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Yasmeen N, Ahmad Chaudhary A, K Niraj RR, Lakhawat SS, Sharma PK, Kumar V. Screening of phytochemicals from Clerodendrum inerme (L.) Gaertn as potential anti-breast cancer compounds targeting EGFR: an in-silico approach. J Biomol Struct Dyn 2023:1-43. [PMID: 38141177 DOI: 10.1080/07391102.2023.2294379] [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: 07/25/2023] [Accepted: 12/04/2023] [Indexed: 12/25/2023]
Abstract
Breast cancer (BC) is the most prevalent malignancy among women around the world. The epidermal growth factor receptor (EGFR) is a tyrosine kinase receptor (RTK) of the ErbB/HER family. It is essential for triggering the cellular signaling cascades that control cell growth and survival. However, perturbations in EGFR signaling lead to cancer development and progression. Hence, EGFR is regarded as a prominent therapeutic target for breast cancer. Therefore, in the current investigation, EGFR was targeted with phytochemicals from Clerodendrum inerme (L.) Gaertn (C. inerme). A total of 121 phytochemicals identified by gas chromatography-mass spectrometry (GC-MS) analysis were screened against EGFR through molecular docking, ADMET analyses (Absorption, Distribution, Metabolism, Excretion, and Toxicity), PASS predictions, and molecular dynamics simulation, which revealed three potential hit compounds with CIDs 10586 [i.e. alpha-bisabolol (-6.4 kcal/mol)], 550281 [i.e. 2,(4,4-Trimethyl-3-hydroxymethyl-5a-(3-methyl-but-2-enyl)-cyclohexene) (-6.5 kcal/mol)], and 161271 [i.e. salvigenin (-7.4 kcal/mol)]. The FDA-approved drug gefitinib was used to compare the inhibitory effects of the phytochemicals. The top selected compounds exhibited good ADMET properties and obeyed Lipinski's rule of five (ROF). The molecular docking analysis showed that salvigenin was the best among the three compounds and formed bonds with the key residue Met 793. Furthermore, the molecular mechanics generalized born surface area (MMGBSA) calculations, molecular dynamics simulation, and normal mode analysis validated the binding affinity of the compounds and also revealed the strong stability and compactness of phytochemicals at the docked site. Additionally, DFT and DOS analyses were done to study the reactivity of the compounds and to further validate the selected phytochemicals. These results suggest that the identified phytochemicals possess high inhibitory potential against the target EGFR and can treat breast cancer. However, further in vitro and in vivo investigations are warranted towards the development of these constituents into novel anti-cancer drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nusrath Yasmeen
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | | | | | | | - Vikram Kumar
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
- Amity Institute of Pharmacy, Amity University Rajasthan, Jaipur, India
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Balkrishna A, Sharma D, Thapliyal M, Arya V, Dabas A. Unraveling the therapeutic potential of Senna singueana phytochemicals to attenuate pancreatic cancer using protein-protein interactions, molecular docking, and MD simulation. In Silico Pharmacol 2023; 12:3. [PMID: 38108042 PMCID: PMC10719185 DOI: 10.1007/s40203-023-00179-9] [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: 08/10/2023] [Accepted: 11/05/2023] [Indexed: 12/19/2023] Open
Abstract
Pancreatic cancer (PC) presents challenges due to limited treatment options and patients seek complementary therapies alongside conventional treatments to improve well-being. This study uses computational drug discovery approaches to find potential phytochemicals from S. singueana for PC treatment. Among the 38 phytochemicals screened from S. singueana, specific inhibitors against PC were selected. Protein-protein interaction (PPI) network analysis highlighted key targets with high degrees, including PTEN (8) and PTK2 (7) genes, along with their respective proteins 5BZX and 3BZ3, which were employed for molecular docking studies. 1-methylchrysene and 3-methyl-1,8,9-anthracenetriol showed strong binding affinities of - 9.2 and - 8.1 Kcal/mol, respectively. Molecular dynamics simulations lasting 300 ns assessed structural stability and interaction energy of compound-target dockings: 1-methylchrysene-PTEN and 3-methyl-1,8,9-anthracenetriol-PTK2. In molecular dynamics simulations, the 3-methyl-1,8,9-anthracenetriol-PTK2 complex showed lower RMSD, RMSF, radius of gyration, solvent-accessible surface area, and more hydrogen bonds than the 1-methylchrysene-PTEN complex. The 3-methyl-1,8,9-anthracenetriol-PTK2 complex exhibited significantly stronger binding with a binding free energy (ΔG) of - 21.92 kcal/mol compared to the less favourable ΔG of - 10.65 kcal/mol for the 1-methylchrysene-PTEN complex. The consistent and stable binding interaction observed in the 3-methyl-1,8,9-anthracenetriol-PTK2 complex highlights its potential as a potent inhibitor of Focal Adhesion Kinase 1. Consequently, it emerges as a promising lead compound for the development of pancreatic cancer therapeutics. Conversely, the fluctuations observed in the 1-methylchrysene-PTEN complex indicate a less stable binding interaction. This indicates the potential of 3-methyl-1,8,9-anthracenetriol as a primary candidate for pancreatic cancer treatment. These findings improve our grasp of S. singueana's multi-target effects and its promise in addressing pancreatic cancer. Nevertheless, additional in-vivo and in-vitro studies are required to validate their effectiveness and therapeutic potential. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00179-9.
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Affiliation(s)
- Acharya Balkrishna
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar, Uttarakhand 249405 India
- University of Patanjali, Patanjali Yogpeeth, Haridwar, Uttarakhand 249405 India
| | - Darshita Sharma
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar, Uttarakhand 249405 India
| | - Manisha Thapliyal
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar, Uttarakhand 249405 India
| | - Vedpriya Arya
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar, Uttarakhand 249405 India
- University of Patanjali, Patanjali Yogpeeth, Haridwar, Uttarakhand 249405 India
| | - Anurag Dabas
- Patanjali Herbal Research Department, Patanjali Research Institute, Haridwar, Uttarakhand 249405 India
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Tewari D, Rawat K, Bisht A, Almoyad MAA, Wahab S, Chandra S, Pande V. Screening of potential inhibitors of Leishmania major N-myristoyltransferase from Azadirachta indica phytochemicals for leishmaniasis drug discovery by molecular docking, molecular dynamics simulation and density functional theory methods. J Biomol Struct Dyn 2023:1-18. [PMID: 37922151 DOI: 10.1080/07391102.2023.2279281] [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: 07/24/2023] [Accepted: 10/30/2023] [Indexed: 11/05/2023]
Abstract
Leishmaniasis is one of the most neglected parasitic diseases worldwide. The toxicity of current drugs used for its treatment is a major obstacle to their effectiveness, necessitating the discovery and development of new therapeutic agents for better disease control. In Leishmania parasites, N-Myristoyltransferase (NMT) has been identified as a promising target for drug development. Thus, exploring well-known medicinal plants such as Azadirachta indica and their phytochemicals can offer a diverse range of treatment options, potentially leading to disease prevention and control. To assess the therapeutic potential of these compounds, their ADMET prediction and drug-likeness properties were analyzed. The top 4 compounds were selected which had better and significantly low binding energy than the reference molecule QMI. Based on the binding energy score of the top compounds, the results show that Isonimocinolide has the highest binding affinity (-9.8 kcal/mol). In addition, a 100 ns MD simulation of the four best compounds showed that Isonimocinolide and Nimbolide have good stability with LmNMT. These compounds were then subjected to MMPBSA (last 30 ns) calculation to analyze protein-ligand stability and dynamic behavior. Nimbolide and Meldenin showed lowest binding free energy i.e. -84.301 kJ/mol and -91.937 kJ/mol respectively. DFT was employed to calculate the HOMO-LUMO energy gap, global reactivity parameters, and molecular electrostatic potential of all hit molecules. The promising results obtained from MD simulations and MMPBSA analyses provide compelling evidence for the potential use of these compounds in future drug development efforts for the treatment of leishmaniasis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Disha Tewari
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
| | - Kalpana Rawat
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Amisha Bisht
- Department of Botany, P.G. College Bageshwar, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Mohammad Ali Abdullah Almoyad
- Department of Basic Medical Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Khamis Mushyt, Saudi Arabia
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
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Swain SP, Ahamad S, Samarth N, Singh S, Gupta D, Kumar S. In silico studies of alkaloids and their derivatives against N-acetyltransferase EIS protein from Mycobacterium tuberculosis. J Biomol Struct Dyn 2023:1-15. [PMID: 37728544 DOI: 10.1080/07391102.2023.2259487] [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: 12/28/2022] [Accepted: 09/09/2023] [Indexed: 09/21/2023]
Abstract
Antibiotic resistance against Mycobacterium tuberculosis (M.tb.) has been a significant cause of death worldwide. The Enhanced intracellular survival (EIS) protein of the bacteria is an acetyltransferase that multiacetylates aminoglycoside antibiotics, preventing them from binding to the bacterial ribosome. To overcome the EIS-mediated antibiotics resistance of M.tb., we compiled 888 alkaloids and derivatives from five different databases and virtually screened them against the EIS receptor. The compound library was filtered down to 87 compounds, which underwent additional analysis and filtration. Moreover, the top 15 most prominent phytocompounds were obtained after the drug-likeness prediction and ADMET screening. Out of 15, nine compounds confirmed the maximum number of hydrogen bond interactions and reliable binding energies during molecular docking. Additionally, the Molecular dynamics (MD) simulation of nine compounds showed the three most stable complexes, further verified by re-docking with mutated protein. The density functional theory (DFT) calculation was performed to identify the HOMO-LUMO energy gaps of the selected three potential compounds. Finally, our selected top lead compounds i.e., Alkaloid AQC2 (PubChem85634496), Nobilisitine A (ChEbi68116), and N-methylcheilanthifoline (ChEbi140673) demonstrated more favourable outcomes when compared with reference compounds (i.e., 39b and 2i) in all parameters used in this study. Therefore, we anticipate that our findings will help to explore and develop natural compound therapy against multi and extensively drug-resistant strains of M.tb.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Supriya P Swain
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nikhil Samarth
- National Centre for Cell Science, NCCS Complex, Pune, India
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, Pune, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Shailesh Kumar
- Bioinformatics Lab, National Institute of Plant Genome Research (NIPGR), New Delhi, India
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Islam SI, Ahmed SS, Habib N, Ferdous MA, Sanjida S, Mou MJ. High-throughput virtual screening of marine algae metabolites as high-affinity inhibitors of ISKNV major capsid protein: An analysis of in-silico models and DFT calculation to find novel drug molecules for fighting infectious spleen and kidney necrosis virus (ISKNV). Heliyon 2023; 9:e16383. [PMID: 37292285 PMCID: PMC10245175 DOI: 10.1016/j.heliyon.2023.e16383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/27/2023] [Accepted: 05/15/2023] [Indexed: 06/10/2023] Open
Abstract
Infectious Spleen and Kidney Necrosis Virus (ISKNV) is linked to severe infections that cause significant financial losses in global aquaculture. ISKNV enters the host cell through its major capsid protein (MCP), and the resulting infection can lead to mass mortality of fish. Even though several drugs and vaccines are at various stages of clinical testing, none are currently available. Thus, we sought to assess the potential of seaweed compounds to block viral entrance by inhibiting the MCP. The Seaweed Metabolite Database (1110 compounds) was assessed for potential antiviral activity against ISKNV using high throughput virtual screening. Forty compounds with docking scores of ≥8.0 kcal/mol were screened further. The inhibitory molecules BC012, BC014, BS032, and RC009 were predicted by the docking and MD techniques to bind the MCP protein significantly with binding affinities of -9.2, -9.2, -9.9, and -9.4 kcal/mol, respectively. Also, ADMET characteristics of the compounds indicated drug-likeness. According to this study, marine seaweed compounds may operate as viral entrance inhibitors. For their efficacy to be established, in-vitro and in-vivo testing is required.
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Affiliation(s)
- Sk Injamamul Islam
- Department of Fisheries and Marine Bioscience, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Sheikh Sunzid Ahmed
- Department of Botany, Faculty of Biological Sciences, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Nasim Habib
- Department of Fisheries and Marine Bioscience, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Akib Ferdous
- Department of Fisheries and Marine Bioscience, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Saloa Sanjida
- Department of Environmental Science and Technology, Faculty of Applied Science and Technology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Moslema Jahan Mou
- Department of Genetic Engineering and Biotechnology, Faculty of Earth and Life Science, University of Rajshahi, Rajshahi, 00, Bangladesh
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Ranjan S, Gautam A. Pharmaceutical prospects of Silymarin for the treatment of neurological patients: an updated insight. Front Neurosci 2023; 17:1159806. [PMID: 37274201 PMCID: PMC10232807 DOI: 10.3389/fnins.2023.1159806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/17/2023] [Indexed: 06/06/2023] Open
Abstract
Background Silymarin is a polyphenolic flavonoid complex extricated from dried fruits and seeds of the plant Silybum marianum L. Chemically, it is a mixture of flavonolignan complexes consisting of silybin, isosilybin, silychristin, silydianin, a minor quantity of taxifolin, and other polyphenolic compounds, which possess different bio medicinal values. Purpose This review critically looks into the current status, pharmaceutical prospects and limitations of the clinical application of Silymarin for treating neurological disorders. In particular, Silymarin's medicinal properties and molecular mechanisms are focused on providing a better-compiled understanding helpful in its neuro-pharmacological or therapeutic aspects. Methods This review was compiled by the literature search done using three databases, i.e., PubMed (Medline), EMBASE and Science Direct, up to January 2023, using the keywords-Silymarin, neurological disorders, cognitive disorders, Type 2 Diabetes, pharmaceutical prospects and treatment. Then, potentially relevant publications and studies (matching the eligible criteria) were retrieved and selected to explain in this review using PRISMA 2020 (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) study flow chart. Result Since its discovery, it has been widely studied as a hepatoprotective drug for various liver disorders. However, in the last 10-15 years, several research studies have shown its putative neuroprotective nature against various brain disorders, including psychiatric, neurodegenerative, cognitive, metabolic and other neurological disorders. The main underlying neuroprotective mechanisms in preventing and curing such disorders are the antioxidant, anti-inflammatory, anti-apoptotic, pro-neurotrophic and pro-estrogenic nature of the bioactive molecules. Conclusion This review provides a lucid summary of the well-studied neuroprotective effects of Silymarin, its underlying molecular mechanisms and current limitations for its usage during neurological disorders. Finally, we have suggested a future course of action for developing it as a novel herbal drug for the treatment of brain diseases.
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Affiliation(s)
- Shovit Ranjan
- University Department of Zoology, Kolhan University, Chaibasa, Jharkhand, India
| | - Akash Gautam
- Center for Neural and Cognitive Sciences, University of Hyderabad, Hyderabad, India
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Lan Q, Wang L, Jiao F, Lu L, Xia S, Jiang S. Pan-coronavirus fusion inhibitors to combat COVID-19 and other emerging coronavirus infectious diseases. J Med Virol 2023; 95:e28143. [PMID: 36098460 PMCID: PMC9539121 DOI: 10.1002/jmv.28143] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 01/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the currently ongoing coronavirus disease 2019 (COVID-19) pandemic, has posed a serious threat to global public health. Recently, several SARS-CoV-2 variants of concern (VOCs) have emerged and caused numerous cases of reinfection in convalescent COVID-19 patients, as well as breakthrough infections in vaccinated individuals. This calls for the development of broad-spectrum antiviral drugs to combat SARS-CoV-2 and its VOCs. Pan-coronavirus fusion inhibitors, targeting the conserved heptad repeat 1 (HR1) in spike protein S2 subunit, can broadly and potently inhibit infection of SARS-CoV-2 and its variants, as well as other human coronaviruses. In this review, we summarized the most recent development of pan-coronavirus fusion inhibitors, such as EK1, EK1C4, and EKL1C, and highlighted their potential application in combating current COVID-19 infection and reinfection, as well as future emerging coronavirus infectious diseases.
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Affiliation(s)
- Qiaoshuai Lan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and BiosecurityFudan UniversityShanghaiChina
| | - Lijue Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and BiosecurityFudan UniversityShanghaiChina
| | - Fanke Jiao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and BiosecurityFudan UniversityShanghaiChina
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and BiosecurityFudan UniversityShanghaiChina
| | - Shuai Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and BiosecurityFudan UniversityShanghaiChina
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Institute of Infectious Disease and BiosecurityFudan UniversityShanghaiChina
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Nath H, Khataniar A, Bania KK, Mukerjee N, Al-Hussain SA, Zaki MEA, Rajkhowa S. Nano-functionalization and evaluation of antimicrobial activity of Tinospora cordifolia against the TolB protein of Pseudomonas aeruginosa - An antibacterial and computational study. Front Microbiol 2023; 14:1138106. [PMID: 37113217 PMCID: PMC10126308 DOI: 10.3389/fmicb.2023.1138106] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/15/2023] [Indexed: 04/29/2023] Open
Abstract
Introduction Antibacterial drug resistance, brought on by the overuse of antibiotics, is one of the biggest threats to human health. It is crucial to consider cutting-edge strategies, such as herbal remedies, to control multidrug-resistant (MDR) bacteria. Methods This study evaluated the phytochemical, antioxidant and antibacterial properties of the various Tinospora cordifolia extracts. Functionalization of the isolated active compound was done using gold (Au) and silver (Ag) nanoparticles (NPs). Further, to understand the interaction of the isolated class, Cordifolisides, with its target, various in-silico methods were used. Results and Discussion The plant was reported from the Charaideo district of Assam, whose methanolic stem extract showed the maximum activity towards the nosocomial pathogen Pseudomonas aeruginosa. Consequently, the active compound was isolated and characterized as belonging to the class Cordifoliside using NMR. The AuNPs and AgNPs functionalized isolates showed enhanced antimicrobial activity against P. aeruginosa compared to the unfunctionalized isolate. The most reactive compound, Cordifoliside C was determined using Density Functional Theory (DFT) analysis, whose interactions with the TolB protein were studied using molecular docking methods, which revealed good binding interactions of Cordifoliside C with the TolB protein. Conclusion This study offers enormous potential for drug design and might be used as a pipeline to address the urgent problem of multidrug-resistance in bacteria. Graphical Abstract.
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Affiliation(s)
- Himporna Nath
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam, India
| | - Ankita Khataniar
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam, India
| | - Kusum K. Bania
- Department of Chemical Sciences, Tezpur University, Tezpur, Assam, India
| | - Nobendu Mukerjee
- Department of Microbiology, West Bengal State University, West Bengal, Kolkata, India
- Department of Health Sciences, Novel Global Community Educational Foundation, Hebersham, NSW, Australia
| | - Sami A. Al-Hussain
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Magdi E. A. Zaki
- Department of Chemistry, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
- *Correspondence: Magdi E. A. Zaki,
| | - Sanchaita Rajkhowa
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam, India
- Sanchaita Rajkhowa,
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Budipramana K, Sangande F. Molecular docking-based virtual screening: Challenges in hits identification for Anti-SARS-Cov-2 activity. PHARMACIA 2022. [DOI: 10.3897/pharmacia.69.e89812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) requires finding new drugs or repurposing drugs for clinical use. Molecular docking belongs to structure-based drug design providing a fast method for identifying the hit compounds with antiviral activity against SARS-Cov-2. However, the weakness of the docking method is compounded by the limited crystallographic information and comparison drugs due to the novelty of this virus can present challenges in identifying hits of anti-SARS-Cov-2. In the current review, we highlighted several aspects, especially those related to the target structure, docking validation, and virtual hit selection, that need to be considered to obtain reliable docking results. Here, we discussed several cases pertaining to the issue highlighted and approaches that could be used to solve them.
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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Essential oil nebulization in mild COVID-19(EONCO): Early phase exploratory clinical trial. J Ayurveda Integr Med 2022; 13:100626. [PMID: 35813974 PMCID: PMC9257088 DOI: 10.1016/j.jaim.2022.100626] [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: 02/17/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/22/2022] Open
Abstract
Background Medications studied for therapeutic benefits in coronavirus disease 2019 (COVID-19) have produced inconclusive efficacy results except for steroids. Objective A prospective randomized open-label, parallel-arm Phase I/II clinical trial was planned to compare essential oil (EO) blend versus placebo nebulization in mild COVID-19. Methods A Phase I safety evaluation was carried out in a single ascending and multiple ascending dose study designs. We assessed Phase II therapeutic efficacy on COVID-19 and general respiratory symptoms on days 0, 3, 5, 7, 10, and 14 on the predesigned case record form. Viremia was evaluated on day 0, day 5, and day 10. Results Dose-limiting toxicities were not reached with the doses, frequencies, and duration studied, thus confirming the formulation's preliminary safety. General respiratory symptoms (p < 0.001), anosmia (p < 0.05), and dysgeusia (p < 0.001) benefited significantly with the use of EO blend nebulization compared to placebo. Symptomatic COVID-19 participants with mild disease did not show treatment benefits in terms of symptomatic relief (p = 1.0) and viremia clearance (p = 0.74) compared to the placebo. EO blend was found to be associated with the reduced evolution of symptoms in previously asymptomatic reverse transcription polymerase chain reaction (RT-PCR)-positive study participants (p = 0.034). Conclusion EO nebulization appears to be a safer add-on symptomatic relief approach for mild COVID-19. However, the direct antiviral action of the EO blend needs to be assessed with different concentrations of combinations of individual phytochemicals in the EO blend.
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Molecular docking and dynamics studies of Nicotinamide Riboside as a potential multi-target nutraceutical against SARS-CoV-2 entry, replication, and transcription: A new insight. J Mol Struct 2022; 1247:131394. [PMID: 34483364 PMCID: PMC8404146 DOI: 10.1016/j.molstruc.2021.131394] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/17/2022]
Abstract
The highly contagious Coronavirus Disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which is a newborn infectious member of the dangerous beta-coronaviruses (β-CoVs) following SARS and MERS‐CoVs, can be regarded as the most significant issue afflicting the whole world shortly after December 2019. Considering CoVs as RNA viruses with a single-stranded RNA genome (+ssRNA), the critical viral enzyme RNA dependent RNA polymerase (RdRp) is a promising therapeutic target for the potentially fatal infection COVID-19. Nicotinamide riboside (NR), which is a naturally occurring analogue of Niacin (vitamin B3), is expected to have therapeutic effects on COVID-19 due to its super close structural similarity to the proven RdRp inhibitors. Thus, at the first phase of the current molecular docking and dynamics simulation studies, we targeted SARS-CoV-2 RdRp. On the next phase, SARS-CoV RdRp, human Angiotensin-converting enzyme 2, Inosine-5’-monophosphate dehydrogenase, and the SARS-CoV-2 Structural Glycoproteins Spike, Nonstructural viral protein 3-Chymotrypsin-like protease, and Papain-like protease were targeted using the docking simulation to find other possible antiviral effects of NR serendipitously. In the current study, the resulted scores from molecular docking and dynamics simulations as the primary determinative factor as well as the observed reliable binding modes have demonstrated that Nicotinamide Riboside and its active metabolite NMN can target human ACE2 and IMPDH, along with the viral Spro, Mpro, PLpro, and on top of all, RdRp as a potential competitive inhibitor.
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Deciphering the pharmacological potentials of Aganosma cymosa (Roxb.) G. Don using in vitro and computational methods. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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In silico study of some selective phytochemicals against a hypothetical SARS-CoV-2 spike RBD using molecular docking tools. Comput Biol Med 2021. [DOI: 10.1016/j.compbiomed.2021.104818
expr 849028860 + 881472580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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Nag A, Paul S, Banerjee R, Kundu R. In silico study of some selective phytochemicals against a hypothetical SARS-CoV-2 spike RBD using molecular docking tools. Comput Biol Med 2021; 137:104818. [PMID: 34481181 PMCID: PMC8401086 DOI: 10.1016/j.compbiomed.2021.104818] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 02/07/2023]
Abstract
Background This world is currently witnessing a pandemic outbreak of ‘COVID-19′ caused by a positive-strand RNA virus ‘SARS-CoV-2’. Millions have succumbed globally to the disease, and the numbers are increasing day by day. The viral genome enters into the human host through interaction between the spike protein (S) and host angiotensin-converting enzyme-2 (ACE2) proteins. S is the common target for most recently rolled-out vaccines across regions. A recent surge in single/multiple mutations in S region is of great concern as it may escape vaccine induced immunity. So far, the treatment regime with repurposed drugs has not been too successful. Hypothesis Natural compounds are capable of targeting mutated spike protein by binding to its active site and destabilizing the spike-host ACE2 interaction. Materials and methods A hypothetical mutated spike protein was constructed by incorporating twelve different mutations from twelve geographical locations simultaneously into the receptor-binding domain (RBD) and docked with ACE2 and seven phytochemicals namely allicin, capsaicin, cinnamaldehyde, curcumin, gingerol, piperine and zingeberene. Molecular Dynamic (MD) simulation and Principal Component Analysis (PCA) were finally used for validation of the docking results. Result The docking results showed that curcumin and piperine were most potent to bind ACE2, mutated spike, and mutated spike-ACE2 complex, thereby restricting viral entry. ADME analysis also proved their drug candidature. The docking complexes were found to be stable by MD simulation. Conclusion This result provides a significant insight about the phytochemicals' role, namely curcumin and piperine, as the potential therapeutic entities against mutated spike protein of SARS-CoV-2.
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Affiliation(s)
- Anish Nag
- Department of Life Sciences, CHRIST (Deemed to Be University), Bangalore 560029, India
| | - Subhabrata Paul
- School of Biotechnology, Presidency University, Canal Bank Rd, DG Block, Action Area 1D, New Town, West Bengal 700156, India
| | - Ritesh Banerjee
- School of Biological and Environmental Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Rita Kundu
- Department of Botany, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, India.
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