the natural amino-acids against the Mpro of SARS-CoV-2 as using of amino-acids is not toxic to humans. In the present work, authors have studied the amino-acids using DFT calculations and then they were explored for their promising role in the inhibition of main protease of SARS-CoV-2 using molecular docking and molecular dynamics simulations. Out of the 20 amino-acids, arginine found to best against the main protease of SARS-CoV-2 using the molecular docking and the binding energy was -0.94 kcal/ mol. Further, molecular dynamics simulations for the main protease of SARS-CoV-2 with and without arginine was performed using the Amber and different thermodynamic parameters like ΔH and TΔS to get ΔG, comes out to be 2.74 kcal/mol. It is expected that arginine can boost the immunity.
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Kumari K, Kumar A, Singh P, Kaushik NK. In silico study of remdesivir with and without ionic liquids having different cations using DFT calculations and molecular docking. J INDIAN CHEM SOC 2022. [PMCID: PMC8720381 DOI: 10.1016/j.jics.2021.100328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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17
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Hong M, Cheng L, Liu Y, Wu Z, Zhang P, Zhang X. A Natural Plant Source-Tea Polyphenols, a Potential Drug for Improving Immunity and Combating Virus. Nutrients 2022; 14:nu14030550. [PMID: 35276917 PMCID: PMC8839699 DOI: 10.3390/nu14030550] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) is still in a global epidemic, which has profoundly affected people’s lives. Tea polyphenols (TP) has been reported to enhance the immunity of the body to COVID-19 and other viral infectious diseases. The inhibitory effect of TP on COVID-19 may be achieved through a series of mechanisms, including the inhibition of multiple viral targets, the blocking of cellular receptors, and the activation of transcription factors. Emerging evidence shows gastrointestinal tract is closely related to respiratory tract, therefore, the relationship between the state of the gut–lung axis microflora and immune homeostasis of the host needs further research. This article summarized that TP can improve the disorder of flora, reduce the occurrence of cytokine storm, improve immunity, and prevent COVID-19 infection. TP may be regarded as a potential and valuable source for the design of new antiviral drugs with high efficiency and low toxicity.
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Affiliation(s)
- Mengyu Hong
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China; (M.H.); (Y.L.); (Z.W.)
| | - Lu Cheng
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA;
| | - Yanan Liu
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China; (M.H.); (Y.L.); (Z.W.)
| | - Zufang Wu
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China; (M.H.); (Y.L.); (Z.W.)
| | - Peng Zhang
- Department of Student Affairs, Xinyang Normal University, Xinyang 464000, China
- Correspondence: (P.Z.); (X.Z.)
| | - Xin Zhang
- Department of Food Science and Engineering, Ningbo University, Ningbo 315211, China; (M.H.); (Y.L.); (Z.W.)
- Correspondence: (P.Z.); (X.Z.)
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18
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In Silico Evaluation of Binding of 2-Deoxy-D-Glucose with Mpro of nCoV to Combat COVID-19. Pharmaceutics 2022; 14:pharmaceutics14010135. [PMID: 35057031 PMCID: PMC8779518 DOI: 10.3390/pharmaceutics14010135] [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: 11/23/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 12/11/2022] Open
Abstract
COVID-19 has threatened the existence of humanity andthis infection occurs due to SARS-CoV-2 or novel coronavirus, was first reported in Wuhan, China. Therefore, there is a need to find a promising drug to cure the people suffering from the infection. The second wave of this viral infection was shaking the world in the first half of 2021. Drugs Controllers of India has allowed the emergency use of 2-deoxy-D-glucose (2DG) in 2021 for patients suffering from this viral infection. The potentiality of 2-deoxy-D-glucose to intervene in D-glucose metabolism exists and energy deprivation is an effective parameter to inhibit cancer cell development. Once 2DG arrives in the cells, it becomes phosphorylated to 2-deoxy-D-glucose-6-phosphate (2-DG6P), a charged molecule expressively captured inside the cells. On the other hand, 2DG lacks the ability to convert into fructose-6-phosphate, resulting in a hampering of the activity of both glucose-6-phosphate isomerase and hexokinase, and finally causing cell death. Hence, the potential and effectiveness of 2DG with the main protease (Mpro) of novel coronavirus (nCoV) should be investigated using the molecular docking and molecular dynamics (MD) simulations. The ability of 2DG to inhibit the Mpro of nCoV is compared with 2-deoxyglucose (2DAG), an acyclic molecule, and 2-deoxy-D-ribose (2DR). The binding energy of the molecules with the Mpro of nCoV is calculated using molecular docking and superimposed analysis data is obtained. The binding energy of 2DG, 2DR and 2DAG was −2.40, −2.22 and −2.88 kcal/mol respectively. Although the molecular docking does not provide reliable information, therefore, the binding affinity can be confirmed by molecular dynamics simulations. Various trajectories such as Rg, RMSD, RMSF, and hydrogen bonds are obtained from the molecular dynamics (MD) simulations. 2DG was found to be a better inhibitor than the 2DAG and 2DR based on the results obtained from the MD simulations at 300 K. Furthermore, temperature-dependent MD simulations of the Mpro of nCoV with promising 2DG was performed at 295, 310 and 315 K, and the effective binding with the Mpro of nCoV occurred at 295 K. With the use of DFT calculations, optimized geometry and localization of electron density of the frontier molecular orbitals were calculated.
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19
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Mukherjee A, Verma A, Bihani S, Burli A, Mantri K, Srivastava S. Proteomics advances towards developing SARS-CoV-2 therapeutics using in silico drug repurposing approaches. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 39:1-12. [PMID: 34906319 PMCID: PMC8222565 DOI: 10.1016/j.ddtec.2021.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/21/2021] [Accepted: 06/11/2021] [Indexed: 12/12/2022]
Abstract
Standing amidst the COVID-19 pandemic, we have faced major medical and economic crisis in recent times which remains to be an unresolved issue till date. Although the scientific community has made significant progress towards diagnosis and understanding the disease; however, effective therapeutics are still lacking. Several omics-based studies, especially proteomics and interactomics, have contributed significantly in terms of identifying biomarker panels that can potentially be used for the disease prognosis. This has also paved the way to identify the targets for drug repurposing as a therapeutic alternative. US Food and Drug Administration (FDA) has set in motion more than 500 drug development programs on an emergency basis, most of them are focusing on repurposed drugs. Remdesivir is one such success of a robust and quick drug repurposing approach. The advancements in omics-based technologies has allowed to explore altered host proteins, which were earlier restricted to only SARS-CoV-2 protein signatures. In this article, we have reviewed major contributions of proteomics and interactomics techniques towards identifying therapeutic targets for COVID-19. Furthermore, in-silico molecular docking approaches to streamline potential drug candidates are also discussed.
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Affiliation(s)
- Amrita Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ayushi Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Surbhi Bihani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ananya Burli
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Krishi Mantri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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20
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Bimonte S, Forte CA, Cuomo M, Esposito G, Cascella M, Cuomo A. An Overview on the Potential Roles of EGCG in the Treatment of COVID-19 Infection. Drug Des Devel Ther 2021; 15:4447-4454. [PMID: 34737551 PMCID: PMC8560077 DOI: 10.2147/dddt.s314666] [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: 05/24/2021] [Accepted: 08/05/2021] [Indexed: 01/18/2023] Open
Abstract
Coronavirus disease-19 (COVID-19) pandemic is currently ongoing worldwide and causes a lot of deaths in many countries. Although different vaccines for the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection have been developed and are now available, there are no effective antiviral drugs to treat the disease, except for Remdesivir authorized by the US FDA to counteract the emergency. Thus, it can be useful to find alternative therapies based on the employment of natural compounds, with antiviral features, to circumvent SARS-CoV-2 infection. Pre-clinical studies highlighted the antiviral activities of epigallocatechin-3-gallate (EGCG), a catechin primarily found in green tea, against various viruses, including SARS-CoV-2. In this review, we summarize this experimental evidence and highlight the potential use of EGCG as an alternative therapeutic choice for the treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Sabrina Bimonte
- Division of Anesthesia and Pain Medicine, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Cira Antonietta Forte
- Division of Anesthesia and Pain Medicine, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Massimiliano Cuomo
- S.C. Project Management e Formazione, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Gennaro Esposito
- Division of Anesthesia and Pain Medicine, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Marco Cascella
- Division of Anesthesia and Pain Medicine, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Arturo Cuomo
- Division of Anesthesia and Pain Medicine, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
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21
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Barazorda-Ccahuana HL, Nedyalkova M, Mas F, Madurga S. Unveiling the Effect of Low pH on the SARS-CoV-2 Main Protease by Molecular Dynamics Simulations. Polymers (Basel) 2021; 13:3823. [PMID: 34771379 PMCID: PMC8587287 DOI: 10.3390/polym13213823] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 12/19/2022] Open
Abstract
(1) Background: Main Protease (Mpro) is an attractive therapeutic target that acts in the replication and transcription of the SARS-CoV-2 coronavirus. Mpro is rich in residues exposed to protonation/deprotonation changes which could affect its enzymatic function. This work aimed to explore the effect of the protonation/deprotonation states of Mpro at different pHs using computational techniques. (2) Methods: The different distribution charges were obtained in all the evaluated pHs by the Semi-Grand Canonical Monte Carlo (SGCMC) method. A set of Molecular Dynamics (MD) simulations was performed to consider the different protonation/deprotonation during 250 ns, verifying the structural stability of Mpro at different pHs. (3) Results: The present findings demonstrate that active site residues and residues that allow Mpro dimerisation was not affected by pH changes. However, Mpro substrate-binding residues were altered at low pHs, allowing the increased pocket volume. Additionally, the results of the solvent distribution around Sγ, Hγ, Nδ1 and Hδ1 atoms of the catalytic residues Cys145 and His41 showed a low and high-water affinity at acidic pH, respectively. It which could be crucial in the catalytic mechanism of SARS-CoV-2 Mpro at low pHs. Moreover, we analysed the docking interactions of PF-00835231 from Pfizer in the preclinical phase, which shows excellent affinity with the Mpro at different pHs. (4) Conclusion: Overall, these findings indicate that SARS-CoV-2 Mpro is highly stable at acidic pH conditions, and this inhibitor could have a desirable function at this condition.
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Affiliation(s)
- Haruna Luz Barazorda-Ccahuana
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08028 Barcelona, Spain;
- Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
| | - Miroslava Nedyalkova
- Department of Inorganic Chemistry, University of Sofia “St. Kl. Okhridski”, 1164 Sofia, Bulgaria;
| | - Francesc Mas
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08028 Barcelona, Spain;
| | - Sergio Madurga
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08028 Barcelona, Spain;
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22
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Zhang Z, Zhang X, Bi K, He Y, Yan W, Yang CS, Zhang J. Potential protective mechanisms of green tea polyphenol EGCG against COVID-19. Trends Food Sci Technol 2021; 114:11-24. [PMID: 34054222 PMCID: PMC8146271 DOI: 10.1016/j.tifs.2021.05.023] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/07/2021] [Accepted: 05/15/2021] [Indexed: 02/08/2023]
Abstract
Background The world is in the midst of the COVID-19 pandemic. In this comprehensive review, we discuss the potential protective effects of (−)-epigallocatechin-3-gallate (EGCG), a major constituent of green tea, against COVID-19. Scope and approach Information from literature of clinical symptoms and molecular pathology of COVID-19 as well as relevant publications in which EGCG shows potential protective activities against COVID-19 is integrated and evaluated. Key findings and conclusions EGCG, via activating Nrf2, can suppress ACE2 (a cellular receptor for SARS-CoV-2) and TMPRSS2, which mediate cell entry of the virus. Through inhibition of SARS-CoV-2 main protease, EGCG may inhibit viral reproduction. EGCG via its broad antioxidant activity may protect against SARS-CoV-2 evoked mitochondrial ROS (which promote SARS-CoV-2 replication) and against ROS burst inflicted by neutrophil extracellular traps. By suppressing ER-resident GRP78 activity and expression, EGCG can potentially inhibit SARS-CoV-2 life cycle. EGCG also shows protective effects against 1) cytokine storm-associated acute lung injury/acute respiratory distress syndrome, 2) thrombosis via suppressing tissue factors and activating platelets, 3) sepsis by inactivating redox-sensitive HMGB1, and 4) lung fibrosis through augmenting Nrf2 and suppressing NF-κB. These activities remain to be further substantiated in animals and humans. The possible concerted actions of EGCG suggest the importance of further studies on the prevention and treatment of COVID-19 in humans. These results also call for epidemiological studies on potential preventive effects of green tea drinking on COVID-19.
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Affiliation(s)
- Zhichao Zhang
- Department of Musculoskeletal Tumor, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Xiangchun Zhang
- Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China
| | - Keyi Bi
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science, Anhui Agricultural University, Hefei, 230036, China
| | - Yufeng He
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science, Anhui Agricultural University, Hefei, 230036, China
| | - Wangjun Yan
- Department of Musculoskeletal Tumor, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Chung S Yang
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854-8020, USA
| | - Jinsong Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science, Anhui Agricultural University, Hefei, 230036, China
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23
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Saggam A, Limgaokar K, Borse S, Chavan-Gautam P, Dixit S, Tillu G, Patwardhan B. Withania somnifera (L.) Dunal: Opportunity for Clinical Repurposing in COVID-19 Management. Front Pharmacol 2021; 12:623795. [PMID: 34012390 PMCID: PMC8126694 DOI: 10.3389/fphar.2021.623795] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/30/2021] [Indexed: 12/13/2022] Open
Abstract
As the COVID-19 pandemic is progressing, the therapeutic gaps in conventional management have highlighted the need for the integration of traditional knowledge systems with modern medicine. Ayurvedic medicines, especially Ashwagandha (Withania somnifera (L.) Dunal, WS), may be beneficial in the management of COVID-19. WS is a widely prescribed Ayurvedic botanical known as an immunomodulatory, antiviral, anti-inflammatory, and adaptogenic agent. The chemical profile and pharmacological activities of WS have been extensively reported. Several clinical studies have reported its safety for use in humans. This review presents a research synthesis of in silico, in vitro, in vivo, and clinical studies on Withania somnifera (L.) Dunal (WS) and discusses its potential for prophylaxis and management of COVID-19. We have collated the data from studies on WS that focused on viral infections (HIV, HSV, H1N1 influenza, etc.) and noncommunicable diseases (hypertension, diabetes, cancer, etc.). The experimental literature indicates that WS has the potential for 1) maintaining immune homeostasis, 2) regulating inflammation, 3) suppressing pro-inflammatory cytokines, 4) organ protection (nervous system, heart, lung, liver, and kidney), and 5) anti-stress, antihypertensive, and antidiabetic activities. Using these trends, the review presents a triangulation of Ayurveda wisdom, pharmacological properties, and COVID-19 pathophysiology ranging from viral entry to end-stage acute respiratory distress syndrome (ARDS). The review proposes WS as a potential therapeutic adjuvant for various stages of COVID-19 management. WS may also have beneficial effects on comorbidities associated with the COVID-19. However, systematic studies are needed to realize the potential of WS for improving clinical outcome of patients with COVID-19.
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Affiliation(s)
- Akash Saggam
- AYUSH Center of Excellence, Center for Complementary and Integrative Health, Interdisciplinary School of Health Sciences, Savitribai Phule Pune University, Pune, India
| | - Kirti Limgaokar
- Division of Biochemistry, Department of Chemistry, Fergusson College (Autonomous), Pune, India
| | - Swapnil Borse
- AYUSH Center of Excellence, Center for Complementary and Integrative Health, Interdisciplinary School of Health Sciences, Savitribai Phule Pune University, Pune, India
| | - Preeti Chavan-Gautam
- AYUSH Center of Excellence, Center for Complementary and Integrative Health, Interdisciplinary School of Health Sciences, Savitribai Phule Pune University, Pune, India
| | | | - Girish Tillu
- AYUSH Center of Excellence, Center for Complementary and Integrative Health, Interdisciplinary School of Health Sciences, Savitribai Phule Pune University, Pune, India
| | - Bhushan Patwardhan
- AYUSH Center of Excellence, Center for Complementary and Integrative Health, Interdisciplinary School of Health Sciences, Savitribai Phule Pune University, Pune, India
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Park J, Park R, Jang M, Park YI. Therapeutic Potential of EGCG, a Green Tea Polyphenol, for Treatment of Coronavirus Diseases. Life (Basel) 2021; 11:197. [PMID: 33806274 PMCID: PMC8002208 DOI: 10.3390/life11030197] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
Abstract
Epigallocatechin gallate (EGCG) is a major catechin found in green tea, and there is mounting evidence that EGCG is potentially useful for the treatment of coronavirus diseases, including coronavirus disease 2019 (COVID-19). Coronaviruses encode polyproteins that are cleaved by 3CL protease (the main protease) for maturation. Therefore, 3CL protease is regarded as the main target of antivirals against coronaviruses. EGCG is a major constituent of brewed green tea, and several studies have reported that EGCG inhibits the enzymatic activity of the coronavirus 3CL protease. Moreover, EGCG has been reported to regulate other potential targets, such as RNA-dependent RNA polymerase and the viral spike protein. Finally, recent studies have demonstrated that EGCG treatment interferes with the replication of coronavirus. In addition, the bioavailability of EGCG and future research prospects are discussed.
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Affiliation(s)
- Junsoo Park
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Korea; (R.P.); (M.J.); (Y.-I.P.)
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Kshirsagar SG, Rao RV. Antiviral and Immunomodulation Effects of Artemisia. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:217. [PMID: 33673527 PMCID: PMC7997252 DOI: 10.3390/medicina57030217] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 12/18/2022]
Abstract
Background and Objectives: Artemisia is one of the most widely distributed genera of the family Astraceae with more than 500 diverse species growing mainly in the temperate zones of Europe, Asia and North America. The plant is used in Chinese and Ayurvedic systems of medicine for its antiviral, antifungal, antimicrobial, insecticidal, hepatoprotective and neuroprotective properties. Research based studies point to Artemisia's role in addressing an entire gamut of physiological imbalances through a unique combination of pharmacological actions. Terpenoids, flavonoids, coumarins, caffeoylquinic acids, sterols and acetylenes are some of the major phytochemicals of the genus. Notable among the phytochemicals is artemisinin and its derivatives (ARTs) that represent a new class of recommended drugs due to the emergence of bacteria and parasites that are resistant to quinoline drugs. This manuscript aims to systematically review recent studies that have investigated artemisinin and its derivatives not only for their potent antiviral actions but also their utility against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Materials andMethods: PubMed Central, Scopus and Google scholar databases of published articles were collected and abstracts were reviewed for relevance to the subject matter. Conclusions: The unprecedented impact that artemisinin had on public health and drug discovery research led the Nobel Committee to award the Nobel Prize in Physiology or Medicine in 2015 to the discoverers of artemisinin. Thus, it is clear that Artemisia's importance in indigenous medicinal systems and drug discovery systems holds great potential for further investigation into its biological activities, especially its role in viral infection and inflammation.
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Affiliation(s)
- Suhas G. Kshirsagar
- College of Ayurveda, Mount Madonna Institute, 445 Summit Road, Watsonville, CA 95076, USA
| | - Rammohan V. Rao
- California College of Ayurveda, 700 Zion Street, Nevada City, CA 95959, USA
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Anderson G, Carbone A, Mazzoccoli G. Tryptophan Metabolites and Aryl Hydrocarbon Receptor in Severe Acute Respiratory Syndrome, Coronavirus-2 (SARS-CoV-2) Pathophysiology. Int J Mol Sci 2021; 22:ijms22041597. [PMID: 33562472 PMCID: PMC7915649 DOI: 10.3390/ijms22041597] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
The metabolism of tryptophan is intimately associated with the differential regulation of diverse physiological processes, including in the regulation of responses to severe acute respiratory syndrome, coronavirus-2 (SARS-CoV-2) infection that underpins the COVID-19 pandemic. Two important products of tryptophan metabolism, viz kynurenine and interleukin (IL)4-inducible1 (IL41)-driven indole 3 pyruvate (I3P), activate the aryl hydrocarbon receptor (AhR), thereby altering the nature of immune responses to SARS-CoV-2 infection. AhR activation dysregulates the initial pro-inflammatory cytokines production driven by neutrophils, macrophages, and mast cells, whilst AhR activation suppresses the endogenous antiviral responses of natural killer cells and CD8+ T cells. Such immune responses become further dysregulated by the increased and prolonged pro-inflammatory cytokine suppression of pineal melatonin production coupled to increased gut dysbiosis and gut permeability. The suppression of pineal melatonin and gut microbiome-derived butyrate, coupled to an increase in circulating lipopolysaccharide (LPS) further dysregulates the immune response. The AhR mediates its effects via alterations in the regulation of mitochondrial function in immune cells. The increased risk of severe/fatal SARS-CoV-2 infection by high risk conditions, such as elderly age, obesity, and diabetes are mediated by these conditions having expression levels of melatonin, AhR, butyrate, and LPS that are closer to those driven by SARS-CoV-2 infection. This has a number of future research and treatment implications, including the utilization of melatonin and nutraceuticals that inhibit the AhR, including the polyphenols, epigallocatechin gallate (EGCG), and resveratrol.
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Affiliation(s)
- George Anderson
- CRC Scotland & London, Eccleston Square, London SW1V 1PX, UK
| | - Annalucia Carbone
- Department of Medical Sciences, Division of Internal Medicine and Chronobiology Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
| | - Gianluigi Mazzoccoli
- Department of Medical Sciences, Division of Internal Medicine and Chronobiology Laboratory, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo, Italy
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