1
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Yılmaz Çolak Ç. Bacterial Membrane Vesicles as a Novel Vaccine Platform against SARS-CoV-2. Curr Microbiol 2024; 81:317. [PMID: 39164527 DOI: 10.1007/s00284-024-03846-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 08/15/2024] [Indexed: 08/22/2024]
Abstract
Throughout history, infectious diseases have plagued humanity, with outbreaks occurring regularly worldwide. Not every outbreak affects people globally; however, in the case of Coronavirus Disease 2019 (COVID-19), caused by a novel coronavirus (SARS-CoV-2), it reached a pandemic level within a remarkably short period. Fortunately, advancements in medicine and biotechnology have facilitated swift responses to the disease, resulting in the development of therapeutics and vaccines. Nevertheless, the persistent spread of the virus and the emergence of new variants underscore the necessity for protective interventions, leading researchers to seek more effective vaccines. Despite the presence of various types of vaccines, including mRNA and inactivated vaccines against SARS-CoV-2, new platforms have been investigated since the pandemic, and research on bacterial membrane vesicles (BMVs) has demonstrated their potential as a novel COVID-19 vaccine platform. Researchers have explored different strategies for BMV-based COVID-19 vaccines, such as mixing the vesicles with antigenic components of the virus due to their adjuvant capacity or decorating the vesicles with the viral antigens to create adjuvanted delivery systems. These approaches have presented promising results in inducing robust immune responses, but obstacles such as reproducibility in obtaining and homogeneous characterization of BMVs remain in developing vesicle-based vaccines. Overall, the development of BMV-based vaccines represents a novel and promising strategy in the fight against COVID-19. Additional research and clinical trials are needed to further evaluate the potential of these vaccines to offer long-lasting protection against SARS-CoV-2 and its evolving variants.
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Affiliation(s)
- Çiğdem Yılmaz Çolak
- Life Sciences, Marmara Research Center, TUBITAK, Kocaeli, Türkiye.
- Molecular Biology and Genetics Department, Istanbul Technical University, Istanbul, Türkiye.
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2
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Lanrewaju AA, Enitan-Folami AM, Nyaga MM, Sabiu S, Swalaha FM. Metabolites profiling and cheminformatics bioprospection of selected medicinal plants against the main protease and RNA-dependent RNA polymerase of SARS-CoV-2. J Biomol Struct Dyn 2024; 42:6740-6760. [PMID: 37464870 DOI: 10.1080/07391102.2023.2236718] [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: 05/16/2023] [Accepted: 07/08/2023] [Indexed: 07/20/2023]
Abstract
Despite the existence of some vaccines, SARS-CoV-2 (S-2) infections persist for various reasons relating to vaccine reluctance, rapid mutation rate, and an absence of specific treatments targeted to the infection. Due to their availability, low cost and low toxicity, research into potentially repurposing phytometabolites as therapeutic alternatives has gained attention. Therefore, this study explored the antiviral potential of metabolites of some medicinal plants [Spondias mombin, Macaranga barteri and Dicerocaryum eriocarpum (Sesame plant)] identified using liquid chromatography-mass spectrometry (LCMS) as possible inhibitory agents against the S-2 main protease (S-2 MP) and RNA-dependent RNA polymerase (RP) using computational approaches. Molecular docking was used to identify the compounds with the best affinities for the selected therapeutics targets. Afterwards, compounds with poor physicochemical characteristics, pharmacokinetics, and drug-likeness were screened out. The top-ranked compounds were further subjected to a 120-ns molecular dynamics (MD) simulation. Only quercetin 3-O-rhamnoside (-48.77 kcal/mol) had higher binding free energy than the reference standard (zafirlukast) (-44.99 kcal/mol) against S-2 MP. Conversely, all the top-ranked compounds (ellagic acid hexoside, spiraeoside, apigenin-4'-glucoside and chrysoeriol 7-glucuronide) except gnetin L (-24.24 kcal/mol) had higher binding free energy (-55.19 kcal/mol, -52.75 kcal/mol, -47.22 kcal/mol and -43.35 kcal/mol) respectively, against S-2 RP relative to the reference standard (-34.79 kcal/mol). The MD simulations study further revealed that the investigated inhibitors are thermodynamically stable and form structurally compatible complexes that impede the regular operation of the respective S-2 therapeutic targets. Although, these S-2 therapeutic candidates are promising, further in vitro and in vivo evaluation is required and highly recommended.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adedayo Ayodeji Lanrewaju
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, Durban, South Africa
| | | | - Martin M Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, Durban, South Africa
| | - Feroz Mahomed Swalaha
- Department of Biotechnology and Food Science, Faculty of Applied Science, Durban University of Technology, Durban, South Africa
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3
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Pakrashy S, Chakraborty S, Manna S, Nanda Goswami J, Bhattacharya B, Emmerling F, Mandal J, Misra S, Maiti Choudhury S, Okla MK, Bose A, Maurya PK, Majhi A, Dolai M. Inhibition of Human Colorectal Cancer by a Natural Product 7-Acetylhorminone and Interactions with BSA/HSA: Multispectral Analysis and In Silico and In Vitro Studies. ACS APPLIED BIO MATERIALS 2024; 7:3414-3430. [PMID: 38687465 DOI: 10.1021/acsabm.4c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
We have semi-synthesized a natural product 7-acetylhorminone from crude extract of Premna obtusifolia (Indian headache tree), which is active against colorectal cancer after probation through computational screening methods as it passed through the set parameters of pharmacokinetics (most important nonblood-brain barrier permeant) and drug likeliness (e.g., Lipinski's, Ghose's, Veber's rule) which most other phytoconstituents failed to pass combined with docking with EGFR protein which is highly upregulated in the colorectal carcinoma cell. The structure of 7-acetylhorminone was confirmed by single crystal X-ray diffraction studies and 1H NMR, 13C NMR, and COSY studies. To validate the theoretical studies, first, in vitro experiments were carried out against human colorectal carcinoma cell lines (HCT116) which revealed the potent cytotoxic efficacy of 7-acetylhorminone and verified preliminary investigation. Second, the drugability of 7-acetylhorminone interaction with serum albumin proteins (HSA and BSA) is evaluated both theoretically and experimentally via steady-state fluorescence spectroscopic studies, circular dichroism, isothermal titration calorimetry, and molecular docking. In summary, this study reveals the applicability of 7-acetylhorminone as a potent drug candidate or as a combinatorial drug against colorectal cancer.
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Affiliation(s)
- Sourav Pakrashy
- Department of Chemistry, Prabhat Kumar College, Purba Medinipur 721404, W.B., India
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata 700 073, India
| | - Souvik Chakraborty
- Department of Physiology, Bhairab Ganguly College, 2, Feeder Rd., Beehive Garden, Belghoria, Kolkata, West Bengal 700056, India
| | - Sounik Manna
- Biochemistry, Molecular Endocrinology, and Reproductive Physiology Laboratory, Department of Human Physiology, Vidyasagar University, Midnapore, W.B. 721102, India
| | - Juli Nanda Goswami
- Department of Chemistry, Prabhat Kumar College, Purba Medinipur 721404, W.B., India
| | - Biswajit Bhattacharya
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Str. 11, 12489 Berlin, Germany
| | - Franziska Emmerling
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Str. 11, 12489 Berlin, Germany
| | - Jishu Mandal
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Sourav Misra
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata 700 073, India
| | - Sujata Maiti Choudhury
- Biochemistry, Molecular Endocrinology, and Reproductive Physiology Laboratory, Department of Human Physiology, Vidyasagar University, Midnapore, W.B. 721102, India
| | - Mohammad K Okla
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Adity Bose
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata 700 073, India
| | - Pawan Kumar Maurya
- Division of Non-Communicable Diseases, Centre for Ageing and Mental Health, Indian Council of Medical Research, Kolkata 700091, India
| | - Anjoy Majhi
- Department of Chemistry, Presidency University, 86/1 College Street, Kolkata 700 073, India
| | - Malay Dolai
- Department of Chemistry, Prabhat Kumar College, Purba Medinipur 721404, W.B., India
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El-Hddad SSA, Sobhy MH, El-Morsy A, Shoman NA, El-Adl K. Quinazolines and thiazolidine-2,4-dions as SARS-CoV-2 inhibitors: repurposing, in silico molecular docking and dynamics simulation. RSC Adv 2024; 14:13237-13250. [PMID: 38655479 PMCID: PMC11037030 DOI: 10.1039/d4ra02029d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 04/18/2024] [Indexed: 04/26/2024] Open
Abstract
This paper presents an extensive analysis of COVID-19 with a specific focus on VEGFR-2 inhibitors as potential treatments. The investigation includes an overview of computational methodologies employed in drug repurposing and highlights in silico research aimed at developing treatments for SARS-CoV-2. The study explores the possible effects of twenty-eight established VEGFR-2 inhibitors, which include amide and urea linkers, against SARS-CoV-2. Among these, nine inhibitors exhibit highly promising in silico outcomes (designated as 3-6, 11, 24, 26, 27, and sorafenib) and are subjected to extensive molecular dynamics (MD) simulations to evaluate the binding modes and affinities of these inhibitors to the SARS-CoV-2 Mpro across a 100 ns timeframe. Additionally, MD simulations are conducted to ascertain the binding free energy of the most compelling ligand-pocket complexes identified through docking studies. The findings provide valuable understanding regarding the dynamic and thermodynamic properties of the interactions between ligands and pockets, reinforcing the outcomes of the docking studies and presenting promising prospects for the creation of therapeutic treatments targeting COVID-19.
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Affiliation(s)
- Sanadelaslam S A El-Hddad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Omar Almukhtar University Al Bayda 991 Libya
| | - Mohamed H Sobhy
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development Cairo Egypt
| | - Ahmed El-Morsy
- Pharmaceutical Chemistry Department, College of Pharmacy, The Islamic University Najaf Iraq
| | - Nabil A Shoman
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Ahram Canadian University Giza Egypt
| | - Khaled El-Adl
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development Cairo Egypt
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University Cairo11884 Egypt
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Vijay A, Sreyas Adury VS, Mukherjee A. Targeting RdRp of SARS-CoV-2 with De Novo Molecule Generation. ACS APPLIED BIO MATERIALS 2024; 7:609-616. [PMID: 37566736 DOI: 10.1021/acsabm.3c00339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
Viruses are known for their extremely high mutation rates, allowing them to evade both the human immune system and many forms of standard medicine. Despite this, the RNA dependent RNA polymerase (RdRp) of the RNA viruses has been largely conserved, and any significant mutation of this protein is unlikely. The recent COVID-19 pandemic presents a need for therapeutics. We have designed a de novo drug design algorithm that generates strong binding ligands from scratch, based on only the structure of the target protein's receptor. In this paper, we applied our method to target SARS-CoV-2 RdRp and generated several de novo molecules. We then chose some drug molecules based on the structural similarity to some of our strongest binding de novo molecules. Subsequently, we showed, using rigorous all-atom explicit-water free energy calculations in near-microsecond time scales using state-of-the-art well-tempered metadynamics simulations, that some of our de novo generated ligands bind more strongly to RdRp than the recent FDA approved drug remdesivir in its active form, remdesivir triphosphate (RTP). We elucidated the binding mechanism for some of the top binders and compared it with RTP. We believe that this work will be useful both by presenting lead structures for RdRp inhibition and by delivering key insights into the residues of the protein potentially involved in the binding/unbinding of these small molecule drugs, leading to more targeted studies in the future.
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Affiliation(s)
- Amal Vijay
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
| | | | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
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Yu K, Liang P, Yu H, Liu H, Guo J, Yan X, Li Z, Li G, Wang Y, Wang C. Integrating Transcriptome and Chemical Analyses to Provide Insights into Biosynthesis of Terpenoids and Flavonoids in the Medicinal Industrial Crop Andrographis paniculate and Its Antiviral Medicinal Parts. Molecules 2024; 29:852. [PMID: 38398604 PMCID: PMC10893308 DOI: 10.3390/molecules29040852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Andrographis paniculata is a medicinal plant traditionally used to produce diterpene lactones and flavonoids, which possess various biological activities. Widely distributed in China, India, and other Southeast Asia countries, A. paniculata has become an important economic crop, significantly treating SARS-CoV-2, and is being cultivated on a large scale in southern China. The biosynthesis of active ingredients in A. paniculata are regulated and controlled by genes, but their specific roles are still not fully understood. To further explore the growth regulation factors and utilization of its medicinal parts of this industrial crop, chemical and transcriptome analyses were conducted on the roots, stems, and leaves of A. paniculata to identify the biosynthesis pathways and related candidate genes of the active ingredients. The chemical analysis revealed that the main components of A. paniculata were diterpene lactones and flavonoids, which displayed potential ability to treat SARS-CoV-2 through molecular docking. Moreover, the transcriptome sequencing annotated a total of 40,850 unigenes, including 7962 differentially expressed genes. Among these, 120 genes were involved in diterpene lactone biosynthesis and 60 genes were involved in flavonoid biosynthesis. The expression of diterpene lactone-related genes was the highest in leaves and the lowest in roots, consistent with our content determination results. It is speculated that these highly expressed genes in leaves may be involved in the biosynthesis pathway of diterpenes. Furthermore, two class Ⅰ terpene synthases in A. paniculata transcriptome were also annotated, providing reference for the downstream pathway of the diterpene lactone biosynthesis. With their excellent market value, our experiments will promote the study of the biosynthetic genes for active ingredients in A. paniculata and provide insights for subsequent in vitro biosynthesis.
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Affiliation(s)
- Kuo Yu
- School of Medicine, Foshan University, Foshan 528225, China; (K.Y.); (P.L.); (H.L.); (J.G.); (G.L.)
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; (H.Y.); (X.Y.); (Z.L.)
| | - Pengjie Liang
- School of Medicine, Foshan University, Foshan 528225, China; (K.Y.); (P.L.); (H.L.); (J.G.); (G.L.)
| | - Heshui Yu
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; (H.Y.); (X.Y.); (Z.L.)
| | - Hui Liu
- School of Medicine, Foshan University, Foshan 528225, China; (K.Y.); (P.L.); (H.L.); (J.G.); (G.L.)
| | - Jialiang Guo
- School of Medicine, Foshan University, Foshan 528225, China; (K.Y.); (P.L.); (H.L.); (J.G.); (G.L.)
| | - Xiaohui Yan
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; (H.Y.); (X.Y.); (Z.L.)
| | - Zheng Li
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; (H.Y.); (X.Y.); (Z.L.)
| | - Guoqiang Li
- School of Medicine, Foshan University, Foshan 528225, China; (K.Y.); (P.L.); (H.L.); (J.G.); (G.L.)
| | - Ying Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Chunhua Wang
- School of Medicine, Foshan University, Foshan 528225, China; (K.Y.); (P.L.); (H.L.); (J.G.); (G.L.)
- College of Pharmaceutical Engineering of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; (H.Y.); (X.Y.); (Z.L.)
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Khalifa HO, Al Ramahi YM. After the Hurricane: Anti-COVID-19 Drugs Development, Molecular Mechanisms of Action and Future Perspectives. Int J Mol Sci 2024; 25:739. [PMID: 38255813 PMCID: PMC10815681 DOI: 10.3390/ijms25020739] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a new coronavirus in the Coronaviridae family. The COVID-19 pandemic, caused by SARS-CoV-2, has undoubtedly been the largest crisis of the twenty-first century, resulting in over 6.8 million deaths and 686 million confirmed cases, creating a global public health issue. Hundreds of notable articles have been published since the onset of this pandemic to justify the cause of viral spread, viable preventive measures, and future therapeutic approaches. As a result, this review was developed to provide a summary of the current anti-COVID-19 drugs, as well as their timeline, molecular mode of action, and efficacy. It also sheds light on potential future treatment options. Several medications, notably hydroxychloroquine and lopinavir/ritonavir, were initially claimed to be effective in the treatment of SARS-CoV-2 but eventually demonstrated inadequate activity, and the Food and Drug Administration (FDA) withdrew hydroxychloroquine. Clinical trials and investigations, on the other hand, have demonstrated the efficacy of remdesivir, convalescent plasma, and monoclonal antibodies, 6-Thioguanine, hepatitis C protease inhibitors, and molnupiravir. Other therapeutics, including inhaled medicines, flavonoids, and aptamers, could pave the way for the creation of novel anti-COVID-19 therapies. As future pandemics are unavoidable, this article urges immediate action and extensive research efforts to develop potent specialized anti-COVID-19 medications.
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Affiliation(s)
- Hazim O. Khalifa
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 1555, United Arab Emirates;
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Yousef M. Al Ramahi
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 1555, United Arab Emirates;
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Zargari F, Mohammadi M, Nowroozi A, Morowvat MH, Nakhaei E, Rezagholi F. The Inhibitory Effects of the Herbals Secondary Metabolites (7α-acetoxyroyleanone, Curzerene, Incensole, Harmaline, and Cannabidiol) on COVID-19: A Molecular Docking Study. Recent Pat Biotechnol 2024; 18:316-331. [PMID: 38817009 DOI: 10.2174/0118722083246773231108045238] [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: 04/04/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 06/01/2024]
Abstract
BACKGROUND Since the COVID-19 outbreak in early 2020, researchers and studies are continuing to find drugs and/or vaccines against the disease. As shown before, medicinal plants can be very good sources against viruses because of their secondary compounds which may cure diseases and help in survival of patients. There is a growing trend in the filed patents in this field. AIMS In the present study, we test and suggest the inhibitory potential of five herbal based extracts including 7α-acetoxyroyleanone, Curzerene, Incensole, Harmaline, and Cannabidiol with antivirus activity on the models of the significant antiviral targets for COVID-19 like spike glycoprotein, Papain-like protease (PLpro), non-structural protein 15 (NSP15), RNA-dependent RNA polymerase and core protease by molecular docking study. METHODS The Salvia rythida root was extracted, dried, and pulverized by a milling machine. The aqueous phase and the dichloromethane phase of the root extractive were separated by two-phase extraction using a separatory funnel. The separation was performed using the column chromatography method. The model of the important antivirus drug target of COVID-19 was obtained from the Protein Data Bank (PDB) and modified. TO study the binding difference between the studied molecules, the docking study was performed. RESULTS These herbal compounds are extracted from Salvia rhytidea, Curcuma zeodaria, Frankincense, Peganum harmala, and Cannabis herbs, respectively. The binding energies of all compounds on COVID-19 main targets are located in the limited area of 2.22-5.30 kcal/mol. This range of binding energies can support our hypothesis for the presence of the inhibitory effects of the secondary metabolites of mentioned structures on COVID-19. Generally, among the investigated herbal structures, Cannabidiol and 7α- acetoxyroyleanone compounds with the highest binding energy have the most inhibitory potential. The least inhibitory effects are related to the Curzerene and Incensole structures by the lowest binding affinity. CONCLUSION The general arrangement of the basis of the potential barrier of binding energies is in the order below: Cannabidiol > 7α-acetoxyroyleanone > Harmaline> Incensole > Curzerene. Finally, the range of docking scores for investigated herbal compounds on the mentioned targets indicates that the probably inhibitory effects on these targets obey the following order: main protease> RNA-dependent RNA polymerase> PLpro> NSP15> spike glycoprotein.
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Affiliation(s)
- Farshid Zargari
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan (USB), P.O.Box 98135- 674, Zahedan, Iran
| | - Mehdi Mohammadi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Box 71468-64685, Shiraz, Iran
| | - Alireza Nowroozi
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan (USB), P.O.Box 98135- 674, Zahedan, Iran
| | - Mohammad Hossein Morowvat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Box 71468-64685, Shiraz, Iran
| | - Ebrahim Nakhaei
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan (USB), P.O.Box 98135- 674, Zahedan, Iran
| | - Fatemeh Rezagholi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Box 71468-64685, Shiraz, Iran
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Hsu CW, Yang WW, Hou CY, Feng IJ, Huang TY, Lee PL, Guo HR, Huang CY, Su SB. Patients with Hepatitis C Undergoing Direct-Acting Antiviral Treatment Have a Lower SARS-CoV-2 Infection Rate. Life (Basel) 2023; 13:2326. [PMID: 38137927 PMCID: PMC10745044 DOI: 10.3390/life13122326] [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: 09/08/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
This study retrospectively analyzed the medical records of 602 patients with first-time positive results for the HCV nucleic acid test between 1 May 2021 and 31 March 2023, exploring the association between DAA treatment and SARS-CoV-2 infection. The results showed that 9.8% of HCV patients were co-infected with SARS-CoV-2. Gender, age, vaccination status, and HCV genotype did not significantly affect SARS-CoV-2 infection. However, patients undergoing DAA treatment showed significantly lower rates of SARS-CoV-2 infection and mortality compared to those not undergoing DAA treatment. The analysis also compared patients undergoing different DAA treatments, with Epclusa and Maviret showing superior protection against SARS-CoV-2. Furthermore, this study explored the severity and mortality of SARS-CoV-2 infection in patients undergoing and having completed DAA treatment. It revealed that patients diagnosed with COVID-19 during DAA treatment experienced only mild symptoms, and none died, suggesting a potential protective effect of DAA treatment against severe outcomes of SARS-CoV-2 infection. The findings contribute to the understanding of the interplay between HCV, DAA treatment, and SARS-CoV-2 infection, highlighting the need for continued monitoring and healthcare measures for individuals with chronic conditions during the ongoing COVID-19 pandemic.
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Affiliation(s)
- Chin-Wen Hsu
- Department of Family Medicine, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - Wan-Wen Yang
- Department of Clinical Pathology, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - Chia-Yi Hou
- Department of Clinical Pathology, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - I-Jung Feng
- Institute of Precision Medicine, National Sun Yat-Sen University, Kaohsiung 804201, Taiwan
| | - Ting-Yi Huang
- Department of Hepato-Gastroenterology, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - Pei-Lun Lee
- Department of Hepato-Gastroenterology, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - How-Ran Guo
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 70428, Taiwan;
| | - Chien-Yuan Huang
- Division of Occupational Medicine, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
| | - Shih-Bin Su
- Division of Occupational Medicine, Chi-Mei Medical Center, Liouying, Tainan 736402, Taiwan
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Shi W, Li T, Li H, Ren J, Lv M, Wang Q, He Y, Yu Y, Liu L, Jin S, Chen H. Bioinformatics approach to identify the hub gene associated with COVID-19 and idiopathic pulmonary fibrosis. IET Syst Biol 2023; 17:336-351. [PMID: 37814484 PMCID: PMC10725713 DOI: 10.1049/syb2.12080] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 09/26/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) has developed into a global health crisis. Pulmonary fibrosis, as one of the complications of SARS-CoV-2 infection, deserves attention. As COVID-19 is a new clinical entity that is constantly evolving, and many aspects of disease are remain unknown. The datasets of COVID-19 and idiopathic pulmonary fibrosis were obtained from the Gene Expression Omnibus. The hub genes were screened out using the Random Forest (RF) algorithm depending on the severity of patients with COVID-19. A risk prediction model was developed to assess the prognosis of patients infected with SARS-CoV-2, which was evaluated by another dataset. Six genes (named NELL2, GPR183, S100A8, ALPL, CD177, and IL1R2) may be associated with the development of PF in patients with severe SARS-CoV-2 infection. S100A8 is thought to be an important target gene that is closely associated with COVID-19 and pulmonary fibrosis. Construction of a neural network model was successfully predicted the prognosis of patients with COVID-19. With the increasing availability of COVID-19 datasets, bioinformatic methods can provide possible predictive targets for the diagnosis, treatment, and prognosis of the disease and show intervention directions for the development of clinical drugs and vaccines.
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Affiliation(s)
- Wenchao Shi
- Department of RespirationThe Fourth Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Tinghui Li
- Department of RespirationHainan Cancer HospitalHaikouHainanChina
| | - Huiwen Li
- Department of RespirationThe Second Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Juan Ren
- Department of RespirationThe Second Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Meiyu Lv
- Department of RespirationThe Fourth Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Qi Wang
- Department of RespirationThe Second Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Yaowu He
- Department of RespirationThe Second Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Yao Yu
- Department of RespirationThe Second Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Lijie Liu
- Department of RespirationThe Fourth Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Shoude Jin
- Department of RespirationThe Fourth Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
| | - Hong Chen
- Department of RespirationThe Second Affiliated Hospital of Harbin Medical UniversityHarbin Medical UniversityHarbinHeilongjiangChina
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11
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Bag SS, Sinha S, Dutta S, Baishya HJ, Paul S. Targeting the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) with synthetic/designer unnatural nucleoside analogs: an in silico study. J Mol Model 2023; 29:366. [PMID: 37950101 DOI: 10.1007/s00894-023-05767-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023]
Abstract
CONTEXT Since the outbreak of COVID-19 in December 2019, it developed into a pandemic affecting all the countries and millions of people around the globe. Until now, there is no medicine available to contain the spread of the virus. As an aid to drug discovery, the molecular docking and molecular dynamic tools were applied extensively. In silico studies made it possible for rapid screening of potential molecules as possible inhibitors/drugs against the targeted proteins. As a continuation of our drug discovery research, we have carried out molecular docking studies of our 12 reported unnatural nucleosides and 14 designer Avigan analogs with SARS-CoV-2, RNA-dependent RNA polymerase (RdRp), which we want to report herein. The same calculation was also carried out, taking 11 known/under trail/commercial nucleoside drug molecules for a comparison of the binding interactions in the catalytic site of RdRp. The docking results and binding efficiencies of our reported nucleosides and designer nucleosidic were compared with the binding energy of commercially available drugs such as remdesevir and favipiravir. Furthermore, we evaluated the protein-drug binding efficiency and stability of the best docked molecules by molecular dynamic studies (MD). From our study, we have found that few of our proposed drugs show promising binding efficiency at the catalytic pocket of SARS-CoV-2 RdRp and can be a promising RdRp inhibitor drug candidate. Hence, this study will be of importance to make progress toward developing successful nucleoside-based drugs and conduct the antiviral test in the wet lab to understand their efficacy against COVID-19. METHOD All the docking studies were carried out with AutoDock 4.2, AutoDock Vina and Molegro Virtual Docker. Following the docking studies, the MD simulations were carried out following the standard protocol with the GROMACS ver. 2019.6. by applying the CHARMM36 all-atom biomolecular force field. The drug-protein interaction was studied using the Biovia Discovery Studio suite, Ligplot software, and Protein-Ligand Interaction Profiler (PLIP).
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Affiliation(s)
- Subhendu Sekhar Bag
- Chemical Biology/Genomics Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India, 781039.
- Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati, Assam, India, 781039.
| | - Sayantan Sinha
- Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati, Assam, India, 781039
| | - Soumya Dutta
- Chemical Biology/Genomics Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India, 781039
| | - Hirak Jyoti Baishya
- Chemical Biology/Genomics Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India, 781039
| | - Suravi Paul
- Chemical Biology/Genomics Laboratory, Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India, 781039
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12
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El-Hddad S, Sobhy M, Ayoub A, El-Adl K. In silico molecular docking, dynamics simulation and repurposing of some VEGFR-2 inhibitors based on the SARS-CoV-2-main-protease inhibitor N3. J Biomol Struct Dyn 2023; 41:9267-9281. [PMID: 36399002 DOI: 10.1080/07391102.2022.2148000] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/09/2022] [Indexed: 11/21/2022]
Abstract
The global and rapid spread of the novel human coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has brought immediate urgency to the discovery of favorable targets for COVID-19 treatment. Here, we consider drug reuse as an attractive methodology for drug discovery by reusing existing drugs to treat diseases other than their initial indications. Here, we review current information concerning the global health issue of COVID-19 including VEGFR-2 inhibitors. Besides, we describe computational approaches to be used in drug repurposing and highlight examples of in silico studies of drug development efforts against SARS-CoV-2. The present study suggests the potential anti-SARS-CoV-2 activities of 35 reported VEGFR-2 inhibitors containing the amide and urea linkers. Nineteen members revealed the best in silico results and hence, were subjected to further molecular dynamics (MD) simulation for their inhibitory activities against SARS-CoV-2 Mpro across 100 ns. Furthermore, MD simulations followed by calculations of the free energy of binding were also carried out for the most promising ligand-pocket complexes from docking studies to clarify some information on their dynamic and thermodynamic properties and approve the docking results. These results we obtained probably provided an excellent lead candidate for the development of therapeutic drugs against COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanadelaslam El-Hddad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Omar Almukhtar University, Al Bayda, Libya
| | - Mohamed Sobhy
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development, Cairo, Egypt
| | - Ahmed Ayoub
- HTuO Biosciences Inc., Vancouver, BC, Canada
| | - Khaled El-Adl
- Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development, Cairo, Egypt
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
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13
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Metwally NH, Elgemeie GH, Fahmy FG. Synthesis and Biological Evaluation of Benzothiazolyl-pyridine Hybrids as New Antiviral Agents against H5N1 Bird Flu and SARS-COV-2 Viruses. ACS OMEGA 2023; 8:36636-36654. [PMID: 37841136 PMCID: PMC10568744 DOI: 10.1021/acsomega.3c01987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/18/2023] [Indexed: 10/17/2023]
Abstract
A novel series of benzothiazolyl-pyridine hybrids 8a-h and 14a-e were produced from the reaction of enamine derivative 4 with each of the arylcyanoacetamides 5a-h and cyanoacetohydrazides 9a-e. The new products were characterized by spectral techniques (IR, 1H NMR, 13C NMR, and MS). Biological evaluation of 8a-h and 14a-e in vitro against H5N1 and SARS-COV-2 viruses showed that several compounds had significant activity. Compounds 8f-h, which contain fluorine atoms, have better activity against H5N1 and anti-SARS-CoV-2 viruses than the other compounds included in this study. Compound 8h has a trifluoromethyl group at position-3 of the phenyl ring and exhibits a high activity against H5N1 virus with 93 and 60% inhibition at concentrations of 0.5 and 0.25 μmol/μL, respectively, among the tested compounds, and it also showed anti-SARS-CoV-2 virus with a half-maximum inhibition rate of 3.669 μM, among the remaining compounds. The mechanism of action of 8f-h, which is expected to be repurposed against COVID-19, was investigated. The results showed that the compounds have virucidal effects at different stages of the three mechanisms of action. Furthermore, compounds 8f-h were found to possess CoV-3CL protease inhibitory activities with IC50 values of 544.6, 868.2, and 240.6 μg/mL, respectively, compared to IC50 = 129.8 μg/mL of the standard drug lopinavir. Interestingly, compounds 8f-h also showed high inhibitory activity against the H5N1 virus as well as the SARS-CoV-2 virus. Moreover, compounds 8f-h fit admirably into the active site of the SARS-CoV-2 main protease (PDB ID: 6LU7) using the molecular docking Moe software 2015.10.
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Affiliation(s)
| | | | - Fatma Gomaa Fahmy
- Chemistry
Department, Faculty of Science, Cairo University, Cairo 12613, Egypt
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14
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Istifli ES, Okumus N, Sarikurkcu C, Kuhn ER, Netz PA, Tepe AS. Comparative docking and molecular dynamics studies of molnupiravir (EIDD-2801): implications for novel mechanisms of action on influenza and SARS-CoV-2 protein targets. J Biomol Struct Dyn 2023:1-13. [PMID: 37811782 DOI: 10.1080/07391102.2023.2267696] [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: 05/11/2023] [Accepted: 07/27/2023] [Indexed: 10/10/2023]
Abstract
Molnupiravir (EIDD-2801) (MLN) is an oral antiviral drug for COVID-19 treatment, being integrated into viral RNA through RNA-dependent RNA polymerase (RdRp). Upon ingestion, MLN is transformed into two active metabolites: β-d-N4-hydroxycytidine (NHC) (EIDD-1931) in the host plasma, and EIDD-1931-triphosphate (MTP) within the host cells. However, recent studies provide increasing evidence of MLN's interactions with off-target proteins beyond the viral genome, suggesting that the complete mechanisms of action of MLN remain unclear. The aim of this study was therefore to investigate the molecular interactions of MLN in the form of NHC and MTP with the non-RNA structural components of avian influenza (hemagglutinin, neuraminidase) and SARS-CoV-2 (spike glycoprotein, Mpro, and RdRp) viruses and to elucidate whether these two metabolites possess the ability to form stable complexes with these major viral components. Molecular docking of NHC and MTP was performed using AutoDock 4.2.6 and the obtained protein-drug complexes were submitted to 200-ns molecular dynamics simulations in triplicate with subsequent free energy calculations using GROMACS. Docking scores, molecular dynamics and MM/GBSA results showed that MTP was tightly bound within the active site of SARS-CoV-2 RdRp and remained highly stable throughout the 200-ns simulations. Besides, it was also shown that NHC and MTP formed moderately-to-highly stable molecular complexes with off-target receptors hemagglutinin, neuraminidase and Mpro, but rather weak interactions with spike glycoprotein. Our computational findings suggest that NHC and MTP may directly inhibit these receptors, and propose that additional studies on the off-target effects of MLN, i.e. real-time protein binding assays, should be performed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Erman Salih Istifli
- Faculty of Science and Literature, Department of Biology, Cukurova University, Adana, Turkey
| | - Nurullah Okumus
- Faculty of Medicine, Department of Pediatrics, Afyonkarahisar Health Sciences University, Afyonkarahisar, Turkey
| | - Cengiz Sarikurkcu
- Faculty of Pharmacy, Department of Analytical Chemistry, Afyonkarahisar Health Sciences University, Afyonkarahisar, Turkey
| | - Eduardo Ramires Kuhn
- Theoretical Chemistry Group, Institute of Chemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Paulo A Netz
- Theoretical Chemistry Group, Institute of Chemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Arzuhan Sihoglu Tepe
- Department of Pharmacy Services, Kilis 7 Aralik University, Vocational High School of Health Services, Kilis, Turkey
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15
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Mittal RK, Purohit P, Sankaranarayanan M, Muzaffar-Ur-Rehman M, Taramelli D, Signorini L, Dolci M, Basilico N. In-vitro antiviral activity and in-silico targeted study of quinoline-3-carboxylate derivatives against SARS-Cov-2 isolate. Mol Divers 2023:10.1007/s11030-023-10703-w. [PMID: 37480422 DOI: 10.1007/s11030-023-10703-w] [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: 06/07/2023] [Accepted: 07/16/2023] [Indexed: 07/24/2023]
Abstract
In recent years, the viral outbreak named COVID-19 showed that infectious diseases have a huge impact on both global health and the financial and economic sectors. The lack of efficacious antiviral drugs worsened the health problem. Based on our previous experience, we investigated in vitro and in silico a series of quinoline-3-carboxylate derivatives against a SARS-CoV-2 isolate. In the present study, the in-vitro antiviral activity of a series of quinoline-3-carboxylate compounds and the in silico target-based molecular dynamics (MD) and metabolic studies are reported. The compounds' activity against SARS-CoV-2 was evaluated using plaque assay and RT-qPCR. Moreover, from the docking scores, it appears that the most active compounds (1j and 1o) exhibit stronger binding affinity to the primary viral protease (NSP5) and the exoribonuclease domain of non structural protein 14 (NSP14). Additionally, the in-silico metabolic analysis of 1j and 1o defines CYP2C9 and CYP3A4 as the major P450 enzymes involved in their metabolism.
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Affiliation(s)
- Ravi Kumar Mittal
- National Institute of Pharmaceutical Education and Research, S A S Nagar Mohali, Punjab, 160062, India
- Galgotias College of Pharmacy, Greater Noida, UttarPradesh, India
| | - Priyank Purohit
- School of Pharmacy, Graphic Era Hill University, Dehradun, Uttarakhand, 248002, India.
| | - Murugesan Sankaranarayanan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, BITS Pilani, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Mohammed Muzaffar-Ur-Rehman
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, BITS Pilani, Pilani Campus, Pilani, Rajasthan, 333031, India
| | - Donatella Taramelli
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Pascal Street 36, 20133, Milan, Italy
| | - Lucia Signorini
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Pascal Street 36, 20133, Milan, Italy
| | - Maria Dolci
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Pascal Street 36, 20133, Milan, Italy
| | - Nicoletta Basilico
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Pascal Street 36, 20133, Milan, Italy
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16
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Kumbhar N, Nimal S, Patil D, Kaiser VF, Haupt J, Gacche RN. Repurposing of neprilysin inhibitor 'sacubitrilat' as an anti-cancer drug by modulating epigenetic and apoptotic regulators. Sci Rep 2023; 13:9952. [PMID: 37336927 DOI: 10.1038/s41598-023-36872-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023] Open
Abstract
Modifications in the epigenetic landscape have been considered a hallmark of cancer. Histone deacetylation is one of the crucial epigenetic modulations associated with the aggressive progression of various cancer subtypes. Herein, we have repurposed the neprilysin inhibitor sacubitrilat as a potent anticancer agent using in-silico protein-ligand interaction profiler (PLIP) analysis, molecular docking, and in vitro studies. The screening of PLIP profiles between vorinostat/panobinostat and HDACs/LTA4H followed by molecular docking resulted in five (Sacubitrilat, B65, BDS, BIR, and NPV) FDA-approved, experimental and investigational drugs. Sacubitrilat has demonstrated promising anticancer activity against colorectal cancer (SW-480) and triple-negative breast cancer (MDA-MB-231) cells, with IC50 values of 14.07 μg/mL and 23.02 μg/mL, respectively. FACS analysis revealed that sacubitrilat arrests the cell cycle at the G0/G1 phase and induces apoptotic-mediated cell death in SW-480 cells. In addition, sacubitrilat inhibited HDAC isoforms at the transcriptomic level by 0.7-0.9 fold and at the proteomic level by 0.5-0.6 fold as compared to the control. Sacubitrilat increased the protein expression of tumor-suppressor (p53) and pro-apoptotic makers (Bax and Bid) by 0.2-2.5 fold while decreasing the expression of anti-apoptotic Bcl2 and Nrf2 proteins by 0.2-0.5 fold with respect to control. The observed cleaved PARP product indicates that sacubitrilat induces apoptotic-mediated cell death. This study may pave the way to identify the anticancer potential of sacubitrilat and can be explored in human clinical trials.
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Affiliation(s)
- Navanath Kumbhar
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra (MS), 411007, India
| | - Snehal Nimal
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra (MS), 411007, India
| | - Deeksha Patil
- Department of Microbiology, Savitribai Phule Pune University, Pune, Maharashtra (MS), 411007, India
| | | | | | - Rajesh N Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra (MS), 411007, India.
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17
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Shehzadi K, Saba A, Yu M, Liang J. Structure-Based Drug Design of RdRp Inhibitors against SARS-CoV-2. Top Curr Chem (Cham) 2023; 381:22. [PMID: 37318607 DOI: 10.1007/s41061-023-00432-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide pandemic since 2019, spreading rapidly and posing a significant threat to human health and life. With over 6 billion confirmed cases of the virus, the need for effective therapeutic drugs has become more urgent than ever before. RNA-dependent RNA polymerase (RdRp) is crucial in viral replication and transcription, catalysing viral RNA synthesis and serving as a promising therapeutic target for developing antiviral drugs. In this article, we explore the inhibition of RdRp as a potential treatment for viral diseases, analysing the structural information of RdRp in virus proliferation and summarizing the reported inhibitors' pharmacophore features and structure-activity relationship profiles. We hope that the information provided by this review will aid in structure-based drug design and aid in the global fight against SARS-CoV-2 infection.
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Affiliation(s)
- Kiran Shehzadi
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Afsheen Saba
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China
| | - Mingjia Yu
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
| | - Jianhua Liang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 10081, China.
- Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing, 314019, China.
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18
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Abduljalil JM, Elghareib AM, Samir A, Ezat AA, Elfiky AA. How helpful were molecular dynamics simulations in shaping our understanding of SARS-CoV-2 spike protein dynamics? Int J Biol Macromol 2023:125153. [PMID: 37268078 DOI: 10.1016/j.ijbiomac.2023.125153] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/22/2023] [Accepted: 05/27/2023] [Indexed: 06/04/2023]
Abstract
The SARS-CoV-2 spike protein (S) represents an important viral component that is required for successful viral infection in humans owing to its essential role in recognition of and entry to host cells. The spike is also an appealing target for drug designers who develop vaccines and antivirals. This article is important as it summarizes how molecular simulations successfully shaped our understanding of spike conformational behavior and its role in viral infection. MD simulations found that the higher affinity of SARS-CoV-2-S to ACE2 is linked to its unique residues that add extra electrostatic and van der Waal interactions in comparison to the SARS-CoV S. This illustrates the spread potential of the pandemic SARS-CoV-2 relative to the epidemic SARS-CoV. Different mutations at the S-ACE2 interface, which is believed to increase the transmission of the new variants, affected the behavior and binding interactions in different simulations. The contributions of glycans to the opening of S were revealed via simulations. The immune evasion of S was linked to the spatial distribution of glycans. This help the virus to escape the immune system recognition. This article is important as it summarizes how molecular simulations successfully shaped our understanding of spike conformational behavior and its role in viral infection. This will pave the way to us preparing for the next pandemic as the computational tools are tailored to help fight new challenges.
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Affiliation(s)
- Jameel M Abduljalil
- Department of Biological Sciences, Faculty of Applied Sciences, Thamar University, Dhamar, Yemen; Department of Botany and Microbiology, College of Science, Cairo University, Giza, Egypt
| | - Ahmed M Elghareib
- Department of Biophysics, Faculty of Science, Cairo University, Giza, Egypt
| | - Ahmed Samir
- Department of Biophysics, Faculty of Science, Cairo University, Giza, Egypt
| | - Ahmed A Ezat
- Department of Biophysics, Faculty of Science, Cairo University, Giza, Egypt
| | - Abdo A Elfiky
- Department of Biophysics, Faculty of Science, Cairo University, Giza, Egypt.
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19
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Mohamed AR, Mostafa A, El Hassab MA, Hedeab GM, Mahmoud SH, George RF, Georgey HH, Abdel Gawad NM, El-Ashrey MK. Insights into targeting SARS-CoV-2: design, synthesis, in silico studies and antiviral evaluation of new dimethylxanthine derivatives. RSC Med Chem 2023; 14:899-920. [PMID: 37252103 PMCID: PMC10211320 DOI: 10.1039/d3md00056g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/15/2023] [Indexed: 05/31/2023] Open
Abstract
Aiming to achieve efficient activity against severe acute respiratory syndrome coronavirus (SARS-CoV-2), the expansion of the structure- and ligand-based drug design approaches was adopted, which has been recently reported by our research group. Purine ring is a corner stone in the development of SARS-CoV-2 main protease (Mpro) inhibitors. The privileged purine scaffold was elaborated to achieve additional affinity based on hybridization and fragment-based approaches. Thus, the characteristic pharmacophoric features that are required for the inhibition of Mpro and RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 were utilized along with the crystal structure information of both targets. The designed pathways involved rationalized hybridization with large sulfonamide moieties and a carboxamide fragment for the synthesis of ten new dimethylxanthine derivatives. The synthesis was performed under diverse conditions to afford N-alkylated xanthine derivatives, and cyclization afforded tricyclic compounds. Molecular modeling simulations were used to confirm and gain insights into the binding interactions at both targets' active sites. The merit of designed compounds and the in silico studies resulted in the selection of three compounds that were evaluated in vitro to estimate their antiviral activity against SARS-CoV-2 (compounds 5, 9a and 19 with IC50 values of 38.39, 8.86 and 16.01 μM, respectively). Furthermore, oral toxicity of the selected antiviral candidates was predicted, in addition to cytotoxicity investigations. Compound 9a showed IC50 values of 8.06 and 3.22 μM against Mpro and RdRp of SARS-CoV-2, respectively, in addition to promising molecular dynamics stability in both target active sites. The current findings encourage further specificity evaluations of the promising compounds for confirming their specific protein targeting.
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Affiliation(s)
- Abdalla R Mohamed
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Egyptian Russian University Badr City Cairo 11829 Egypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre Giza 12622 Egypt
| | - Mahmoud A El Hassab
- Medicinal Chemistry Department, Faculty of Pharmacy, King Salman International University Ras-Sedr South Sinai Egypt
| | - Gomaa M Hedeab
- Pharmacology Department and Health Research Unit, Medical College, Jouf University Kingdom of Saudi Arabia
- Pharmacology Department, Faculty of Medicine, Beni-Suef University Egypt
| | - Sara H Mahmoud
- Center of Scientific Excellence for Influenza Viruses, National Research Centre Giza 12622 Egypt
| | - Riham F George
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
| | - Hanan H Georgey
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy and Drug Technology, Egyptian Chinese University 11786 Cairo Egypt
| | - Nagwa M Abdel Gawad
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
| | - Mohamed K El-Ashrey
- Medicinal Chemistry Department, Faculty of Pharmacy, King Salman International University Ras-Sedr South Sinai Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
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20
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Moon Y. Gut distress and intervention via communications of SARS-CoV-2 with mucosal exposome. Front Public Health 2023; 11:1098774. [PMID: 37139365 PMCID: PMC10150023 DOI: 10.3389/fpubh.2023.1098774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/27/2023] [Indexed: 05/05/2023] Open
Abstract
Acute coronavirus disease 2019 (COVID-19) has been associated with prevalent gastrointestinal distress, characterized by fecal shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA or persistent antigen presence in the gut. Using a meta-analysis, the present review addressed gastrointestinal symptoms, such as nausea, vomiting, abdominal pain, and diarrhea. Despite limited data on the gut-lung axis, viral transmission to the gut and its influence on gut mucosa and microbial community were found to be associated by means of various biochemical mechanisms. Notably, the prolonged presence of viral antigens and disrupted mucosal immunity may increase gut microbial and inflammatory risks, leading to acute pathological outcomes or post-acute COVID-19 symptoms. Patients with COVID-19 exhibit lower bacterial diversity and a higher relative abundance of opportunistic pathogens in their gut microbiota than healthy controls. Considering the dysbiotic changes during infection, remodeling or supplementation with beneficial microbial communities may counteract adverse outcomes in the gut and other organs in patients with COVID-19. Moreover, nutritional status, such as vitamin D deficiency, has been associated with disease severity in patients with COVID-19 via the regulation of the gut microbial community and host immunity. The nutritional and microbiological interventions improve the gut exposome including the host immunity, gut microbiota, and nutritional status, contributing to defense against acute or post-acute COVID-19 in the gut-lung axis.
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Affiliation(s)
- Yuseok Moon
- Laboratory of Mucosal Exposome and Biomodulation, Department of Integrative Biomedical Sciences, Pusan National University, Yangsan-si, Republic of Korea
- Biomedical Research Institute, Pusan National University, Busan, Republic of Korea
- Graduate Program of Genomic Data Sciences, Pusan National University, Yangsan-si, Republic of Korea
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21
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Rodrigues-da-Silva RN, Conte FP, da Silva G, Carneiro-Alencar AL, Gomes PR, Kuriyama SN, Neto AAF, Lima-Junior JC. Identification of B-Cell Linear Epitopes in the Nucleocapsid (N) Protein B-Cell Linear Epitopes Conserved among the Main SARS-CoV-2 Variants. Viruses 2023; 15:v15040923. [PMID: 37112903 PMCID: PMC10145278 DOI: 10.3390/v15040923] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 04/29/2023] Open
Abstract
The Nucleocapsid (N) protein is highlighted as the main target for COVID-19 diagnosis by antigen detection due to its abundance in circulation early during infection. However, the effects of the described mutations in the N protein epitopes and the efficacy of antigen testing across SARS-CoV-2 variants remain controversial and poorly understood. Here, we used immunoinformatics to identify five epitopes in the SARS-CoV-2 N protein (N(34-48), N(89-104), N(185-197), N(277-287), and N(378-390)) and validate their reactivity against samples from COVID-19 convalescent patients. All identified epitopes are fully conserved in the main SARS-CoV-2 variants and highly conserved with SARS-CoV. Moreover, the epitopes N(185-197) and N(277-287) are highly conserved with MERS-CoV, while the epitopes N(34-48), N(89-104), N(277-287), and N(378-390) are lowly conserved with common cold coronaviruses (229E, NL63, OC43, HKU1). These data are in accordance with the observed conservation of amino acids recognized by the antibodies 7R98, 7N0R, and 7CR5, which are conserved in the SARS-CoV-2 variants, SARS-CoV and MERS-CoV but lowly conserved in common cold coronaviruses. Therefore, we support the antigen tests as a scalable solution for the population-level diagnosis of SARS-CoV-2, but we highlight the need to verify the cross-reactivity of these tests against the common cold coronaviruses.
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Affiliation(s)
- Rodrigo N Rodrigues-da-Silva
- Laboratory of Immunological Technology, Institute of Technology in Immunobiologicals, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
| | - Fernando P Conte
- Eukaryotic Pilot Laboratory, Institute of Technology in Immunobiologicals, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
| | - Gustavo da Silva
- Laboratory of Immunological Technology, Institute of Technology in Immunobiologicals, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
| | - Ana L Carneiro-Alencar
- Laboratory of Immunological Technology, Institute of Technology in Immunobiologicals, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
- Laboratory of Immunoparasitology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
| | - Paula R Gomes
- Getulio Vargas State Hospital, Rio de Janeiro 21070-061, Brazil
| | - Sergio N Kuriyama
- SENAI Innovation Institute for Green Chemistry, Rio de Janeiro 20271-030, Brazil
| | - Antonio A F Neto
- SENAI Innovation Institute for Green Chemistry, Rio de Janeiro 20271-030, Brazil
| | - Josué C Lima-Junior
- Laboratory of Immunoparasitology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
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22
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Pozzi C, Vanet A, Francesconi V, Tagliazucchi L, Tassone G, Venturelli A, Spyrakis F, Mazzorana M, Costi MP, Tonelli M. Antitarget, Anti-SARS-CoV-2 Leads, Drugs, and the Drug Discovery-Genetics Alliance Perspective. J Med Chem 2023; 66:3664-3702. [PMID: 36857133 PMCID: PMC10005815 DOI: 10.1021/acs.jmedchem.2c01229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
The most advanced antiviral molecules addressing major SARS-CoV-2 targets (Main protease, Spike protein, and RNA polymerase), compared with proteins of other human pathogenic coronaviruses, may have a short-lasting clinical efficacy. Accumulating knowledge on the mechanisms underlying the target structural basis, its mutational progression, and the related biological significance to virus replication allows envisaging the development of better-targeted therapies in the context of COVID-19 epidemic and future coronavirus outbreaks. The identification of evolutionary patterns based solely on sequence information analysis for those targets can provide meaningful insights into the molecular basis of host-pathogen interactions and adaptation, leading to drug resistance phenomena. Herein, we will explore how the study of observed and predicted mutations may offer valuable suggestions for the application of the so-called "synthetic lethal" strategy to SARS-CoV-2 Main protease and Spike protein. The synergy between genetics evidence and drug discovery may prioritize the development of novel long-lasting antiviral agents.
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Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Anne Vanet
- Université Paris Cité,
CNRS, Institut Jacques Monod, F-75013 Paris,
France
| | - Valeria Francesconi
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
| | - Lorenzo Tagliazucchi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
- Doctorate School in Clinical and Experimental Medicine
(CEM), University of Modena and Reggio Emilia, Via Campi 287,
41125 Modena, Italy
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy,
University of Siena, via Aldo Moro 2, 53100 Siena,
Italy
| | - Alberto Venturelli
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology,
University of Turin, Via Giuria 9, 10125 Turin,
Italy
| | - Marco Mazzorana
- Diamond Light Source, Harwell Science and
Innovation Campus, Didcot, Oxfordshire OX11 0DE,
U.K.
| | - Maria P. Costi
- Department of Life Science, University of
Modena and Reggio Emilia, via Campi 103, 41125 Modena,
Italy
| | - Michele Tonelli
- Department of Pharmacy, University of
Genoa, viale Benedetto XV n.3, 16132 Genoa, Italy
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23
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Bekheit MS, Panda SS, Girgis AS. Potential RNA-dependent RNA polymerase (RdRp) inhibitors as prospective drug candidates for SARS-CoV-2. Eur J Med Chem 2023; 252:115292. [PMID: 36965227 PMCID: PMC10023213 DOI: 10.1016/j.ejmech.2023.115292] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023]
Abstract
The SARS-CoV-2 pandemic is considered as one of the most disastrous pandemics for human health and the world economy. RNA-dependent RNA polymerase (RdRp) is one of the key enzymes that control viral replication. RdRp is an attractive and promising therapeutic target for the treatment of SARS-CoV-2 disease. It has attracted much interest of medicinal chemists, especially after the approval of Remdesivir. This study highlights the most promising SARS-CoV-2 RdRp repurposed drugs in addition to natural and synthetic agents. Although many in silico predicted agents have been developed, the lack of in vitro and in vivo experimental data has hindered their application in drug discovery programs.
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Affiliation(s)
- Mohamed S Bekheit
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza, 12622, Egypt
| | - Siva S Panda
- Department of Chemistry and Physics, Augusta University, Augusta, GA, 30912, USA.
| | - Adel S Girgis
- Department of Pesticide Chemistry, National Research Centre, Dokki, Giza, 12622, Egypt.
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24
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Velagacherla V, Suresh A, Mehta CH, Nayak UY, Nayak Y. Multi-Targeting Approach in Selection of Potential Molecule for COVID-19 Treatment. Viruses 2023; 15:213. [PMID: 36680253 PMCID: PMC9861341 DOI: 10.3390/v15010213] [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: 10/20/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
The coronavirus disease (COVID-19) is a pandemic that started in the City of Wuhan, Hubei Province, China, caused by the spread of coronavirus (SARS-CoV-2). Drug discovery teams around the globe are in a race to develop a medicine for its management. It takes time for a novel molecule to enter the market, and the ideal way is to exploit the already approved drugs and repurpose them therapeutically. We have attempted to screen selected molecules with an affinity towards multiple protein targets in COVID-19 using the Schrödinger suit for in silico predictions. The proteins selected were angiotensin-converting enzyme-2 (ACE2), main protease (MPro), and spike protein. The molecular docking, prime MM-GBSA, induced-fit docking (IFD), and molecular dynamics (MD) simulations were used to identify the most suitable molecule that forms a stable interaction with the selected viral proteins. The ligand-binding stability for the proteins PDB-IDs 1ZV8 (spike protein), 5R82 (Mpro), and 6M1D (ACE2), was in the order of nintedanib > quercetin, nintedanib > darunavir, nintedanib > baricitinib, respectively. The MM-GBSA, IFD, and MD simulation studies imply that the drug nintedanib has the highest binding stability among the shortlisted. Nintedanib, primarily used for idiopathic pulmonary fibrosis, can be considered for repurposing for us against COVID-19.
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Affiliation(s)
- Varalakshmi Velagacherla
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi 576104, India
| | - Akhil Suresh
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi 576104, India
| | - Chetan Hasmukh Mehta
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi 576104, India
| | - Usha Y. Nayak
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi 576104, India
- Manipal Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Udupi 576104, India
| | - Yogendra Nayak
- Manipal Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Udupi 576104, India
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Udupi 576104, India
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25
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Shahabadi N, Zendehcheshm S, Mahdavi M, Khademi F. Repurposing FDA-approved drugs cetilistat, abiraterone, diiodohydroxyquinoline, bexarotene, and remdesivir as potential inhibitors against RNA dependent RNA polymerase of SARS-CoV-2: A comparative in silico perspective. INFORMATICS IN MEDICINE UNLOCKED 2023; 36:101147. [PMID: 36510496 PMCID: PMC9729590 DOI: 10.1016/j.imu.2022.101147] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/19/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
Vaccines are undoubtedly the most effective means of combating viral diseases like COVID-19. However, there are risks associated with vaccination, such as incomplete viral deactivation or potential adverse effects in humans. However, designing and developing a panel of new drug molecules is always encouraged. In an emergency, drug repurposing research is one of the most potent and rapid options. RdRp (RNA-dependent RNA polymerase) has been discovered to play a pivotal role in viral replication. In this study, FDA-approved drugs bexarotene, diiodohydroxyquinoline, abiraterone, cetilistat, and remdesivir were repurposed against the RdRp by molecular modeling, docking, and dynamic simulation. Furthermore, to validate the potency of these drugs, we compared them to the antiviral remdesivir, which inhibits RdRp. Our finding indicated that the selected drugs have a high potential to be developed as RdRp inhibitors and, with further validation studies, could serve as potential drugs for the treatment of COVID-19.
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Affiliation(s)
- Nahid Shahabadi
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran,Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran,Corresponding author. Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Saba Zendehcheshm
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran,Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohammad Mahdavi
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Fatemeh Khademi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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26
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Khushboo, Siddiqi NJ, Sharma B. Pathophysiology of SARS-CoV2 Mediated Depression, Therapeutics, and Consequences: A Comprehensive Narrative. Mini Rev Med Chem 2023; 23:217-229. [PMID: 35658879 DOI: 10.2174/1381612828666220603150637] [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: 02/08/2022] [Revised: 03/31/2022] [Accepted: 04/13/2022] [Indexed: 11/22/2022]
Abstract
The Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2), belongs to emerging and reemerging diseases, which was first identified and reported in Wuhan, China, in December 2019. The genetic sequence of SARS-CoV-2 was similar to the SARS virus, a β-coronavirus. The epidemiological studies suggest that the transmission of SARS-CoV-2 mainly occurs from an infected person to others through close contact with the respiratory droplets or by having contact with SARS-CoV-2 adhering to objects and surfaces. The incubation period ranges from 5 to14 days. The symptoms include fever, dry cough, tiredness, aches, chest pain, conjunctivitis, diarrhea, headache, difficulty in breathing or short breath, loss of taste, smell, rashes on the skin, and sore throat. Some reports indicated that males exhibited lower scores than females, the younger populations displayed increased symptoms, Chinese/Taiwanese people registered only scarce symptoms, and Canadians experienced more symptoms. The results of several studies suggested that while COVID-19 had a significant effect on depression, job instability affected anxiety and depression. The diagnostics to detect the presence of coronavirus involve ELISA and RT-PCR. There is no specific treatment available to eradicate COVID-19. The therapeutics used to treat COVID 19 exhibited severe side effects. Recently, some Indian traditional medicinal plants have shown promise in reducing the risk of viral infection and also boosting the immunity of an individual. This paper presents an overview of the current status of depression in the SARS CoV2 infected people and the measures required to overcome COVID-19 induced depression in patients even after recovery.
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Affiliation(s)
- Khushboo
- Departments of Biochemistry, University of Allahabad, Allahabad 211002, UP-India
| | - Nikhat J Siddiqi
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Bechan Sharma
- Departments of Biochemistry, University of Allahabad, Allahabad 211002, UP-India
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27
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Chamkouri N, Absalan F, Koolivand Z, Yousefi M. Nonsteroidal Anti-Inflammatory Drugs in Viral Infections Disease, Specially COVID-19. Adv Biomed Res 2023; 12:20. [PMID: 36926440 PMCID: PMC10012024 DOI: 10.4103/abr.abr_148_21] [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: 06/01/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 02/05/2023] Open
Abstract
During the current SARS-CoV-2 (COVID-19) pandemic, some reports were presented based on those nonsteroidal anti-inflammatory drugs (NSAIDs) and corticosteroids may exacerbate symptoms in COVID-19 patients. According to this, we aimed to collate information available in published articles to identify any evidence behind these statements with the aim of helping clinicians on how best to treat patients. We could not find published conclusive evidence for or against the use of NSAIDs in COVID-19 patients. Meanwhile, there appeared to be some evidence that corticosteroids may be beneficial if utilized in the early acute phase of infection, however, conflicting WHO (World Health Organization) evidence surrounding corticosteroid use in certain viral infections means this evidence is not conclusive. Given the current availability of literature, caution should be exercised until further evidence emerges surrounding the use of NSAIDs and corticosteroids in COVID-19 patients. However, the availability of reliable information for clinicians and patients is paramount.
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Affiliation(s)
- Narges Chamkouri
- Medical Faculty, Abadan University of Medical Sciences, Abadan, Iran
| | - Forouzan Absalan
- Medical Faculty, Abadan University of Medical Sciences, Abadan, Iran
| | - Zahra Koolivand
- Medical Faculty, Abadan University of Medical Sciences, Abadan, Iran
| | - Mahsa Yousefi
- Medical Faculty, Abadan University of Medical Sciences, Abadan, Iran
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28
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Fayyazi N, Mostashari-Rad T, Ghasemi JB, Ardakani MM, Kobarfard F. Molecular dynamics simulation, 3D-pharmacophore and scaffold hopping analysis in the design of multi-target drugs to inhibit potential targets of COVID-19. J Biomol Struct Dyn 2022; 40:11787-11808. [PMID: 34405765 DOI: 10.1080/07391102.2021.1965914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SARS-CoV-2 has posed serious threat to the health and has inflicted huge costs in the world. Discovering potent compounds is a critical step to inhibit coronavirus. 3CLpro and RdRp are the most conserved targets associated with COVID-19. In this study, three-dimensional pharmacophore modeling, scaffold hopping, molecular docking, structure-based virtual screening, QSAR-based ADMET predictions and molecular dynamics analysis were used to identify inhibitors for these targets. Binding free energies estimated by molecular docking for each ligand in different binding sites of RdRp were used to predict the active site. Previously reported active 3CLpro and RdRp inhibitors were used to build a pharmacophore model to develop different scaffolds. Structure-based simulations and pharmacophore modeling based on Hip Hop algorithm converged in a state that suggest hydrogen bond acceptor and donor features have a critical role in the two binding sites. Further validations indicated that the best pharmacophore model has fairly good correlation values compared with approved inhibitors. Structure-based simulation results approved that GLu166 and Gln189 in 3CLpro and Lys551 and Glu811 in RdRp, are critical residues for dual activities. Ten compounds were extracted from pharmacophore-based virtual screening in six databases. The results, gained by repurposing approach, suggest the effectiveness of these ten compounds with different scaffolds as possible inhibitors of the two targets. Some quinoline-based hybrid derivatives also were designed. QSAR descriptors plot predicted that the scaffolds have had accepted pharmacokinetic profiles. Multiple molecular dynamics simulations in 100 ns and MM/PBSA studies of some reference inhibitors and the novel compounds in complex with both targets demonstrated stable complexes and confirmed the interaction modes. Based on different computational methods, COVID-19 multi-target inhibitors are proposed. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neda Fayyazi
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan, Iran.,Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tahereh Mostashari-Rad
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan, Iran.,Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jahan B Ghasemi
- College of Sciences, Faculty of Chemistry, University of Tehran, Tehran, Iran
| | - Mehran Mirabzadeh Ardakani
- Department of Traditional Pharmacy, Faculty of Pharmacy, Tehran University of Medical Science, Tehran, Iran
| | - Farzad Kobarfard
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medicinal Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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29
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Mitra D, Paul M, Thatoi H, Mohapatra PKD. Study of potentiality of dexamethasone and its derivatives against Covid-19. J Biomol Struct Dyn 2022; 40:10239-10249. [PMID: 34182880 DOI: 10.1080/07391102.2021.1942210] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In December 2019, COVID-19 epidemic was reported in Wuhan, China, and subsequently the infection has spread all over the world and became pandemic. The death toll associated with the pandemic is increasing day by day in a high rate. Herein, an effort has been made to identify the potentiality of commercially available drugs and also their probable derivatives for creation of better opportunity to make more powerful drugs against coronavirus. This study involves the in-silico interactions of dexamethasone and its derivatives against the multiple proteins of SARS-CoV-2 with the help of various computational methods. Descriptor parameters revealed their non-toxic effect in the human body. Ultimately docking studies and molecular dynamic simulation on those target protein by dexamethasone and its derivatives showed a high binding energy. Dexamethasone showed -9.8 kcal/mol and its derivative D5 showed -12.1 kcal/mol binding energy. Those scores indicate that dexamethasone has more therapeutic effect on SARS CoV-2 than other currently used drugs. Derivatives give the clue for the synthesis of a novel drug to remove SARS CoV-2. Until then, dexamethasone will be used as a potential inhibitor of SARS CoV-2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debanjan Mitra
- Department of Microbiology, Raiganj University, Raiganj, West Bengal, India
| | - Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, Odisha, India
| | - Hrudayanath Thatoi
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, Odisha, India
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30
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Pyasi S, Jonniya NA, Sk MF, Nayak D, Kar P. Finding potential inhibitors against RNA-dependent RNA polymerase (RdRp) of bovine ephemeral fever virus (BEFV): an in- silico study. J Biomol Struct Dyn 2022; 40:10403-10421. [PMID: 34238122 DOI: 10.1080/07391102.2021.1946714] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The bovine ephemeral fever virus (BEFV) is an enzootic agent that affects millions of bovines and causes major economic losses. Though the virus is seasonally reported with a very high morbidity rate (80-100%) from African, Australian, and Asiatic continents, it remains a neglected pathogen in many of its endemic areas, with no proper therapeutic drugs or vaccines presently available for treatment. The RNA-dependent RNA polymerase (RdRp) catalyzes the viral RNA synthesis and is an appropriate candidate for antiviral drug developments. We utilized integrated computational tools to build the 3D model of BEFV-RdRp and then predicted its probable active binding sites. The virtual screening and optimization against these active sites, using several small-molecule inhibitors from a different category of Life Chemical database and FDA-approved drugs from the ZINC database, was performed. We found nine molecules that have docking scores varying between -6.84 to -10.43 kcal/mol. Furthermore, these complexes were analyzed for their conformational dynamics and thermodynamic stability using molecular dynamics simulations in conjunction with the molecular mechanics generalized Born surface area (MM-GBSA) scheme. The binding free energy calculations depict that the electrostatic interactions play a dominant role in the RdRp-inhibitor binding. The hot spot residues, such as Arg565, Asp631, Glu633, Asp740, and Glu707, were found to control the RdRp-inhibitor interaction. The ADMET analysis strongly suggests favorable pharmacokinetics of these compounds that may prove useful for treating the BEFV ailment. Overall, we anticipate that these findings would help explore and develop a wide range of anti-BEFV therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shruti Pyasi
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Nisha Amarnath Jonniya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Debasis Nayak
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, India
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31
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Arumuganainar D, Yadalam PK, Alzahrani KJ, Alsharif KF, Alzahrani FM, Alshammeri S, Ahmed SSSJ, Vinothkumar TS, Baeshen HA, Patil S. Inhibitory effect of lupeol, quercetin, and solasodine on Rhizopus oryzae: A molecular docking and dynamic simulation study. J Infect Public Health 2022; 16:117-124. [PMID: 36512968 DOI: 10.1016/j.jiph.2022.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Mucormycosis is an infection caused by fungi belonging to the order Mucorales. Rhizopus oryzae is one of the most prevalent organisms identified in mucormycosis patients. Because it spreads quickly through the blood vessels, this opportunistic illness has an exceptionally high fatality rate, even when vigorous treatment is administered. Nonetheless, it has a high tolerance to antifungal medicines, limiting treatment options. As a result, improved methods for preventing and treating mucormycosis are desperately needed. Hence, this study was aimed at assessing the effect of lupeol, quercetin, and solasodine against mucormycosis based on computational approaches. METHODS The Rhizopus oryzae RNA-dependent RNA polymerase (RdRp) was the target for the design of drugs against the deadly mucormycosis. The three-dimensional structure of the RdRp was modelled with a Swiss model and validated using PROCHECK, VERIFY 3D, and QMEAN. Using the Schrodinger maestro module, a molecular docking study was performed between RdRp and the antimicrobial phytochemicals lupeol, quercetin, and solasodine. A molecular dynamics (MD) simulation study was used to assess the stability and interaction of the RdRp with these phytochemicals. RESULTS The RdRp protein binds strongly to lupeol (-7.2 kcal/mol), quercetin (-9.1 kcal/mol), and solasodine (-9.6 kcal/mol), according to molecular docking assessment based on the lowest binding energy, confirmation, and bond interaction. Simulations suggest that lupeol, quercetin, and solasodine complexes with RdRp and showed stable confirmation with minimal fluctuation throughout the 200 nanoseconds based on the RMSD and RMSF trajectory assessments. CONCLUSION The molecular docking and MD simulation investigation improved our understanding of phytochemical-RdRp interactions. Due to its high affinity for RdRp, solasodine may be a better treatment option for mucormycosis.
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Affiliation(s)
- Deepavalli Arumuganainar
- Department of Periodontics, Ragas Dental College and Hospital, 2/102, East Coast Road, Uthandi, Chennai 600119, India.
| | - Pradeep Kumar Yadalam
- Department of Periodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Khalid J Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied medical sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Khalaf F Alsharif
- Department of Clinical Laboratory Sciences, College of Applied medical sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Fuad M Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied medical sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.
| | - Saleh Alshammeri
- Department of Optometry, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia.
| | - Sheik S S J Ahmed
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam 603103, Tamil Nadu, India.
| | - Thilla Sekar Vinothkumar
- Department of Restorative Dental Sciences, College of Dentistry, Jazan University, Jazan 45142, Saudi Arabia; Department of Conservative Dentistry and Endodontics, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Hosam Ali Baeshen
- Department of Orthodontics, College of Dentistry, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan UTAH - 84095, USA; Centre of Molecular Medicine and Diagnostics (COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
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32
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Li L, Wu Y, Wang J, Yan H, Lu J, Wang Y, Zhang B, Zhang J, Yang J, Wang X, Zhang M, Li Y, Miao L, Zhang H. Potential Treatment of COVID-19 with Traditional Chinese Medicine: What Herbs Can Help Win the Battle with SARS-CoV-2? ENGINEERING (BEIJING, CHINA) 2022; 19:139-152. [PMID: 34729244 PMCID: PMC8552808 DOI: 10.1016/j.eng.2021.08.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/28/2021] [Accepted: 08/03/2021] [Indexed: 05/05/2023]
Abstract
Traditional Chinese medicine (TCM) has been successfully applied worldwide in the treatment of coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the pharmacological mechanisms underlying this success remain unclear. Hence, the aim of this review is to combine pharmacological assays based on the theory of TCM in order to elucidate the potential signaling pathways, targets, active compounds, and formulas of herbs that are involved in the TCM treatment of COVID-19, which exhibits combatting viral infections, immune regulation, and amelioration of lung injury and fibrosis. Extensive reports on target screening are elucidated using virtual prediction via docking analysis or network pharmacology based on existing data. The results of these reports indicate that an intricate regulatory mechanism is involved in the pathogenesis of COVID-19. Therefore, more pharmacological research on the natural herbs used in TCM should be conducted in order to determine the association between TCM and COVID-19 and account for the observed therapeutic effects of TCM against COVID-19.
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Affiliation(s)
- Lin Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yuzheng Wu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Laboratory of Pharmacology of TCM Formulae Co-Constructed by the Province-Ministry, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jiabao Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Huimin Yan
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jia Lu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yu Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Boli Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Junhua Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Evidence-Based Medicine Center, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jian Yang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiaoying Wang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- College of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Min Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yue Li
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Lin Miao
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Han Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Key Laboratory of Pharmacology of Traditional Chinese Medical Formulae, Ministry of Education, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
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33
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Abdullah Al Awadh A. Nucleotide and nucleoside-based drugs: past, present, and future. Saudi J Biol Sci 2022; 29:103481. [PMID: 36389209 PMCID: PMC9641258 DOI: 10.1016/j.sjbs.2022.103481] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/28/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Nucleotide and nucleoside-based analogue drugs are widely used for the treatment of both acute and chronic viral infections. These drugs inhibit viral replication due to one or more distinct mechanisms. It modifies the virus's genetic structure by reducing viral capacity in every replication cycle. Their clinical success has shown strong effectiveness against several viruses, including ebolavirus, hepatitis C virus, HIV, MERS, SARS-Cov, and the most recent emergent SARS-Cov2. In this review, seven different types of inhibitors have been selected that show broad-spectrum activity against RNA viruses. A detailed overview and mechanism of actionof both analogues are given, and the clinical perspectives are discussed. These inhibitors incorporated the novel SARS-CoV-2 RdRp, further terminating the polymerase activity with variable efficacy. The recent study provides a molecular basis for the inhibitory activity of virus RdRp using nucleotide and nucleoside analogues inhibitors. Furthermore, to identify those drugs that need more research and development to combat novel infections. Consequently, there is a pressing need to focus on present drugs by establishing their cell cultures. If their potencies were evidenced, then they would be explored in the future as potential therapeutics for novel outbreaks.
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34
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Singh R, Bhardwaj VK, Purohit R. Inhibition of nonstructural protein 15 of SARS-CoV-2 by golden spice: A computational insight. Cell Biochem Funct 2022; 40:926-934. [PMID: 36203381 PMCID: PMC9874790 DOI: 10.1002/cbf.3753] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/16/2022] [Accepted: 09/15/2022] [Indexed: 01/27/2023]
Abstract
The quick widespread of the coronavirus and speedy upsurge in the tally of cases demand the fast development of effective drugs. The uridine-directed endoribonuclease activity of nonstructural protein 15 (Nsp15) of the coronavirus is responsible for the invasion of the host immune system. Therefore, developing potential inhibitors against Nsp15 is a promising strategy. In this concern, the in silico approach can play a significant role, as it is fast and cost-effective in comparison to the trial and error approaches of experimental investigations. In this study, six turmeric derivatives (curcuminoids) were chosen for in silico analysis. The molecular interactions, pharmacokinetics, and drug-likeness of all the curcuminoids were measured. Further, the stability of Nsp15-curcuminoids complexes was appraised by employing molecular dynamics (MD) simulations and MM-PBSA approaches. All the molecules were affirmed to have strong interactions and pharmacokinetic profile. The MD simulations data stated that the Nsp15-curcuminoids complexes were stable during simulations. All the curcuminoids showed stable and high binding affinity, and these curcuminoids could be admitted as potential modulators for Nsp15 inhibition.
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Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR‐Institute of Himalayan Bioresource Technology (CSIR‐IHBT)The Himalayan Centre for High‐throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT)PalampurIndia,Biotechnology divisionCSIR‐IHBTPalampurIndia,Academy of Scientific & Innovative Research (AcSIR)GhaziabadIndia
| | - Vijay K. Bhardwaj
- Structural Bioinformatics Lab, CSIR‐Institute of Himalayan Bioresource Technology (CSIR‐IHBT)The Himalayan Centre for High‐throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT)PalampurIndia,Biotechnology divisionCSIR‐IHBTPalampurIndia,Academy of Scientific & Innovative Research (AcSIR)GhaziabadIndia
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR‐Institute of Himalayan Bioresource Technology (CSIR‐IHBT)The Himalayan Centre for High‐throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT)PalampurIndia,Biotechnology divisionCSIR‐IHBTPalampurIndia,Academy of Scientific & Innovative Research (AcSIR)GhaziabadIndia
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35
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Kciuk M, Mujwar S, Rani I, Munjal K, Gielecińska A, Kontek R, Shah K. Computational Bioprospecting Guggulsterone against ADP Ribose Phosphatase of SARS-CoV-2. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238287. [PMID: 36500379 PMCID: PMC9739500 DOI: 10.3390/molecules27238287] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022]
Abstract
Coronavirus Disease-2019 (COVID-19) is a highly contagious disease caused by Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). The World Health Organization (WHO) classified the disease a as global public health hazard on 11 March 2020. Currently, there are no adequate measures to combat viral infections, including COVID-19, and the medication guidelines for the management of COVID-19 are dependent on previous findings from SARS-CoV and MERS-CoV research. Natural products have achieved widespread acceptance around the world as a means of enhancing healthcare and disease prevention. Plants are a potential source of antiviral factors such as flavonoids, phenolic acids, terpenoids, and others. Some of these agents exhibit a broad spectrum of antiviral activity. This study aimed to screen herbal leads for possible inhibitors of the SARS-CoV-2 ADP Ribose Phosphatase enzyme (ARP). Guggulsterone was found to be highly stabilized within the active site of the viral ARP enzyme by molecular dynamic simulation with very little fluctuation throughout the simulation timeframe of 100 ns. Thus, guggulsterone can be further used to develop a safe and competent medication for evolving therapy against SARS-CoV-2 in post-preclinical and clinical trials.
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Affiliation(s)
- Mateusz Kciuk
- Department of Molecular Biotechnology and Genetics, University of Lodz, 90-237 Lodz, Poland
- Doctoral School of Exact and Natural Sciences, University of Lodz, 90-237 Lodz, Poland
- Correspondence:
| | - Somdutt Mujwar
- Chitkara College of Pharmacy, Chitkara University, Chandigarh 140401, Punjab, India
| | - Isha Rani
- Spurthy College of Pharmacy, Marasur Gate, Bengaluru 562106, Karnataka, India
| | - Kavita Munjal
- Department of Pharmacognosy, M.M. College of Pharmacy, Maharishi Markandeshwar (Deemed to Be University) Mullana, Ambala 133207, Haryana, India
| | - Adrianna Gielecińska
- Department of Molecular Biotechnology and Genetics, University of Lodz, 90-237 Lodz, Poland
| | - Renata Kontek
- Department of Molecular Biotechnology and Genetics, University of Lodz, 90-237 Lodz, Poland
| | - Kamal Shah
- Institute of Pharmaceutical Research, GLA University, Mathura 281406, Uttar Pradesh, India
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36
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Discovering new potential inhibitors to SARS-CoV-2 RNA dependent RNA polymerase (RdRp) using high throughput virtual screening and molecular dynamics simulations. Sci Rep 2022; 12:19986. [PMID: 36411383 PMCID: PMC9676757 DOI: 10.1038/s41598-022-24695-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 03/14/2022] [Indexed: 11/23/2022] Open
Abstract
RNA dependent RNA polymerase (RdRp), is an essential in the RNA replication within the life cycle of the severely acute respiratory coronavirus-2 (SARS-CoV-2), causing the deadly respiratory induced sickness COVID-19. Remdesivir is a prodrug that has seen some success in inhibiting this enzyme, however there is still the pressing need for effective alternatives. In this study, we present the discovery of four non-nucleoside small molecules that bind favorably to SARS-CoV-2 RdRp over the active form of the popular drug remdesivir (RTP) and adenosine triphosphate (ATP) by utilizing high-throughput virtual screening (HTVS) against the vast ZINC compound database coupled with extensive molecular dynamics (MD) simulations. After post-trajectory analysis, we found that the simulations of complexes containing both ATP and RTP remained stable for the duration of their trajectories. Additionally, it was revealed that the phosphate tail of RTP was stabilized by both the positive amino acid pocket and magnesium ions near the entry channel of RdRp which includes residues K551, R553, R555 and K621. It was also found that residues D623, D760, and N691 further stabilized the ribose portion of RTP with U10 on the template RNA strand forming hydrogen pairs with the adenosine motif. Using these models of RdRp, we employed them to screen the ZINC database of ~ 17 million molecules. Using docking and drug properties scoring, we narrowed down our selection to fourteen candidates. These were subjected to 200 ns simulations each underwent free energy calculations. We identified four hit compounds from the ZINC database that have similar binding poses to RTP while possessing lower overall binding free energies, with ZINC097971592 having a binding free energy two times lower than RTP.
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37
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Aghamohammadi M, Sirouspour M, Goncalves AS, França TCC, LaPlante SR, Shahdousti P. Modeling studies on the role of vitamins B1 (thiamin), B3 (nicotinamide), B6 (pyridoxamine), and caffeine as potential leads for the drug design against COVID-19. J Mol Model 2022; 28:380. [PMID: 36342543 PMCID: PMC9640828 DOI: 10.1007/s00894-022-05356-9] [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: 02/28/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022]
Abstract
In response to the COVID-19 pandemic, and the lack of effective and safe antivirals against it, we adopted a new approach in which food supplements with vital antiviral characteristics, low toxicity, and fast excretion have been targeted. The structures and chemical properties of the food supplements were compared to the promising antivirals against SARS-COV-2. Our goal was to exploit the food supplements to mimic the topical antivirals' functions but circumventing their severe side effects, which has limited the necessary dosage needed to exhibit the desired antiviral activity. On this line, after a comparative structural analysis of the chemicals mentioned above, and investigation of their potential mechanisms of action, we selected caffeine and some compounds of the vitamin B family and further applied molecular modeling techniques to evaluate their interactions with the RDB domain of the Spike protein of SARS-CoV-2 (SC2Spike) and its corresponding binding site on human ACE-2 (HssACE2). Our results pointed to vitamins B1 and B6 in the neutral form as potential binders to the HssACE2 RDB binding pocket that might be able to impair the SARS-CoV-2 mechanism of cell invasion, qualifying as potential leads for experimental investigation against COVID-19.
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Affiliation(s)
| | | | - Arlan S Goncalves
- Department of Chemistry, Federal Institute of Espirito Santo, Vila Velha, ES, Brazil.,Graduate Program in Chemistry, Federal University of Espirito Santo, Vitoria, ES, Brazil
| | - Tanos Celmar Costa França
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard Des Prairies, Laval, Québec, H7V 1B7, Canada.,Laboratory of Molecular Modeling Applied to the Chemical and Biological Defense (LMCBD), Military Institute of Engineering, Rio de Janeiro, RJ, Brazil.,Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Steven R LaPlante
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard Des Prairies, Laval, Québec, H7V 1B7, Canada
| | - Parvin Shahdousti
- Department of Chemistry, Borujerd Branch, Islamic Azad University, Borujerd, Iran
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38
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Jose AM. Analyzing the Impermeable Structure and Myriad of Antiviral Therapies for SARS-CoV-2. JOURNAL OF THE ASSOCIATION OF PHYSICIANS OF INDIA 2022. [DOI: 10.5005/japi-11001-0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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39
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Xu X, Chen Y, Lu X, Zhang W, Fang W, Yuan L, Wang X. An update on inhibitors targeting RNA-dependent RNA polymerase for COVID-19 treatment: Promises and challenges. Biochem Pharmacol 2022; 205:115279. [PMID: 36209840 PMCID: PMC9535928 DOI: 10.1016/j.bcp.2022.115279] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 01/18/2023]
Abstract
The highly transmissible variants of SARS-CoV-2, the causative pathogen of the COVID-19 pandemic, bring new waves of infection worldwide. Identification of effective therapeutic drugs to combat the COVID-19 pandemic is an urgent global need. RNA-dependent RNA polymerase (RdRp), an essential enzyme for viral RNA replication, is the most promising target for antiviral drug research since it has no counterpart in human cells and shows the highest conservation across coronaviruses. This review summarizes recent progress in studies of RdRp inhibitors, focusing on interactions between these inhibitors and the enzyme complex, based on structural analysis, and their effectiveness. In addition, we propose new possible strategies to address the shortcomings of current inhibitors, which may guide the development of novel efficient inhibitors to combat COVID-19.
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Affiliation(s)
- Xiaoying Xu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou 310053, China.
| | - Yuheng Chen
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xinyu Lu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China
| | - Wanlin Zhang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China
| | - Wenxiu Fang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China
| | - Luping Yuan
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China
| | - Xiaoyan Wang
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou 311402, China.
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Kostarev S, Komyagina O, Fayzrakhmanov R, Kurushin D, Tatarnikova N, Novikova (Kochetova) O, Sereda T. Impact of the New Coronavirus Infection on the Immune System of Children and Adolescents in the Region of the Russian Federation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:13669. [PMID: 36294250 PMCID: PMC9603771 DOI: 10.3390/ijerph192013669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/02/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
The emergence of COVID-19 (SARS-CoV-2) has presented public health professionals with new challenges in the diagnosis of the disease and treatment of patients. Nowadays, the epidemiology, clinical features, prevention and treatment of the disease are studied poorly due to continuous mutation of the pathogen. One of the consequences of the new coronavirus infection could be changes in the immune system of the human population. A detailed analysis of the immunological status of different racial groups under the influence of the new coronavirus infection is currently studied insufficiently, making this work of particular relevance. There is also a reluctance among some Russian residents to be vaccinated, including the population of Perm Krai, due to a lack of research on possible deviations in cellular immunity due to SARS-CoV-2 vaccination. At the start of the third wave caused by the new coronavirus infection, only 40% of the Russian population had been vaccinated, which was insufficient to acquire collective immunity. In the autumn of 2021, a QR code measure was introduced for vaccinated residents, which resulted in exceeding the necessary barrier for acquiring collective immunity. Due to the high growth and severity of the disease, we analysed the immunograms of children and adolescents, aged from 5 months to 17 years, in Perm Krai during the pandemic years 2020-2021. The patients' immunological status results were divided into three categories. Laboratory diagnosis of the human immune system was carried out using serological and flow cytophotometric analyses. A total of 247 samples were analysed. The aim of this work was to investigate changes in the immune system of children and adolescents during the pandemic caused by the new coronavirus infection. The methodology was based on the analysis of immunograms, including biochemical studies, immune status and flow cytophotometric analysis. The immunograms were pre-sorted by IgA, IgM, IgG immunoglobulin status into four categories: absence of disease-k1 in which IgA, IgM, IgG immunoglobulin values were within the reference interval, active disease stage-k2 in which IgA, IgM immunoglobulins had gone beyond the reference interval, passive disease stage-k3 characterised by IgG and IgM immunoglobulin status, and patient recovery process-k4. In the immunograms, three immune status indicators were selected for further investigation: phagocytosis absolute value, phagocytic number and phagocytic index and five flow cytometry indices: leukocytes, lymphocytes, NK cells (CD16+CD56+), T helpers (CD3+CD4+) and CD4+/CD8+ immunoregulation index. A quantitative analysis of the deviations of these indicators from the reference intervals was performed in the three studied age groups of children and adolescents living in Perm Krai of the Russian Federation during the pandemic of 2020-2021.
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Affiliation(s)
- Sergey Kostarev
- Perm National Research Polytechnic University, 29, Komsomolski Avenue, Perm 614990, Russia
- Perm State Agro-Technological University Named after Academician D N Pryanishnikov, 23, Petropavlovskaja St., Perm 614990, Russia
- Perm Institute of the FPS of Russia, 125, Karpinskogo St., Perm 614012, Russia
| | - Oksana Komyagina
- Medical Institution “Philosophy of Beauty and Health”, 64, KIM St., Perm 614990, Russia
| | - Rustam Fayzrakhmanov
- Perm National Research Polytechnic University, 29, Komsomolski Avenue, Perm 614990, Russia
| | - Daniel Kurushin
- Perm National Research Polytechnic University, 29, Komsomolski Avenue, Perm 614990, Russia
| | - Natalya Tatarnikova
- Perm State Agro-Technological University Named after Academician D N Pryanishnikov, 23, Petropavlovskaja St., Perm 614990, Russia
| | - Oksana Novikova (Kochetova)
- Perm State Agro-Technological University Named after Academician D N Pryanishnikov, 23, Petropavlovskaja St., Perm 614990, Russia
- Perm Institute of the FPS of Russia, 125, Karpinskogo St., Perm 614012, Russia
| | - Tatyana Sereda
- Perm State Agro-Technological University Named after Academician D N Pryanishnikov, 23, Petropavlovskaja St., Perm 614990, Russia
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41
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Parise A, Ciardullo G, Prejanò M, Lande ADL, Marino T. On the Recognition of Natural Substrate CTP and Endogenous Inhibitor ddhCTP of SARS-CoV-2 RNA-Dependent RNA Polymerase: A Molecular Dynamics Study. J Chem Inf Model 2022; 62:4916-4927. [PMID: 36219674 DOI: 10.1021/acs.jcim.2c01002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The novel coronavirus SARS-CoV-2 is the causative agent of the COVID-19 outbreak that is affecting the entire planet. As the pandemic is still spreading worldwide, with multiple mutations of the virus, it is of interest and of help to employ computational methods for identifying potential inhibitors of the enzymes responsible for viral replication. Attractive antiviral nucleotide analogue RNA-dependent RNA polymerase (RdRp) chain terminator inhibitors are investigated with this purpose. This study, based on molecular dynamics (MD) simulations, addresses the important aspects of the incorporation of an endogenously synthesized nucleoside triphosphate, ddhCTP, in comparison with the natural nucleobase cytidine triphosphate (CTP) in RdRp. The ddhCTP species is the product of the viperin antiviral protein as part of the innate immune response. The absence of the ribose 3'-OH in ddhCTP could have important implications in its inhibitory mechanism of RdRp. We built an in silico model of the RNA strand embedded in RdRp using experimental methods, starting from the cryo-electron microscopy structure and exploiting the information obtained by spectrometry on the RNA sequence. We determined that the model was stable during the MD simulation time. The obtained results provide deeper insights into the incorporation of nucleoside triphosphates, whose molecular mechanism by the RdRp active site still remains elusive.
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Affiliation(s)
- Angela Parise
- Dipartimento di Chimica e Tecnologie Chimiche, Università Della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy.,Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
| | - Giada Ciardullo
- Dipartimento di Chimica e Tecnologie Chimiche, Università Della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy
| | - Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università Della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy
| | - Aurélien de la Lande
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay 91405, France
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università Della Calabria, Via Pietro Bucci, 87036 Arcavacata di Rende, CS, Italy
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42
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Gillis TD, Bearne SL. Effects of the 5'-Triphosphate Metabolites of Ribavirin, Sofosbuvir, Vidarabine, and Molnupiravir on CTP Synthase Catalysis and Filament Formation: Implications for Repurposing Antiviral Agents against SARS-CoV-2. ChemMedChem 2022; 17:e202200399. [PMID: 36184568 PMCID: PMC9538051 DOI: 10.1002/cmdc.202200399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/22/2022] [Indexed: 01/14/2023]
Abstract
Repurposing of antiviral drugs affords a rapid and effective strategy to develop therapies to counter pandemics such as COVID-19. SARS-CoV-2 replication is closely linked to the metabolism of cytosine-containing nucleotides, especially cytidine-5'-triphosphate (CTP), such that the integrity of the viral genome is highly sensitive to intracellular CTP levels. CTP synthase (CTPS) catalyzes the rate-limiting step for the de novo biosynthesis of CTP. Hence, it is of interest to know the effects of the 5'-triphosphate (TP) metabolites of repurposed antiviral agents on CTPS activity. Using E. coli CTPS as a model enzyme, we show that ribavirin-5'-TP is a weak allosteric activator of CTPS, while sofosbuvir-5'-TP and adenine-arabinofuranoside-5'-TP are both substrates. β-d-N4 -Hydroxycytidine-5'-TP is a weak competitive inhibitor relative to CTP, but induces filament formation by CTPS. Alternatively, sofosbuvir-5'-TP prevented CTP-induced filament formation. These results reveal the underlying potential for repurposed antivirals to affect the activity of a critical pyrimidine nucleotide biosynthetic enzyme.
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Affiliation(s)
- Thomas D. Gillis
- Dalhousie UniversityDepartment of Biochemistry & Molecular Biology5850 College St.Tupper Medical Building, 9JB3H 4R2HalifaxCANADA
| | - Stephen L. Bearne
- Dalhousie UniversityBiochemistry & Molecular Biology5850 College StreetTupper Medical BuildingB3H 4R2HalifaxCANADA
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Bal S, Sharangi AB, Upadhyay TK, Khan F, Pandey P, Siddiqui S, Saeed M, Lee HJ, Yadav DK. Biomedical and Antioxidant Potentialities in Chilli: Perspectives and Way Forward. Molecules 2022; 27:molecules27196380. [PMID: 36234927 PMCID: PMC9570844 DOI: 10.3390/molecules27196380] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Worldwide, since ages and nowadays, traditional medicine is well known, owing to its biodiversity, which immensely contributed to the advancement and development of complementary and alternative medicines. There is a wide range of spices, herbs, and trees known for their medicinal uses. Chilli peppers, a vegetable cum spice crop, are bestowed with natural bioactive compounds, flavonoids, capsaicinoids, phytochemicals, phytonutrients, and pharmacologically active compounds with potential health benefits. Such compounds manifest their functionality over solo-treatment by operating in synergy and consortium. Co-action of these compounds and nutrients make them potentially effective against coagulation, obesity, diabetes, inflammation, dreadful diseases, such as cancer, and microbial diseases, alongside having good anti-oxidants with scavenging ability to free radicals and oxygen. In recent times, capsaicinoids especially capsaicin can ameliorate important viral diseases, such as SARS-CoV-2. In addition, capsaicin provides an ability to chilli peppers to ramify as topical agents in pain-relief and also benefitting man as a potential effective anesthetic agent. Such phytochemicals involved not only make them useful and a much economical substitute to wonder/artificial drugs but can be exploited as obscene drugs for the production of novel stuffs. The responsibility of the TRPV1 receptor in association with capsaicin in mitigating chronic diseases has also been justified in this study. Nonetheless, medicinal studies pertaining to consumption of chilli peppers are limited and demand confirmation of the findings from animal studies. In this artifact, an effort has been made to address in an accessible format the nutritional and biomedical perspectives of chilli pepper, which could precisely upgrade and enrich our pharmaceutical industries towards human well-being.
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Affiliation(s)
- Solanki Bal
- Department of Vegetable Science, BCKV-Agricultural University, Mohanpur 741252, India
| | - Amit Baran Sharangi
- Department of Plantation, Spices, Medicinal & Aromatic Crops, BCKV-Agricultural University, Mohanpur 741252, India
| | - Tarun Kumar Upadhyay
- Department of Biotechnology, Parul Institute of Applied Sciences and Centre of Research for Development, Parul University, Vadodara 391760, India
| | - Fahad Khan
- Department of Biotechnology, Noida Institute of Engineering & Technology, Greater Noida 201306, India
| | - Pratibha Pandey
- Department of Biotechnology, Noida Institute of Engineering & Technology, Greater Noida 201306, India
- Department of Biotechnology, School of Engineering and Technology (SET), Sharda University, Greater Noida 201310, India
| | - Samra Siddiqui
- Department Health Services Management, College of Public Health and Health Informatics, University of Hail, Hail P.O. Box 2240, Saudi Arabia
| | - Mohd Saeed
- Department of Biology, College of Sciences, University of Hail, Hail P.O. Box 2240, Saudi Arabia
| | - Hae-Jeung Lee
- Department of Food & Nutrition, College of Bionano Technology, Gachon University, 1342 Seongnamdaero, Seongnam-si 13120, Korea
- Correspondence: (H.-J.L.); (D.K.Y.)
| | - Dharmendra K. Yadav
- Department of Pharmacy, Gachon Institute of Pharmaceutical Science, College of Pharmacy, Hambakmoeiro 191, Gachon University, Incheon 21924, Korea
- Correspondence: (H.-J.L.); (D.K.Y.)
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Madariaga-Mazón A, Naveja JJ, Becerra A, Alberto Campillo-Balderas J, Hernández-Morales R, Jácome R, Lazcano A, Martinez-Mayorga K. Subtle structural differences of nucleotide analogs may impact SARS-CoV-2 RNA-dependent RNA polymerase and exoribonuclease activity. Comput Struct Biotechnol J 2022; 20:5181-5192. [PMID: 36097553 PMCID: PMC9452397 DOI: 10.1016/j.csbj.2022.08.056] [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: 03/22/2022] [Revised: 08/05/2022] [Accepted: 08/27/2022] [Indexed: 11/17/2022] Open
Abstract
The rapid spread and public health impact of the novel SARS-CoV-2 variants that cause COVID-19 continue to produce major global impacts and social distress. Several vaccines were developed in record time to prevent and limit the spread of the infection, thus playing a pivotal role in controlling the pandemic. Although the repurposing of available drugs attempts to provide therapies of immediate access against COVID-19, there is still a need for developing specific treatments for this disease. Remdesivir, molnupiravir and Paxlovid remain the only evidence-supported antiviral drugs to treat COVID-19 patients, and only in severe cases. To contribute on the search of potential Covid-19 therapeutic agents, we targeted the viral RNA-dependent RNA polymerase (RdRp) and the exoribonuclease (ExoN) following two strategies. First, we modeled and analyzed nucleoside analogs sofosbuvir, remdesivir, favipiravir, ribavirin, and molnupiravir at three key binding sites on the RdRp-ExoN complex. Second, we curated and virtually screened a database containing 517 nucleotide analogs in the same binding sites. Finally, we characterized key interactions and pharmacophoric features presumably involved in viral replication halting at multiple sites. Our results highlight structural modifications that might lead to more potent SARS-CoV-2 inhibitors against an expansive range of variants and provide a collection of nucleotide analogs useful for screening campaigns.
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Affiliation(s)
- Abraham Madariaga-Mazón
- Instituto de Química Unidad Mérida, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz Km. 4.5, Ucú, Yucatán, Mexico.,Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas Unidad Mérida, Universidad Nacional Autónoma de México, Sierra Papacál Mérida, Yucatán 97302, Mexico
| | - José J Naveja
- Instituto de Química Unidad Mérida, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz Km. 4.5, Ucú, Yucatán, Mexico.,Institute for Molecular Biology and University Cancer Center (UCT) Mainz, Germany
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | - Rodrigo Jácome
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Antonio Lazcano
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico.,El Colegio Nacional, Mexico City, Mexico
| | - Karina Martinez-Mayorga
- Instituto de Química Unidad Mérida, Universidad Nacional Autónoma de México, Carretera Mérida-Tetiz Km. 4.5, Ucú, Yucatán, Mexico.,Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas Unidad Mérida, Universidad Nacional Autónoma de México, Sierra Papacál Mérida, Yucatán 97302, Mexico
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Efficacy of Dexamethasone and Methylprednisolone in Hospitalization Outcomes of COVID-19 Patients: A Comparative Retrospective Study. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2022. [DOI: 10.5812/archcid-129727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background: Control of the COVID-19 pandemic, its treatment, and prevention of mortality and morbidity have been the main focus of researchers over the past two years. Due to disagreement on the usefulness of different corticosteroids in the treatment of COVID-19, this work compared the efficacy of dexamethasone and methylprednisolone in the treatment outcomes of intensive critical care (ICU) patients. Methods: The present retrospective cohort study examined clinical records of 105 COVID-19 patients hospitalized in the ICUs of Firoozabadi Hospital in 2021. Clinical outcomes, including the length of hospital stay, the need for a ventilator, and mortality, were compared between patients who received either dexamethasone (DXM) or methylprednisolone (MP). Data were analyzed by SPSS V.20 software at P < 0.05 as statistical significance. Results: The mean ± SD ages of the patients in the DXM and MP groups were 58.82 ± 19.29 and 60.66 ± 14.17 years, respectively, without a statistically significant difference (P > 0.05). The mean duration of hospitalization was 8.14 ± 4.36 days in the DXM group and 6.80 ± 3.34 days in the MP group (P = 0.295). Also, 19 (33.3%) cases in the DXM group an, 19 (39.6%) in the MP group needed mechanical ventilation during hospitalization (P = 0.546). Finally, 30 (52.6%) patients in the DXM group and 27 (56.2%) in the MP group died. Conclusions: The findings indicated no significant difference in the mean duration of hospitalization, the need for a ventilator, and mortality in COVID-19 ICU patients treated with methylprednisolone or dexamethasone. There is a need to perform meta-analyses owing to conflicting results regarding the effects of different corticosteroids on the COVID-19 course.
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Mosayebnia M, Hajiagha Bozorgi A, Rezaeianpour M, Kobarfard F. In silico prediction of SARS-CoV-2 main protease and polymerase inhibitors: 3D-Pharmacophore modelling. J Biomol Struct Dyn 2022; 40:6569-6586. [PMID: 33599180 PMCID: PMC7898304 DOI: 10.1080/07391102.2021.1886991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/02/2021] [Indexed: 01/18/2023]
Abstract
The outbreak of the second severe acute respiratory syndrome coronavirus (SARS-CoV-2) known as COVID-19 has caused global concern. No effective vaccine or treatment to control the virus has been approved yet. Social distancing and precautionary protocols are still the only way to prevent person-to-person transmission. We hope to identify anti-COVID-19 activity of the existing drugs to overcome this pandemic as soon as possible. The present study used HEX and AutoDock Vina softwares to predict the affinity of about 100 medicinal structures toward the active site of 3-chymotrypsin-like protease (3Clpro) and RNA-dependent RNA polymerase (RdRp), separately. Afterwards, MOE software and the pharmacophore-derived query methodology were employed to determine the pharmacophore model of their inhibitors. Tegobuvir (19) and compound 45 showed the best binding affinity toward RdRp and 3Clpro of SARS-CoV-2 in silico, respectively. Tegobuvir -previously applied for hepatitis C virus- formed highly stable complex with uncommon binding pocket of RdRp (E total: -707.91 Kcal/mol) in silico. In addition to compound 45, tipranavir (28) and atazanavir (26) as FDA-approved HIV protease inhibitors were tightly interacted with the active site of SARS-CoV-2 main protease as well. Based on pharmacophore modelling, a good structural pattern for potent candidates against SARS-CoV-2 main enzymes is suggested. Re-tasking or taking inspiration from the structures of tegobuvir and tipranavir can be a proper approach toward coping with the COVID-19 in the shortest possible time and at the lowest cost.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mona Mosayebnia
- Department of Radiopharmacy and Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atefeh Hajiagha Bozorgi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Alborz University of Medical Sciences, Karaj, Iran
| | - Maliheh Rezaeianpour
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberclosis and Lung Diseases (NRTLD), Shahid Beheshti University of Medical sciences, Tehran, Iran
| | - Farzad Kobarfard
- Department of Radiopharmacy and Pharmaceutical Chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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47
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Kaur I, Behl T, Sehgal A, Singh S, Sharma N, Subramanian V, Fuloria S, Fuloria NK, Sekar M, Dailah HG, Alsubayiel AM, Bhatia S, Al-Harrasi A, Aleya L, Bungau S. A motley of possible therapies of the COVID-19: reminiscing the origin of the pandemic. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:67685-67703. [PMID: 35933528 PMCID: PMC9362373 DOI: 10.1007/s11356-022-22345-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/28/2022] [Indexed: 05/20/2023]
Abstract
The 2019 outbreak of corona virus disease began from Wuhan (China), transforming into a leading pandemic, posing an immense threat to the global population. The WHO coined the term nCOVID-19 for the disease on 11th February, 2020 and the International Committee of Taxonomy of Viruses named it SARS-CoV-2, on account of its similarity with SARS-CoV-1 of 2003. The infection is associated with fever, cough, pneumonia, lung damage, and ARDS along with clinical implications of lung opacities. Brief understanding of the entry target of virus, i.e., ACE2 receptors has enabled numerous treatment options as discussed in this review. The manuscript provides a holistic picture of treatment options in COVID-19, such as non-specific anti-viral drugs, immunosuppressive agents, anti-inflammatory candidates, anti-HCV, nucleotide inhibitors, antibodies and anti-parasitic, RNA-dependent RNA polymerase inhibitors, anti-retroviral, vitamins and hormones, JAK inhibitors, and blood plasma therapy. The text targets to enlist the investigations conducted on all the above categories of drugs, with respect to the COVID-19 pandemic, to accelerate their significance in hindering the disease progression. The data collected primarily targets recently published articles and most recent records of clinical trials, focusing on the last 10-year database. The current review provides a comprehensive view on the critical need of finding a suitable treatment for the currently prevalent COVID-19 disease, and an opportunity for the researchers to investigate the varying possibilities to find and optimized treatment approach to mitigate and ameliorate the chaos created by the pandemic worldwide.
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Affiliation(s)
- Ishnoor Kaur
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India.
| | - Aayush Sehgal
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Sukhbir Singh
- MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, Haryana, 133207, India
| | - Neelam Sharma
- MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, Haryana, 133207, India
| | | | - Shivkanya Fuloria
- Faculty of Pharmacy & Center of Excellence for Biomaterials Engineering, AIMST University, Bedong, Kedah, Malaysia
| | - Neeraj Kumar Fuloria
- Faculty of Pharmacy & Center of Excellence for Biomaterials Engineering, AIMST University, Bedong, Kedah, Malaysia
| | - Mahendran Sekar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Health Sciences, Universiti Kuala Lumpur, Royal College of Medicine, Perak, Ipoh, Malaysia
| | - Hamed Ghaleb Dailah
- Research and Scientific Studies Unit, College of Nursing, Jazan University, Jazan, Saudi Arabia
| | - Amal M Alsubayiel
- Department of Pharmaceutics, College of Pharmacy, Qassim University, Buraydah, Kingdom of Saudi Arabia
| | - Saurabh Bhatia
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
- School of Health Science, University of Petroleum and Energy Studies, Dehradun, Uttarakhand, India
| | - Ahmed Al-Harrasi
- Natural & Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Lotfi Aleya
- Chrono-Environment Laboratory, UMR CNRS 6249, Bourgogne Franche-Comté University, Besançon, France
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
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48
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Couroux P, Brkovic A, Vittitow JL, Israel RJ, Pamidi C, Patel J, Barakat M. A randomized, placebo-controlled study to evaluate safety and pharmacokinetics of inhaled ribavirin. Clin Transl Sci 2022; 15:2159-2171. [PMID: 35677972 PMCID: PMC9468560 DOI: 10.1111/cts.13350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/29/2022] [Accepted: 05/17/2022] [Indexed: 01/25/2023] Open
Abstract
Ribavirin is an inosine monophosphate dehydrogenase inhibitor. Studies suggest ribavirin aerosol could be a safe and efficacious treatment option in the fight against coronaviruses. However, current treatment is long (12-18 h per day, 3-7 days), limiting clinical utility. A reduction in treatment time would reduce treatment burden. We aimed to evaluate safety and pharmacokinetics (PK) of four, single-dose regimens of ribavirin aerosol in healthy volunteers. Thirty-two subjects were randomized, to four cohorts of aerosolized ribavirin (active) or placebo. Cohort 1 received 50 mg/ml ribavirin/placebo (10 ml total volume); cohort 2, 50 mg/ml ribavirin/placebo (20 ml total volume); cohort 3, 100 mg/ml ribavirin/placebo (10 ml total volume); and cohort 4, 100 mg/ml ribavirin/placebo (20 ml total volume). Intense safety monitoring and PK sampling took place on days 1, 2, 3, and 40. Subjects were (mean ± SD, active vs. placebo) aged 57 ± 4.5 vs. 60 ± 2.5 years; 83% vs. 88% were female; and 75% vs. 50% were Caucasian. Some 12.5% (3/24) and 25% (2/8) experienced at least one treatment-emergent adverse event (TEAE) (two moderate; five mild) in the active and placebo groups, respectively. No clinically significant safety concerns were reported. Mean maximum observed concentration (Cmax ) and area under the curve (AUC) values were higher in cohort 4, whereas cohorts 2 and 3 showed similar PK values. Ribavirin absorption reached Cmax within 2 h across cohorts. Four single-dose regimens of ribavirin aerosol demonstrated systemic exposure with minimal systemic effects. Results support continued clinical development of ribavirin aerosol as a treatment option in patients with coronaviruses.
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Gheshlaghi SZ, Nakhaei E, Ebrahimi A, Jafari M, Shahraki A, Rezazadeh S, Saberinasab E, Nowroozi A, Hosseini SS. Analysis of medicinal and therapeutic potential of Withania somnifera derivatives against COVID-19. J Biomol Struct Dyn 2022:1-11. [PMID: 35993530 DOI: 10.1080/07391102.2022.2112977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Apart from chemical and allopathic drugs, several medicinal plants contain phytochemicals that are potentially useful to counter the COVID-19 pandemic. Withania somnifera (Ashwagandha), which has a good effect on some viral infections, can be considered as a candidate against the virus. In the present study, thirty-nine natural compounds of Ashwagandha were investigated in terms of their binding to the important drug targets to treat the COVID-19. Although the molecular docking calculations reveal the binding affinities of the compounds to Mpro, TMPRSS2, NSP15, PLpro, Spike RBD + ACE2, RdRp and NSP12 as targets in controlling the coronavirus enzymes, Withanoside II is expected to be the most effective compound due to the high affinity in binding with many of considered targets. Furthermore, the Withanoside III, IV, V, X, and XI have favorable binding affinities as ligands with respect to the MM/GBSA calculations. The molecular dynamics simulations MD explore a stable hydrogen bond network between ligands and the active sites residues. Also, the dynamic fluctuations of the binding site residues verify their tight binding to ligands. Moreover, the stability of ligand-protein complexes is approved by the RMSD ranges lower than 0.5 Å in equilibration zone for all mentioned complexes. The TMPRSS2-Withanolide Q and Mpro-Withanoside IV complexes are the most stable pairs using the MM/GBSA calculations and MD simulation.
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Affiliation(s)
- Saman Zare Gheshlaghi
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Ebrahim Nakhaei
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Ali Ebrahimi
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Majid Jafari
- Department of Plant Protection, Higher Education Complex of Saravan, College of Agriculture
| | - Asiyeh Shahraki
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Shiva Rezazadeh
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
| | - Erfan Saberinasab
- School of Health, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Nowroozi
- Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and Baluchestan, Zahedan, Iran
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50
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Singh M, Jayant K, Singh D, Bhutani S, Poddar NK, Chaudhary AA, Khan SUD, Adnan M, Siddiqui AJ, Hassan MI, Khan FI, Lai D, Khan S. Withania somnifera (L.) Dunal (Ashwagandha) for the possible therapeutics and clinical management of SARS-CoV-2 infection: Plant-based drug discovery and targeted therapy. Front Cell Infect Microbiol 2022; 12:933824. [PMID: 36046742 PMCID: PMC9421373 DOI: 10.3389/fcimb.2022.933824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/11/2022] [Indexed: 11/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic has killed huge populations throughout the world and acts as a high-risk factor for elderly and young immune-suppressed patients. There is a critical need to build up secure, reliable, and efficient drugs against to the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Bioactive compounds of Ashwagandha [Withania somnifera (L.) Dunal] may implicate as herbal medicine for the management and treatment of patients infected by SARS-CoV-2 infection. The aim of the current work is to update the knowledge of SARS-CoV-2 infection and information about the implication of various compounds of medicinal plant Withania somnifera with minimum side effects on the patients' organs. The herbal medicine Withania somnifera has an excellent antiviral activity that could be implicated in the management and treatment of flu and flu-like diseases connected with SARS-CoV-2. The analysis was performed by systematically re-evaluating the published articles related to the infection of SARS-CoV-2 and the herbal medicine Withania somnifera. In the current review, we have provided the important information and data of various bioactive compounds of Withania somnifera such as Withanoside V, Withanone, Somniferine, and some other compounds, which can possibly help in the management and treatment of SARS-CoV-2 infection. Withania somnifera has proved its potential for maintaining immune homeostasis of the body, inflammation regulation, pro-inflammatory cytokines suppression, protection of multiple organs, anti-viral, anti-stress, and anti-hypertensive properties. Withanoside V has the potential to inhibit the main proteases (Mpro) of SARS-CoV-2. At present, synthetic adjuvant vaccines are used against COVID-19. Available information showed the antiviral activity in Withanoside V of Withania somnifera, which may explore as herbal medicine against to SARS-CoV-2 infection after standardization of parameters of drug development and formulation in near future.
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Affiliation(s)
- Manali Singh
- Department of Biotechnology, Invertis University, Bareilly, Uttar Pradesh, India
- Department of Biochemistry, C.B.S.H, G.B Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, India
| | - Kuldeep Jayant
- Department of Agricultural and Food Engineering, IIT Kharagpur, West Bengal, Kharagpur, India
| | - Dipti Singh
- Department of Biochemistry, C.B.S.H, G.B Pant University of Agriculture and Technology, Pantnagar, Uttrakhand, India
| | - Shivani Bhutani
- Department of Biotechnology, Invertis University, Bareilly, Uttar Pradesh, India
| | - Nitesh Kumar Poddar
- Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Salah-Ud-Din Khan
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
| | - Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Hail, Hail, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Faez Iqbal Khan
- Department of Biological Sciences, School of Science, Xi’an Jiaotong-Liverpool University, Suzhou, China
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Dakun Lai
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Shahanavaj Khan
- Department of Health Sciences, Novel Global Community Educational Foundation 7 Peterlee Place, Hebersham, NSW, Australia
- Department of Medical Lab Technology, Indian Institute of Health and Technology (IIHT), Deoband, Saharanpur, UP, India
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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