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Saif MZ, Esha NJI, Quayum ST, Rahman S, Al-Gawati MA, Alsowygh G, Albrithen H, Alodhayb AN, Poirier RA, Uddin KM. Investigating the potential of 6-substituted 3-formyl chromone derivatives as anti-diabetic agents using in silico methods. Sci Rep 2024; 14:13221. [PMID: 38851807 PMCID: PMC11162442 DOI: 10.1038/s41598-024-63237-y] [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: 08/12/2023] [Accepted: 05/27/2024] [Indexed: 06/10/2024] Open
Abstract
In exploring nature's potential in addressing diabetes-related conditions, this study investigates the therapeutic capabilities of 3-formyl chromone derivatives. Utilizing in silico methodologies, we focus on 6-substituted 3-formyl chromone derivatives (1-16) to assess their therapeutic potential in treating diabetes. The research examined the formyl group at the chromone's C-3 position. ADMET, biological activities, were conducted along with B3LYP calculations using 3 different basis sets. The analogues were analyzed based on their parent structure obtained from PubChem. The HOMO-LUMO gap confirmed the bioactive nature of the derivatives, NBO analysis was performed to understand the charge transfer. PASS prediction revealed that 3-formyl chromone derivatives are potent aldehyde oxidase inhibitors, insulin inhibitors, HIF1A expression inhibitors, and histidine kinase. Molecular docking studies indicated that the compounds had a strong binding affinity with proteins, including CAD, BHK, IDE, HIF-α, p53, COX, and Mpro of SARS-CoV2. 6-isopropyl-3-formyl chromone (4) displayed the highest affinity for IDE, with a binding energy of - 8.5 kcal mol-1. This result outperformed the affinity of the reference standard dapagliflozin (- 7.9 kcal mol-1) as well as two other compounds that target human IDE, namely vitexin (- 8.3 kcal mol-1) and myricetin (- 8.4 kcal mol-1). MD simulations were revealed RMSD value between 0.2 and 0.5 nm, indicating the strength of the protein-ligand complex at the active site.
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Affiliation(s)
- Minhaz Zabin Saif
- Department of Biochemistry and Microbiology, North South University, Bashundhara,, Dhaka, 1217, Bangladesh
| | - Nusrat Jahan Ikbal Esha
- Department of Biochemistry and Microbiology, North South University, Bashundhara,, Dhaka, 1217, Bangladesh
| | - Syeda Tasnim Quayum
- Department of Biochemistry and Microbiology, North South University, Bashundhara,, Dhaka, 1217, Bangladesh
| | - Shofiur Rahman
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, 11451, Riyadh, Saudi Arabia.
| | - Mahmoud A Al-Gawati
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Ghadah Alsowygh
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Hamad Albrithen
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, 11451, Riyadh, Saudi Arabia
- Research Chair for Tribology, Surface, and Interface Sciences, Department of Physics and Astronomy, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Abdullah N Alodhayb
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, 11451, Riyadh, Saudi Arabia.
- Research Chair for Tribology, Surface, and Interface Sciences, Department of Physics and Astronomy, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia.
| | - Raymond A Poirier
- Department of Chemistry, Memorial University, St. John's, Newfoundland, A1B 3X7, Canada.
| | - Kabir M Uddin
- Department of Biochemistry and Microbiology, North South University, Bashundhara,, Dhaka, 1217, Bangladesh.
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Quayum ST, Esha NJI, Siraji S, Abbad SSA, Alsunaidi ZH, Almatarneh MH, Rahman S, Alodhayb AN, Alibrahim KA, Kawsar SM, Uddin KM. Exploring the effectiveness of flavone derivatives for treating liver diseases: Utilizing DFT, molecular docking, and molecular dynamics techniques. MethodsX 2024; 12:102537. [PMID: 38299040 PMCID: PMC10828815 DOI: 10.1016/j.mex.2023.102537] [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: 11/01/2023] [Accepted: 12/24/2023] [Indexed: 02/02/2024] Open
Abstract
In exploring nature's potential in addressing liver-related conditions, this study investigates the therapeutic capabilities of flavonoids. Utilizing in silico methodologies, we focus on flavone and its analogs (1-14) to assess their therapeutic potential in treating liver diseases. Molecular change calculations using density functional theory (DFT) were conducted on these compounds, accompanied by an evaluation of each analog's physiochemical and biochemical properties. The study further assesses these flavonoids' binding effectiveness and locations through molecular docking studies against six target proteins associated with human cancer. Tropoflavin and taxifolin served as reference drugs. The structurally modified flavone analogs (1-14) displayed a broad range of binding affinities, ranging from -7.0 to -9.4 kcal mol⁻¹, surpassing the reference drugs. Notably, flavonoid (7) exhibited significantly higher binding affinities with proteins Nrf2 (PDB:1 × 2 J) and DCK (PDB:1 × 2 J) (-9.4 and -8.1 kcal mol⁻¹) compared to tropoflavin (-9.3 and -8.0 kcal mol⁻¹) and taxifolin (-9.4 and -7.1 kcal mol⁻¹), respectively. Molecular dynamics (MD) simulations revealed that the docked complexes had a root mean square deviation (RMSD) value ranging from 0.05 to 0.2 nm and a root mean square fluctuation (RMSF) value between 0.35 and 1.3 nm during perturbation. The study concludes that 5,7-dihydroxyflavone (7) shows substantial promise as a potential therapeutic agent for liver-related conditions. However, further validation through in vitro and in vivo studies is necessary. Key insights from this study include:•Screening of flavanols and their derivatives to determine pharmacological and bioactive properties using ADMET, molinspiration, and pass prediction analysis.•Docking of shortlisted flavone derivatives with proteins having essential functions.•Analysis of the best protein-flavonoid docked complexes using molecular dynamics simulation to determine the flavonoid's efficiency and stability within a system.
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Affiliation(s)
- Syeda Tasnim Quayum
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Nusrat Jahan Ikbal Esha
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Siam Siraji
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Sanaa S. Al Abbad
- Department of Chemistry, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Zainab H.A. Alsunaidi
- Department of Chemistry, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | | | - Shofiur Rahman
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah N. Alodhayb
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khuloud A. Alibrahim
- Department of Chemistry, Princess Nora bint Abdulrahman University, College of Science, Riyadh, Al Riyadh, 11671, Saudi Arabia
| | - Sarkar M.A. Kawsar
- Lab of Carbohydrate and Nucleoside Chemistry, Department of Chemistry, University of Chittagong, Chittagong 4331, Bangladesh
| | - Kabir M. Uddin
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
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Dehghan Z, Mirmotalebisohi SA, Mozafar M, Sameni M, Saberi F, Derakhshanfar A, Moaedi J, Zohrevand H, Zali H. Deciphering the similarities and disparities of molecular mechanisms behind respiratory epithelium response to HCoV-229E and SARS-CoV-2 and drug repurposing, a systems biology approach. Daru 2024; 32:215-235. [PMID: 38652363 PMCID: PMC11087451 DOI: 10.1007/s40199-024-00507-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 02/08/2024] [Indexed: 04/25/2024] Open
Abstract
PURPOSE Identifying the molecular mechanisms behind SARS-CoV-2 disparities and similarities will help find new treatments. The present study determines networks' shared and non-shared (specific) crucial elements in response to HCoV-229E and SARS-CoV-2 viruses to recommend candidate medications. METHODS We retrieved the omics data on respiratory cells infected with HCoV-229E and SARS-CoV-2, constructed PPIN and GRN, and detected clusters and motifs. Using a drug-gene interaction network, we determined the similarities and disparities of mechanisms behind their host response and drug-repurposed. RESULTS CXCL1, KLHL21, SMAD3, HIF1A, and STAT1 were the shared DEGs between both viruses' protein-protein interaction network (PPIN) and gene regulatory network (GRN). The NPM1 was a specific critical node for HCoV-229E and was a Hub-Bottleneck shared between PPI and GRN in HCoV-229E. The HLA-F, ADCY5, TRIM14, RPF1, and FGA were the seed proteins in subnetworks of the SARS-CoV-2 PPI network, and HSPA1A and RPL26 proteins were the seed in subnetworks of the PPI network of HCOV-229E. TRIM14, STAT2, and HLA-F played the same role for SARS-CoV-2. Top enriched KEGG pathways included cell cycle and proteasome in HCoV-229E and RIG-I-like receptor, Chemokine, Cytokine-cytokine, NOD-like receptor, and TNF signaling pathways in SARS-CoV-2. We suggest some candidate medications for COVID-19 patient lungs, including Noscapine, Isoetharine mesylate, Cycloserine, Ethamsylate, Cetylpyridinium, Tretinoin, Ixazomib, Vorinostat, Venetoclax, Vorinostat, Ixazomib, Venetoclax, and epoetin alfa for further in-vitro and in-vivo investigations. CONCLUSION We suggested CXCL1, KLHL21, SMAD3, HIF1A, and STAT1, ADCY5, TRIM14, RPF1, and FGA, STAT2, and HLA-F as critical genes and Cetylpyridinium, Cycloserine, Noscapine, Ethamsylate, Epoetin alfa, Isoetharine mesylate, Ribavirin, and Tretinoin drugs to study further their importance in treating COVID-19 lung complications.
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Affiliation(s)
- Zeinab Dehghan
- Department of Comparative Biomedical Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Amir Mirmotalebisohi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Mozafar
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Marzieh Sameni
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Saberi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amin Derakhshanfar
- Department of Comparative Biomedical Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
- Center of Comparative and Experimental Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Javad Moaedi
- Center of Comparative and Experimental Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Zohrevand
- Student Research Committee, Department of Biomedical Engineering and Medical Physics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Biomedical Engineering and Medical Physics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hakimeh Zali
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Uddin KM, Meem MH, Akter M, Rahman S, Al-Gawati MA, Alarifi N, Albrithen H, Alodhayb A, Poirier RA, Bhuiyan MH. Design, synthesis, and bioevaluation of novel unsaturated cyanoacetamide derivatives: In vitro and in silico exploration. MethodsX 2024; 12:102691. [PMID: 38660042 PMCID: PMC11041845 DOI: 10.1016/j.mex.2024.102691] [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: 11/06/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
In this study, we synthesized novel α,β-unsaturated 2-cyanoacetamide derivatives (1-5) using microwave-assisted Knoevenagel condensation. Characterization of these compounds was carried out using FTIR and 1H NMR spectroscopy. We then evaluated their in vitro antibacterial activity against both gram-positive and gram-negative pathogenic bacteria. Additionally, we employed in silico methods, including ADMET prediction and density functional theory (DFT) calculations of molecular orbital properties, to investigate these cyanoacetamide derivatives (1-5). Molecular docking was used to assess the binding interactions of these derivatives (1-5) with seven target proteins (5MM8, 4NZZ, 7FEQ, 5NIJ, ITM2, 6SE1, and 5GVZ) and compared them to the reference standard tyrphostin AG99. Notably, derivative 5 exhibited the most favorable binding affinity, with a binding energy of -7.7 kcal mol-1 when interacting with the staphylococcus aureus (PDB:5MM8), while also meeting all drug-likeness criteria. Additionally, molecular dynamics simulations were carried out to evaluate the stability of the interaction between the protein and ligand, utilizing parameters such as Root-Mean-Square Deviation (RMSD), Root-Mean-Square Fluctuation (RMSF), Radius of Gyration (Rg), and Principal Component Analysis (PCA). A 50 nanosecond molecular dynamics (MD) simulation was performed to investigate stability further, incorporating RMSD and RMSF analyses on compound 5 within the active binding site of the modeled protein across different temperatures (300, 305, 310, and 320 K). Among these temperatures, compound 5 exhibited an RMSD value ranging from approximately 0.2 to 0.3 nm at 310 K (body temperature) with the 5MM8 target, which differed from the other temperature conditions. The in silico results suggest that compound 5 maintained significant conformational stability throughout the 50 ns simulation period. It is consistent with its low docking energy and in vitro findings concerning α,β-unsaturated cyanoacetamides. Key insights from this study include:•The creation of innovative α,β-unsaturated 2-cyanoacetamide derivatives (1-5) employing cost-effective, licensed, versatile, and efficient software for both in silico and in vitro assessment of antibacterial activity.•Utilization of FTIR and NMR techniques for characterizing compounds 1-5.
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Affiliation(s)
- Kabir M. Uddin
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Mehnaz Hossain Meem
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1217, Bangladesh
| | - Mokseda Akter
- Bioorganic and Medicinal Chemistry Laboratory, Department of Chemistry, University of Chittagong, Chattogram 4331, Bangladesh
| | - Shofiur Rahman
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mahmoud A. Al-Gawati
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nahed Alarifi
- Research Chair for Tribology, Surface, and Interface Sciences, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Hamad Albrithen
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
- Research Chair for Tribology, Surface, and Interface Sciences, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah Alodhayb
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
- Research Chair for Tribology, Surface, and Interface Sciences, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Raymond A. Poirier
- Department of Chemistry, Memorial University, St. John's, Newfoundland A1B 3 × 7, Canada
| | - Md. Mosharef H. Bhuiyan
- Bioorganic and Medicinal Chemistry Laboratory, Department of Chemistry, University of Chittagong, Chattogram 4331, Bangladesh
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5
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Zaman B, Mostafa I, Hassan T, Ahmed S, Esha NJI, Chowdhury FA, Bosu T, Chowdhury HN, Mallick A, Islam MS, Sharmin A, Uddin KM, Hossain MM, Rahman M. Tolperisone hydrochloride improves motor functions in Parkinson's disease via MMP-9 inhibition and by downregulating p38 MAPK and ERK1/2 signaling cascade. Biomed Pharmacother 2024; 174:116438. [PMID: 38513594 DOI: 10.1016/j.biopha.2024.116438] [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: 12/06/2023] [Revised: 03/12/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024] Open
Abstract
The mitogen-activated protein kinase (MAPK) signaling pathway, particularly the p38 MAPK and ERK1/2, has been implicated in the pathogenesis of Parkinson's disease (PD). Recent studies have shown that MAPK signaling pathway can influence the expression of matrix metalloproteinase 9 (MMP-9), known for its involvement in various physiological and pathological processes, including neurodegenerative diseases. This study explores the modulation of MMP-9 expression via the MAPK/ERK signaling cascade and its potential therapeutic implications in the context of PD-associated motor dysfunction. Here, tolperisone hydrochloride (TL), a muscle relaxant that blocks voltage-gated sodium and calcium channels, was used as a treatment to observe its effect on MAPK signaling and MMP-9 expression. Rotenone (RT) exposure in mice resulted in a significant reduction in substantia nigra and primary motor cortex neurons, which were further evidenced by impairments in motor function. When TL was administered, neuron count was restored (89.0 ± 4.78 vs 117.0 ± 4.46/mm2), and most of the motor dysfunction was alleviated. Mechanistically, TL reduced the protein expression of phospho-p38MAPK (1.06 fold vs 1.00 fold) and phospho-ERK1/2 (1.16 fold vs 1.02 fold), leading to the inhibition of MAPK signaling, as well as reduced MMP-9 concentrations (2.76 ± 0.10 vs 1.94 ± 0.10 ng/mL) in the process of rescuing RT-induced neuronal cell death and motor dysfunction. Computational analysis further revealed TL's potential inhibitory properties against MMP-9 along with N and L-type calcium channels. These findings shed light on TL's neuroprotective effects via MMP-9 inhibition and MAPK signaling downregulation, offering potential therapeutic avenues for PD-associated motor dysfunction.
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Affiliation(s)
- Bushra Zaman
- Department of Pharmaceutical Sciences, North South University, Bashundhara, Dhaka 1229, Bangladesh; Department of Neurobiology and Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Irona Mostafa
- Department of Pharmaceutical Sciences, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Tazree Hassan
- Department of Pharmaceutical Sciences, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Shamim Ahmed
- Department of Pharmaceutical Sciences, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Nusrat Jahan Ikbal Esha
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Fowzia Afsana Chowdhury
- Department of Pharmaceutical Sciences, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Tory Bosu
- Department of Pharmaceutical Sciences, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Humayra Noor Chowdhury
- Department of Pharmaceutical Sciences, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Anup Mallick
- Department of Pharmaceutical Sciences, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Mm Shanjid Islam
- Department of Pharmaceutical Sciences, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Ayesha Sharmin
- Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka 1000, Bangladesh
| | - Kabir M Uddin
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Md Mainul Hossain
- Department of Biochemistry and Microbiology, North South University, Bashundhara, Dhaka 1229, Bangladesh
| | - Mahbubur Rahman
- Department of Pharmaceutical Sciences, North South University, Bashundhara, Dhaka 1229, Bangladesh.
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Meem MH, Yusuf SB, Al Abbad SS, Rahman S, Al-Gawati M, Albrithen H, Alodhayb AN, Uddin KM. Exploring the anticancer and antibacterial potential of naphthoquinone derivatives: a comprehensive computational investigation. Front Chem 2024; 12:1351669. [PMID: 38449478 PMCID: PMC10914998 DOI: 10.3389/fchem.2024.1351669] [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: 12/06/2023] [Accepted: 01/30/2024] [Indexed: 03/08/2024] Open
Abstract
This study investigates the potential of 2-(4-butylbenzyl)-3-hydroxynaphthalene-1,4-dione (11) and its 12 derivatives as anticancer and biofilm formation inhibitors for methicillin-resistant staphylococcus aureus using in silico methods. The study employed various computational methods, including molecular dynamics simulation molecular docking, density functional theory, and global chemical descriptors, to evaluate the interactions between the compounds and the target proteins. The docking results revealed that compounds 9, 11, 13, and ofloxacin exhibited binding affinities of -7.6, -7.9, -7.5, and -7.8 kcal mol-1, respectively, against peptide methionine sulfoxide reductase msrA/msrB (PDB: 3E0M). Ligand (11) showed better inhibition for methicillin-resistant staphylococcus aureus msrA/msrB enzyme. The complex of the 3E0M-ligand 11 remained highly stable across all tested temperatures (300, 305, 310, and 320 K). Principal Component Analysis (PCA) was employed to evaluate the behavior of the complex at various temperatures (300, 305, 310, and 320 K), demonstrating a total variance of 85%. Convergence was confirmed by the eigenvector's cosine content value of 0.43, consistently displaying low RMSD values, with the minimum observed at 310 K. Furthermore, ligand 11 emerges as the most promising candidate among the compounds examined, showcasing notable potential when considering a combination of in vitro, in vivo, and now in silico data. While the naphthoquinone derivative (11) remains the primary candidate based on comprehensive in silico studies, further analysis using Frontier molecular orbital (FMO) suggests while the Egap value of compound 11 (2.980 eV) and compound 13 (2.975 eV) is lower than ofloxacin (4.369 eV), indicating their potential, so it can be a statement that compound 13 can also be investigated in further research.
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Affiliation(s)
- Mehnaz Hossain Meem
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Sumaiya Binte Yusuf
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
| | - Sanaa S. Al Abbad
- Department of Chemistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Shofiur Rahman
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
| | - Mahmoud Al-Gawati
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
- Research Chair for Tribology, Surface, and Interface Sciences, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Hamad Albrithen
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
- Research Chair for Tribology, Surface, and Interface Sciences, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah N. Alodhayb
- Biological and Environmental Sensing Research Unit, King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
- Research Chair for Tribology, Surface, and Interface Sciences, Department of Physics and Astronomy, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Kabir M. Uddin
- Department of Biochemistry and Microbiology, North South University, Dhaka, Bangladesh
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AYKANAT S, TÜRKTAŞ M. Divergent proteomic profiles of opium poppy cultivars. Turk J Biol 2024; 48:80-90. [PMID: 38665780 PMCID: PMC11042869 DOI: 10.55730/1300-0152.2684] [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: 11/06/2023] [Revised: 02/27/2024] [Accepted: 02/06/2024] [Indexed: 04/28/2024] Open
Abstract
We examined the proteomic profiles of three registered opium poppy cultivars (Papaver somniferum L.) with varying alkaloid contents. The study was conducted on both the stem and capsule organs. A high number of differentially expressed proteins (DEPs) were identified between the cultivars and the organs. We analyzed DEPs for their contribution in GO terms and KEGG pathways. The upregulated DEPs were significantly enriched in photosynthesis and translation for morphine-rich and noscapine-rich cultivars, respectively. The data indicated that photosynthesis is crucial for benzylisoquinoline alkaloid (BIA) biosynthesis, but different processes are also effective in morphine and noscapine biosynthesis, which occur at different branches in the biosynthetic pathway. The proteomics profiles revealed that energy demand is more effective in morphine biosynthesis, while translational control plays a leading role in noscapine biosynthesis. This study represents the first report demonstrating organ-based and cultivar-based protein expression differences in mature poppy plants.
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Affiliation(s)
- Setenay AYKANAT
- Department of Biology, Faculty of Science, Gazi University, Ankara,
Turkiye
| | - Mine TÜRKTAŞ
- Department of Biology, Faculty of Science, Gazi University, Ankara,
Turkiye
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8
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Paul I, Roy A, Ray S. Molecular Design of Novel Inhibitor by Targeting IL-6Rα using Combined Pharmacophore and Experimentally Verified Plant Products with Scaffold-Hopping Techniques: A Dual Therapeutic Strategy for COVID-19 and Cancer. Chem Biodivers 2023; 20:e202300806. [PMID: 37967248 DOI: 10.1002/cbdv.202300806] [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: 06/02/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 11/17/2023]
Abstract
The IL-6/IL-6R/gp130 complex serves as a significant indicator of cytokine release syndrome in COVID-19 and chronic inflammation, increasing the risk of cancer. Therefore, we identified IL-6Rα as a potential target to block gp130 interaction. Notably, there has been no reception of approval for an orally available drug to serve this purpose, to date. In this study, we targeted IL-6Rα to inhibit IL-6Rα/gp130 interaction. The selection of the lead candidate L821 involved the amalgamation of three drug discovery approaches. This library was screened employing tertiary structure-based pharmacophore models followed by molecular docking models, scaffold-hopping, MM/PBSA as well as MM/GBSA analysis, and assessments of pKi and ADMET properties. After evaluating the binding interactions with key amino acids, 15 potential ligands were chosen, with the top ligand undergoing further investigation by means of molecular dynamics simulations. Considering the stability of the complexes, the strong interactions observed between ligand and residues of IL-6Rα/gp130, and the favorable binding free energy calculations, L821 emerged as the prime candidate for inhibiting IL-6Rα. Notably, L821 exhibited a docking-based binding affinity of -9.5 kcal/mol. Our study presents L821 as a promising inhibitor for future in vitro analysis, potentially combatting SARS-CoV-2-related cytokine storms and serving as an oncogenic drug therapy.
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Affiliation(s)
- Ishani Paul
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Alankar Roy
- Amity Institute of Biotechnology, Amity University, Kolkata, India
| | - Sujay Ray
- Amity Institute of Biotechnology, Amity University, Kolkata, India
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Farhat N, Khan AU. Repurposing FDA approved drug molecules against A B C classes of β-lactamases: a computational biology and molecular dynamics simulations study. J Biomol Struct Dyn 2023:1-15. [PMID: 37909541 DOI: 10.1080/07391102.2023.2276890] [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: 05/10/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023]
Abstract
β-lactamase are the main resistance factor for β-lactam antibiotics in Gram-negative bacteria. Since β-lactam antibiotics are being utilised as an antimicrobial agents extensively for the past 70 years, a large number of β-lactam-inactivating β-lactamases have been produced by bacteria. Here, we employed a structure-based drug discovery approach to identify and assess the efficacy of a potential medication that might block the β-lactamases which hydrolyse antibiotics. The FDA-approved medications were subjected to virtual screening, molecular docking, molecular dynamics simulations, density functional theory, and covalent docking against the β-lactamases. We identified diosmin, hidrosmin, monoxuritin and solasulfone as β-lactamase inhibitors which are authorised for therapeutic use in humans. These medications interact in a remarkable variety of non-covalent ways with the conserved residues in the substrate-binding pocket of the β-lactamases. Diosmin has been identified as an inhibitor that binds covalently to the NDM-1 a class B metallo-betalactamase. After experimental validation and clinical demonstration, this study offers adequate evidence for the therapeutic use of these drugs for controlling multidrug resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nabeela Farhat
- Medical Microbiology and Molecular Biology Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Lab. Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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10
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Choudhari S, Patil SK, Rathod S. Identification of hits as anti-obesity agents against human pancreatic lipase via docking, drug-likeness, in-silico ADME(T), pharmacophore, DFT, molecular dynamics, and MM/PB(GB)SA analysis. J Biomol Struct Dyn 2023:1-23. [PMID: 37735906 DOI: 10.1080/07391102.2023.2258407] [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: 06/19/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
Obesity, characterized by excessive fat accumulation, is a major health concern. Inhibition of human pancreatic lipase, an enzyme involved in fat digestion, offers a potential strategy for weight loss and obesity treatment. This study aimed to identify polyphenols capable of forming stable complexes with human pancreatic lipase to block its activity. Molecular docking, density functional theory (DFT), molecular dynamics (MD) simulations, and MMPBGBSA calculations were employed to evaluate ligand binding, stability, and energy profiles. Pharmacophore modeling was also performed to identify key structural features for effective inhibition. Virtual screening identified ZINC000015120539, ZINC000000899200, ZINC000001531702, and ZINC000013340267 as potential candidates, exhibiting favorable binding and stable interactions over 100 ns MD simulations. These findings provide insights into the inhibitory potential of selected polyphenols on human pancreatic lipase and support further experimental investigations for obesity treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sujata Choudhari
- Department of Pharmaceutical Chemistry, Sarojini College of Pharmacy, Kolhapur, MS, India
- Department of Pharmaceutics, Ashokrao Mane College of Pharmacy, Peth Vadgaon, MS, India
| | - Sachin Kumar Patil
- Department of Pharmaceutics, Ashokrao Mane College of Pharmacy, Peth Vadgaon, MS, India
| | - Sanket Rathod
- Department of Pharmaceutical Chemistry, Bharati Vidyapeeth College of Pharmacy, Kolhapur, MS, India
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11
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Law SK, Au DCT, Chow WYL, Poon CH, Chow KKC, Zhao Z, Chan SW, Wang Y, Li S. Behavioral Prevention, Treatment, and Rehabilitation of Using Western and Chinese Medicines or Herbal Products among the Public in Response to COVID-19 in Hong Kong: A Cross-Sectional Study. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2023; 2023:5637720. [PMID: 37680699 PMCID: PMC10482558 DOI: 10.1155/2023/5637720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 06/26/2023] [Accepted: 07/19/2023] [Indexed: 09/09/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic occurred in Hong Kong for more than two years. This article conducted a cross-sectional study for participants to investigate the behavioral prevention, treatment, and rehabilitation of using Western medicines or herbal products for COVID-19 in Hong Kong. A questionnaire was designed and performed over 2 weeks from 1 May to 15 May 2022. It consisted of five parts with around 20 questions conducted including sociodemographic information, prevention, treatment, rehabilitation of COVID-19, and also the sources of information. The pattern usage of Chinese or Western medicines for COVID-19 was studied after data collection. 318 people participated in this survey, and only 311 were qualified. The sociodemographic information, e.g., personal educational level, and behavior for the prevention of COVID-19, which included wearing masks (98.7%), using alcohol hand sanitizer (83.0%), washing hands frequently (82.4%), avoiding crowds (53.1%), and staying home more often (50.6%). Western medicines, such as antipyretic drugs, antitussive drugs, and pain reliever drugs, whilst Chinese medicines, such as Lianhua Qingwen Jiaonang, Huoxiang Zhengqi San or Wan, and Nin Jiom Pei Pa Koa, were most commonly used in the treatment and rehabilitation periods of COVID-19. Herbal products, including lemon, honey, ginger, and herbal tea, were used as a daily diet to fight against COVID-19. Based on the result findings, Chinese medicines or herbal products were used during the COVID-19 pandemic, but most of the participants used an unknown Chinese medicine practitioner's prescription and self-administered Chinese medicine. The pattern of Chinese medicines and Western medicines' usage in the prevention, treatment, and rehabilitation of COVID-19 was also investigated; this showed a statistically significant association between the variables according to gender, age, and Chinese or Western medicines for further investigation.
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Affiliation(s)
- Siu Kan Law
- Faculty of Science and Technology, The Technological and Higher Education Institute of Hong Kong, Tsing Yi, New Territories, Hong Kong
| | - Dawn Ching Tung Au
- Faculty of Science and Technology, The Technological and Higher Education Institute of Hong Kong, Tsing Yi, New Territories, Hong Kong
- Hong Kong Chinese Medicine Pharmacists Association, San Po Kong, Hong Kong
| | - Wesley Yeuk Lung Chow
- Faculty of Science and Technology, The Technological and Higher Education Institute of Hong Kong, Tsing Yi, New Territories, Hong Kong
- Hong Kong Chinese Medicine Pharmacists Association, San Po Kong, Hong Kong
| | - Chung Hang Poon
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Kylie Ka Ching Chow
- Faculty of Science and Technology, The Technological and Higher Education Institute of Hong Kong, Tsing Yi, New Territories, Hong Kong
| | - Zhongzhen Zhao
- School of Chinese Medicine, Hong Kong Baptist Univesity, Kowloon Tong, Hong Kong
| | - Shun Wan Chan
- Faculty of Science and Technology, The Technological and Higher Education Institute of Hong Kong, Tsing Yi, New Territories, Hong Kong
| | - Yanping Wang
- School of Nursing and Health Studies, Hong Kong Metropolitan University, Ho Man Tin, Kowloon, Hong Kong
| | - Saimei Li
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
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12
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Al-Dulaimy WYM, Hussein AA, Mahdi MA, Kadhom M. In Vitro Inhibition of Xanthine Oxidase Purified from Arthritis Serum Patients by Nanocurcumin and Artemisinin Active Compounds. Molecules 2023; 28:5124. [PMID: 37446786 DOI: 10.3390/molecules28135124] [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: 05/15/2023] [Revised: 06/18/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Curcumin and artemisinin are commonly used in traditional East Asian medicine. In this study, we investigated the inhibitory effects of these active compounds on xanthine oxidase (XO) using allopurinol as a control. XO was purified from the serum of arthritis patients through ammonium sulfate precipitation (65%) and ion exchange chromatography on diethylaminoethyl (DEAE)-cellulose. The specific activity of the purified enzyme was 32.5 U/mg protein, resulting in a 7-fold purification with a yield of 66.8%. Molecular docking analysis revealed that curcumin had the strongest interaction energy with XO, with a binding energy of -9.28 kcal/mol. The amino acid residues Thr1077, Gln762, Phe914, Ala1078, Val1011, Glu1194, and Ala1079 were located closer to the binding site of curcumin than artemisinin, which had a binding energy of -7.2 kcal/mol. In vitro inhibition assays were performed using nanocurcumin and artemisinin at concentrations of 5, 10, 15, 20, and 25 µg/mL. Curcumin inhibited enzyme activity by 67-91%, while artemisinin had a lower inhibition ratio, which ranged from 40-70% compared to allopurinol as a control.
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Affiliation(s)
| | - Asmaa A Hussein
- Department of Molecular and Medical Biotechnology, College of Biotechnology, Al-Nahrain University, Jadriya, Baghdad 64074, Iraq
| | - Mohammed Asaad Mahdi
- Department of Chemistry, College of Science, University of Diyala, Baquba 32001, Iraq
| | - Mohammed Kadhom
- Department of Environmental Science, College of Energy and Environmental Science, Al-Karkh University of Science, Baghdad 10081, Iraq
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13
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Rathod S, Chavan P, Mahuli D, Rochlani S, Shinde S, Pawar S, Choudhari P, Dhavale R, Mudalkar P, Tamboli F. Exploring biogenic chalcones as DprE1 inhibitors for antitubercular activity via in silico approach. J Mol Model 2023; 29:113. [PMID: 36971900 DOI: 10.1007/s00894-023-05521-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 03/17/2023] [Indexed: 03/28/2023]
Abstract
Cases of drug-resistant tuberculosis (TB) have increased worldwide in the last few years, and it is a major threat to global TB control strategies and the human population. Mycobacterium tuberculosis is a common causative agent responsible for increasing cases of TB and as reported by WHO, approximately, 1.5 million death occurred from TB in 2020. Identification of new therapies against drug-resistant TB is an urgent need to be considered primarily. The current investigation aims to find the potential biogenic chalcone against the potential targets of drug-resistant TB via in silico approach. The ligand library of biogenic chalcones was screened against DprE1. Results of molecular docking and in silico ADMET prediction revealed that ZINC000005158606 has lead-like properties against the targeted protein. Pharmacophore modeling was done to identify the pharmacophoric features and their geometric distance present in ZINC000005158606. The binding stability study performed using molecular dynamics (MD) simulation of the DprE1-ZINC000005158606 complex revealed the conformational stability of the complex system over 100 ns with minimum deviation. Further, the in silico anti-TB sensitivity of ZINC000005158606 was found to be higher as compared to the standards against Mycobacterium tuberculosis. The overall in silico investigation indicated the potential of identified hit to act as a lead molecule against Mycobacterium tuberculosis.
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14
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Rathod S, Shinde K, Porlekar J, Choudhari P, Dhavale R, Mahuli D, Tamboli Y, Bhatia M, Haval KP, Al-Sehemi AG, Pannipara M. Computational Exploration of Anti-cancer Potential of Flavonoids against Cyclin-Dependent Kinase 8: An In Silico Molecular Docking and Dynamic Approach. ACS OMEGA 2023; 8:391-409. [PMID: 36643495 PMCID: PMC9835631 DOI: 10.1021/acsomega.2c04837] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Over the centuries, cancer has been considered one of the significant health threats. It holds the position in the list of deadliest diseases over the globe. In women, breast cancer is the most common among many cancers and is the second most common cancer all over the world, while lung cancer is the first. Cyclin-dependent kinase 8 (CDK8) has been identified as a critical oncogenic driver that is found in breast cancer and associated with tumor progression. Flavonoids were virtually screened against CDK8 using molecular docking, drug-likeness, ADMET prediction, and a molecular dynamics (MD) simulation approach to determine the potential flavonoid structure against CDK8. The results indicated that ZINC000005854718 showed the highest negative binding affinity of -10.7 kcal/mol with the targeted protein and passed all the drug-likeness parameters. Performed molecular dynamics simulation showed that docked complex systems have good conformational stability over 100 ns in different temperatures (298, 300, 305, 310, and 320 K). The comparison between calculated binding free energy via MM/PB(GB)SA methods and binding affinity calculated via molecular docking suggested tight binding of ZINC000005854718 with targeted protein. The results concluded that ZINC000005854718 has drug-like properties with tight and stable binding with the targeted protein.
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Affiliation(s)
- Sanket Rathod
- Department
of Pharmaceutical Chemistry, Bharati Vidyapeeth
College of Pharmacy, Kolhapur 416 013, Maharashtra, India
| | - Ketaki Shinde
- Department
of Quality Assurance Techniques, Poona College of Pharmacy, Bharati Vidyapeeth Deemed University, Pune 411 038, Maharashtra, India
| | - Jaykedar Porlekar
- Department
of Pharmaceutics, Bharati Vidyapeeth College
of Pharmacy, Kolhapur 416 013, Maharashtra, India
| | - Prafulla Choudhari
- Department
of Pharmaceutical Chemistry, Bharati Vidyapeeth
College of Pharmacy, Kolhapur 416 013, Maharashtra, India
| | - Rakesh Dhavale
- Department
of Pharmaceutics, Bharati Vidyapeeth College
of Pharmacy, Kolhapur 416 013, Maharashtra, India
| | - Deepak Mahuli
- Department
of Pharmacology, Bharati Vidyapeeth College
of Pharmacy, Kolhapur 416 013, Maharashtra, India
| | - Yasinalli Tamboli
- Wockhardt
Research Centre, D-4, MIDC, Chikalthana, Aurangabad 431 006, Maharashtra, India
| | - Manish Bhatia
- Department
of Pharmaceutical Chemistry, Bharati Vidyapeeth
College of Pharmacy, Kolhapur 416 013, Maharashtra, India
| | - Kishan P. Haval
- Department
of Chemistry, Dr. Babasaheb Ambedkar Marathwada
University Sub Campus, Osmanabad 413501, Maharashtra, India
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15
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Barati S, Feizabadi F, Khalaj H, Sheikhzadeh H, Jamaati HR, Farajidavar H, Dastan F. Evaluation of noscapine-licorice combination effects on cough relieving in COVID-19 outpatients: A randomized controlled trial. Front Pharmacol 2023; 14:1102940. [PMID: 36873992 PMCID: PMC9981666 DOI: 10.3389/fphar.2023.1102940] [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: 11/19/2022] [Accepted: 02/08/2023] [Indexed: 02/19/2023] Open
Abstract
Background: As February 2023, SARS-CoV-2 is still infecting people and children worldwide. Cough and dyspnea are annoying symptoms almost present in a large proportion of COVID-19 outpatients, and the duration of these symptoms might be long enough to affect the patients' quality of life. Studies have shown positive effects for noscapine plus licorice in the previous COVID-19 trials. This study aimed to assess the effects of the combination of noscapine and licorice-for relieving cough in outpatients with COVID-19. Methods: This randomized controlled trial was conducted on 124 patients at the Dr. Masih Daneshvari Hospital. Participants over 18 years of age with confirmed COVID-19 and cough were allowed to enter the study if the onset of symptoms was less than 5 days. The primary outcome was to assess the response to treatment over 5 days using the visual analogue scale. Secondary outcomes included the assessment of cough severity after 5 days using Cough Symptom Score, as well as the cough-related quality of life and dyspnea relieving. Patients in the noscapine plus licorice group received Noscough® syrup 20 mL every 6 h for 5 days. The control group received diphenhydramine elixir 7 mL every 8 h. Results: By day five, 53 (85.48%) patients in the Noscough® group and 49 (79.03%) patients in the diphenhydramine group had response to treatment. This difference was not statistically significant (p-value = 0.34). The presence of dyspnea was significantly lower in the Noscough® group versus diphenhydramine at day five (1.61% in the Noscough® group vs. 12.9% in the diphenhydramine group; p-value = 0.03). The cough-related quality of life and severity also significantly favored Noscough® syrup (p-values <0.001). Conclusion: Noscapine plus licorice syrup was slightly superior to diphenhydramine in relieving cough symptoms and dyspnea in the COVID-19 outpatients. The severity of cough and cough-related quality of life were also significantly better in the noscapine plus licorice syrup. Noscapine plus licorice may be a valuable treatment in relieving cough in COVID-19 outpatients.
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Affiliation(s)
- Saghar Barati
- Department of Clinical Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Alborz, Iran
| | - Faezeh Feizabadi
- Department of Clinical Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Alborz, Iran
| | - Hakimeh Khalaj
- Department of Clinical Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Alborz, Iran
| | - Hakimeh Sheikhzadeh
- National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Alborz, Iran
| | - Hamid R Jamaati
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases, Tehran, Alborz, Iran
| | - Hirad Farajidavar
- Department of Clinical Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Alborz, Iran
| | - Farzaneh Dastan
- Department of Clinical Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Alborz, Iran.,Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases, Tehran, Alborz, Iran
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16
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Kokulnathan T, Wang TJ, Murugesan T, Anthuvan AJ, Kumar RR, Ahmed F, Arshi N. Structural growth of zinc oxide nanograins on carbon cloth as flexible electrochemical platform for hydroxychloroquine detection. CHEMOSPHERE 2023; 312:137186. [PMID: 36368534 DOI: 10.1016/j.chemosphere.2022.137186] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/25/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
Pharmaceutical pollution that imposes a health threat worldwide is making accurate and rapid detection crucial to prevent adverse effects. Herein, binder-free zinc oxide nanograins on carbon cloth (ZnO NGs@CC) have been synthesized hydrothermally and employed to fabricate a flexible electrochemical sensor for the quantification of hydroxychloroquine (HCQ) that is typical pharmaceutical pollution. The characteristics of ZnO NGs@CC were investigated by various in-depth electron microscopic, spectroscopic and electroanalytical approaches. Compared with the pristine CC platform, the ZnO NGs@CC platform exhibits superior electrochemical performance in detecting HCQ with a large oxidation current at a low over-potential of +0.92 V with respect to the Ag/AgCl (Sat. KCl) reference electrode. With the support of desirable characteristics, the fabricated ZnO NGs@CC-based electrochemical sensor for HCQ detection displays good performances in terms of wide sensing range (0.5-116 μM), low detection limit (0.09 μM), high sensitivity (0.279 μA μM-1 cm-2), and strong selectivity. By the resulting 3D hierarchical nanoarchitecture, ZnO NGs@CC has progressive structural advantages that led to its excellent electrochemical performance in sensing applications. Furthermore, the electrochemical sensor is employed to detect HCQ in biological and environmental samples and also achieves good recovery rates. Thus, the designed ZnO NGs@CC demonstrates admirable electrochemical activity toward HCQ real-time monitoring and would be an excellent electrochemical platform for HCQ sensing.
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Affiliation(s)
- Thangavelu Kokulnathan
- Department of Electro-Optical Engineering, National Taipei University of Technology, Taipei 10608, Taiwan
| | - Tzyy-Jiann Wang
- Department of Electro-Optical Engineering, National Taipei University of Technology, Taipei 10608, Taiwan.
| | - Thangapandian Murugesan
- Department of Materials Science and Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Allen Joseph Anthuvan
- Department of Electro-Optical Engineering, National Taipei University of Technology, Taipei 10608, Taiwan; Nanotech Division, Accubits Invent Pvt. Ltd, Trivandrum 695 592, Kerala, India
| | - Rishi Ranjan Kumar
- Department of Materials Science and Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Faheem Ahmed
- Department of Physics, College of Science, King Faisal University, P.O Box 400, Hofuf, Al-Ahsa 31982, Saudi Arabia
| | - Nishat Arshi
- Department of Basic Sciences, Preparatory Year Deanship, King Faisal University, P.O. Box-400, Al-Ahsa 31982, Saudi Arabia
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17
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Awasthi A, Kumar N, Mishra A, Ravi R, Dalal A, Shankar S, Chandra R. Noscapine-Amino Acid Conjugates Suppress the Progression of Cancer Cells. ACS Pharmacol Transl Sci 2022; 5:1292-1304. [PMID: 36524011 PMCID: PMC9745893 DOI: 10.1021/acsptsci.2c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 11/16/2022]
Abstract
Lung cancer is the leading cause of cancer deaths globally; 1 in 16 people are diagnosed with lung cancer in their lifetime. Microtubules, a critical cytoskeletal assembly, have an essential role in cell division. Interference with the microtubule assembly leads to genetic instability during mitosis and cancer cell death. Currently, available antimitotic drugs such as vincas and taxanes are limited due to side effects such as alopecia, myelosuppression, and drug resistance. Noscapine, an opium alkaloid, is a tubulin-binding agent and can alter the microtubule assembly, causing cancer cell death. Amino acids are fundamental building blocks for protein synthesis, making them essential for the biosynthesis of cancer cells. However, the ability of amino acids in drug transportation has yet to be exploited in developing noscapine analogues as a potential drug candidate for cancer. Hence, in the present study, we have explored the ninth position of noscapine by introducing a hydroxymethylene group using the Blanc reaction and further coupled it with a series of amino acids to construct five target conjugates in good yields. The synthesized amino acid conjugate molecules were biologically evaluated against the A549 lung cancer cell line, among which the noscapine-tryptophan conjugate showed IC50 = 32 μM, as compared to noscapine alone (IC50 = 73 μM). Morphological changes in cancer cells, cell cycle arrest in the G1 phase, and ethidium bromide/acridine orange staining indicated promising anticancer properties. Molecular docking confirmed strong binding to tubulin, with a score of -41.47 kJ/mol with all 3D coordinates and significant involvement of molecular forces, including the hydrogen bonds and hydrophobic interactions. Molecular dynamics simulations demonstrated a stable binding of noscapine-tryptophan conjugate for a prolonged time (100 ns) with the involvement of free energy through the reaction coordinates analyses, solving the bioavailability of parent noscapine to the body.
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Affiliation(s)
- Amardeep Awasthi
- Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Neeraj Kumar
- Department of Neurology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois60611, United States
| | - Abhijeet Mishra
- Department of Biochemistry, Shivaji College, University of Delhi, Delhi-110027, India
| | - Rangnath Ravi
- Department of Chemistry, Shivaji College, University of Delhi, Delhi-110027, India
| | - Anu Dalal
- Department of Chemistry, Indian Institute of Technology, Delhi, Delhi-110016, India
| | - Saurav Shankar
- Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Ramesh Chandra
- Department of Chemistry, University of Delhi, Delhi-110007, India
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi-110007, India
- Institute of Nano Medical Sciences, University of Delhi, Delhi-110007, India
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18
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Singh MB, Sharma R, Kumar D, Khanna P, Mansi, Khanna L, Kumar V, Kumari K, Gupta A, Chaudhary P, Kaushik N, Choi EH, Kaushik NK, Singh P. An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review. J Infect Public Health 2022; 15:1326-1349. [PMID: 36288640 PMCID: PMC9579205 DOI: 10.1016/j.jiph.2022.10.013] [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: 05/02/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
The first infection case of new coronavirus was reported at the end of 2019 and after then, the cases are reported in all nations across the world in a very short period. Further, the regular news of mutations in the virus has made life restricted with appropriate behavior. To date, a new strain (Omicron and its new subvariant Omicron XE) has brought fear amongst us due to a higher trajectory of increase in the number of cases. The researchers thus started giving attention to this viral infection and discovering drug-like candidates to cure the infections. Finding a drug for any viral infection is not an easy task and takes plenty of time. Therefore, computational chemistry/bioinformatics is followed to get promising molecules against viral infection. Molecular dynamics (MD) simulations are being explored to get drug candidates in a short period. The molecules are screened via molecular docking, which provides preliminary information which can be further verified by molecular dynamics (MD) simulations. To understand the change in structure, MD simulations generated several trajectories such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bonding, and radius of gyration for the main protease (Mpro) of the new coronavirus (nCoV) in the presence of small molecules. Additionally, change in free energy for the formation of complex of Mpro of nCoV with the small molecule can be determined by applying molecular mechanics with generalized born and surface area solvation (MM-GBSA). Thus, the promising molecules can be further explored for clinical trials to combat coronavirus disease-19 (COVID-19).
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Affiliation(s)
- Madhur Babu Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Ritika Sharma
- Department of Biochemistry, University of Delhi, New Delhi, India
| | - Durgesh Kumar
- Department of Chemistry, Maitreyi College, University of Delhi, Delhi, India
| | - Pankaj Khanna
- Department of Chemistry, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Mansi
- University School of Basic and Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Leena Khanna
- University School of Basic and Applied Sciences, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Vinod Kumar
- Special Centre for Nanoscience (SCNS), Jawaharlal Nehru University, New Delhi, India
| | - Kamlesh Kumari
- Department of Zoology, University of Delhi, New Delhi, India
| | - Akanksha Gupta
- Department of Chemistry, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Preeti Chaudhary
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Hwaseong-si 18323, Republic of Korea.
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea.
| | - Prashant Singh
- Department of Chemistry, Atma Ram Sanatan Dharma College, University of Delhi, New Delhi, India.
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19
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Traditional Chinese medicine treatment for COVID-19: An overview of systematic reviews and meta-analyses. JOURNAL OF INTEGRATIVE MEDICINE 2022; 20:416-426. [PMID: 35811240 PMCID: PMC9225921 DOI: 10.1016/j.joim.2022.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 05/06/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19) is a rapidly spreading disease that has caused an extensive burden to the world. Consequently, a large number of clinical trials have examined the efficacy of traditional Chinese medicine (TCM) for treating and preventing COVID-19, with coinciding proliferation of reviews summarizing these studies. OBJECTIVE This study aimed to evaluate the methodological quality and evidence quality of systematic reviews and meta-analyses on the efficacy of TCM. SEARCH STRATEGY Seven electronic databases, including PubMed, Cochrane Library, Web of Science, China National Knowledge Infrastructure, Chongqing VIP, Wanfang Data and SinoMed, were searched for systematic reviews and meta-analyses in October 2021. Search terms such as "Chinese medicine," "Lianhua Qingwen" and "COVID-19" were used. INCLUSION CRITERIA Systematic reviews and meta-analyses of randomized controlled trials that evaluated the efficacy of TCM treatment of COVID-19 were included. DATA EXTRACTION AND ANALYSIS A Measurement Tool to Assess Systematic Reviews Version 2.0 (AMSTAR 2) was used to evaluate the methodological quality. The quality of evidence was graded using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) system. Data extraction and analysis were performed by two reviewers independently. RESULTS There were 17 meta-analyses included in our overview. The intervention group was defined as TCM combined with Western medicine, while the control group was Western medicine alone. The methodological quality of all the included studies was moderate to poor. A total of 89 outcome indicators were evaluated, of which, 8 were rated as moderate quality, 39 as low quality, and 41 as very low quality. Only one outcome measure was graded as being of high quality. The moderate quality of evidence indicated that, for the treatment of COVID-19, the clinical efficacy of TCM in combination with Western medicine was better, in terms of lung recovery, rate of conversion to severe/critical cases, symptom scores, duration of symptoms, mortality, and length of hospital stay. CONCLUSION Evidence from the included studies shows that, compared with conventional Western medical therapy alone, the addition of TCM to COVID-19 treatment may improve clinical outcomes. Overall, the quality of evidence of TCM for COVID-19 was moderate to poor. Meta-analyses of the use of TCM in the treatment of COVID-19 can be used for clinical decision making by accounting for the experiences of clinical experts, medical policies, and other factors.
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Andola P, Pagag J, Laxman D, Guruprasad L. Fragment-based inhibitor design for SARS-CoV2 main protease. Struct Chem 2022; 33:1467-1487. [PMID: 35811782 PMCID: PMC9251026 DOI: 10.1007/s11224-022-01995-z] [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: 03/25/2022] [Accepted: 06/14/2022] [Indexed: 11/28/2022]
Abstract
COVID-19 disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV2) has resulted in tremendous loss of lives across the world and is continuing to do so. Extensive work is under progress to develop inhibitors which can prevent the disease by arresting the virus in its life cycle. One such way is by targeting the main protease of the virus which is crucial for the cleavage and conversion of polyproteins into functional units of polypeptides. In this endeavor, our effort was to identify hit molecule inhibitors for SARS-CoV2 main protease using fragment-based drug discovery (FBDD), based on the available crystal structure of chromene-based inhibitor (PDB_ID: 6M2N). The designed molecules were validated by molecular docking and molecular dynamics simulations. The stability of the complexes was further assessed by calculating their binding free energies, normal mode analysis, mechanical stiffness, and principal component analysis.
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Affiliation(s)
- Priyanka Andola
- School of Chemistry, University of Hyderabad, Hyderabad, 500046 India
| | - Jishu Pagag
- School of Chemistry, University of Hyderabad, Hyderabad, 500046 India
| | - Durgam Laxman
- School of Chemistry, University of Hyderabad, Hyderabad, 500046 India
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21
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Ghahremanian S, Rashidi MM, Raeisi K, Toghraie D. Molecular dynamics simulation approach for discovering potential inhibitors against SARS-CoV-2: A structural review. J Mol Liq 2022; 354:118901. [PMID: 35309259 PMCID: PMC8916543 DOI: 10.1016/j.molliq.2022.118901] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 01/11/2023]
Abstract
Since the commencement of the novel Coronavirus, the disease has quickly turned into a worldwide crisis so that there has been growing attention in discovering possible hit compounds for tackling this pandemic. Discovering standard treatment strategies is a serious challenge because little information is available about this emerged infectious virus. Regarding the high impact of time, applying computational procedures to choose promising drugs from a catalog of licensed medications provides a precious chance for combat against the life-threatening disorder of COVID-19. Molecular dynamics (MD) simulation is a promising approach for assessing the binding affinity of ligand-receptor as well as observing the conformational trajectory of docked complexes over time. Given that many computational studies are performed using MD along with the molecular docking on various candidates as antiviral inhibitors of COVID-19 protease, there is a demand to conduct a comprehensive review of the most important studies to reveal and compare the potential introduced agents that this study covers this defect. In this context, the present review intends to prepare an overview of these studies by considering RMSD, RMSF, radius of gyration, binding free energy, and Solvent-Accessible Surface Area (SASA) as effective parameters for evaluation. The outcomes will offer a road map for adjusting antiviral inhibitors, which can facilitate the selection and development of drug candidates for use in the medical therapy. Finally, the molecular modeling approaches rendered by this study may be valuable for future computational studies.
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Affiliation(s)
- Shabnam Ghahremanian
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, Sichuan, PR China
| | - Mohammad Mehdi Rashidi
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, Sichuan, PR China
- Faculty of Mechanical and Industrial Engineering, Quchan University of Technology, Quchan, Iran
| | - Kimai Raeisi
- Department of Basic Science, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Davood Toghraie
- Department of Mechanical Engineering, Khomeinishahr Branch, Islamic Azad University, Khomeinishahr, Iran
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22
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Molecular Docking as a Potential Approach in Repurposing Drugs Against COVID-19: a Systematic Review and Novel Pharmacophore Models. CURRENT PHARMACOLOGY REPORTS 2022; 8:212-226. [PMID: 35381996 PMCID: PMC8970976 DOI: 10.1007/s40495-022-00285-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 03/14/2022] [Indexed: 12/12/2022]
Abstract
Purpose of Review This article provides a review of the recent literature related to the FDA-approved drugs that had been repurposed as potential drug candidates against COVID-19. Moreover, we performed a quality pharmacophore study for frequently studied targets, namely, the main protease, RNA-dependent RNA polymerase, and spike protein. Recent Findings Ever since the COVID-19 pandemic, the whole spectrum of scientific community is still unable to invent an absolute therapeutic agent for COVID-19. Considering such a fact, drug repurposing strategies seem a truly viable approach to develop novel therapeutic interventions. Summery Drug repurposing explores previously approved drugs of known safety and pharmacokinetics profile for possible new effects, reducing the cost, time, and predicting prospective side effects and drug interactions. COVID-19 virulent machinery appeared similar to other viruses, making antiviral agents widely repurposed in pursuit for curative candidates. Our main protease pharmacophoric study revealed multiple features and could be a probable starting point for upcoming research.
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Inhibitory effects of selected isoquinoline alkaloids against main protease (Mpro) of SARS-CoV-2, in silico study. In Silico Pharmacol 2022; 10:5. [PMID: 35310017 PMCID: PMC8918422 DOI: 10.1007/s40203-022-00122-4] [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: 05/06/2021] [Accepted: 02/22/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global threat. Despite the production of various vaccines and different treatments, finding natural compounds to control COVID-19 is still a challenging task. Isoquinoline alkaloids are naturally occurring compounds known to have some potential antiviral activity. In this study, ten abundant isoquinoline alkaloids with antiviral activity were selected to analyze the preventive effect on COVID-19. A scrutinized evaluation based on Lipinski’s rule showed that one out of ten compounds was toxic. Based on molecular docking analysis using Autodock software one of the best molecules with maximum negative binding energy was selected for further analysis. The Gromacs simulation analysis revealed that Coptisine has more action against active site Mpro of COVID-19. Overall, to make a rational design of various preventive analogues that inhibit the COVID-19, associated in vitro and in vivo analyses are needed to confirm this claim.
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Das S, Singh A, Samanta SK, Singha Roy A. Naturally occurring anthraquinones as potential inhibitors of SARS-CoV-2 main protease: an integrated computational study. Biologia (Bratisl) 2022; 77:1121-1134. [PMID: 35034970 PMCID: PMC8744046 DOI: 10.1007/s11756-021-01004-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/21/2021] [Indexed: 12/18/2022]
Abstract
The novel coronavirus disease (COVID-19) has spread throughout the globe, affecting millions of people. The World Health Organization (WHO) has declared this infectious disease a pandemic. At present, several clinical trials are going on to identify possible drugs for treating this infection. SARS-CoV-2 Mpro is one of the most critical drug targets for the blockage of viral replication. The aim of this study was to identify potential natural anthraquinones that could bind to the active site of SARS-CoV-2 main protease and stop the viral replication. Blind molecular docking studies of 13 anthraquinones and one control drug (Boceprevir) with SARS-CoV-2 Mpro were carried out using the SwissDOCK server, and alterporriol-Q that showed the highest binding affinity towards Mpro were subjected to molecular dynamics simulation studies. This study indicated that several antiviral anthraquinones could prove to be effective inhibitors for SARS-CoV-2 Mpro of COVID-19 as they bind near the active site having the catalytic dyad, HIS41 and CYS145 through non-covalent forces. The anthraquinones showed less inhibitory potential as compared to the FDA-approved drug, boceprevir. Among the anthraquinones studied, alterporriol-Q was found to be the most potent inhibitor of SARS-CoV-2 Mpro. Further, MD simulation studies for Mpro- alterporriol-Q system suggested that alterporriol-Q does not alter the structure of Mpro to a significant extent. Considering the impact of COVID-19, identification of alternate compounds like alterporriol-Q that could inhibit the viral infection will help in accelerating the process of drug discovery.
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Affiliation(s)
- Sourav Das
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong, 793003 India
| | - Anirudh Singh
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, 211012 India
| | - Sintu Kumar Samanta
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, 211012 India
| | - Atanu Singha Roy
- Department of Chemistry, National Institute of Technology Meghalaya, Shillong, 793003 India
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Abdul-Hammed M, Adedotun IO, Falade VA, Adepoju AJ, Olasupo SB, Akinboade MW. Target-based drug discovery, ADMET profiling and bioactivity studies of antibiotics as potential inhibitors of SARS-CoV-2 main protease (M pro). Virusdisease 2021; 32:642-656. [PMID: 34226871 PMCID: PMC8246438 DOI: 10.1007/s13337-021-00717-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/15/2021] [Indexed: 12/24/2022] Open
Abstract
A recent outbreak of a new strain of Coronavirus (SARS-CoV-2) has become a global health burden, which has resulted in deaths. No proven drug has been found to effectively cure this fast-spreading infection, hence the need to explore old drugs with the known profile in tackling this pandemic. A computer-aided drug design approach involving virtual screening was used to obtain the binding scores and inhibiting efficiencies of previously known antibiotics against SARS-CoV-2 main protease (Mpro). The drug-likeness analysis of the repurposed drugs were done using the Molinspiration chemoinformatics tool, while the Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) analysis was carried out using ADMET SAR-2 webserver. Other analyses performed include bioactivities of the repurposed drug as a probable anti-SARS-CoV-2 agent and oral bioavailability analyses among others. The results were compared with those of drugs currently involved in clinical trials in the ongoing pandemic. Although antibiotics have been speculated to be of no use in the treatment of viral infections, literature has emerged lately to reveal the antiviral potential and immune-boosting ability of antibiotics. This study identified Tarivid and Ciprofloxacin with binding affinities of - 8.3 kcal/mol and - 8.1 kcal/mol, respectively as significant inhibitors of SARS-CoV-2 (Mpro) with better pharmacokinetics, drug-likeness and oral bioavailability, bioactivity properties, ADMET properties and inhibitory strength compared to Remdesivir (- 7.6 kcal/mol) and Azithromycin (- 6.3 kcal/mol). These observations will provide insight for further research (clinical trial) in the cure and management of COVID-19.
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Affiliation(s)
- Misbaudeen Abdul-Hammed
- Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
| | - Ibrahim Olaide Adedotun
- Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
| | - Victoria Adeola Falade
- Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
| | - Adewusi John Adepoju
- Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
| | | | - Modinat Wuraola Akinboade
- Department of Biochemistry, Ladoke Akintola University of Technology, P.M.B. 4000, Ogbomoso, Nigeria
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Barazorda-Ccahuana HL, Nedyalkova M, Mas F, Madurga S. Unveiling the Effect of Low pH on the SARS-CoV-2 Main Protease by Molecular Dynamics Simulations. Polymers (Basel) 2021; 13:3823. [PMID: 34771379 PMCID: PMC8587287 DOI: 10.3390/polym13213823] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 12/19/2022] Open
Abstract
(1) Background: Main Protease (Mpro) is an attractive therapeutic target that acts in the replication and transcription of the SARS-CoV-2 coronavirus. Mpro is rich in residues exposed to protonation/deprotonation changes which could affect its enzymatic function. This work aimed to explore the effect of the protonation/deprotonation states of Mpro at different pHs using computational techniques. (2) Methods: The different distribution charges were obtained in all the evaluated pHs by the Semi-Grand Canonical Monte Carlo (SGCMC) method. A set of Molecular Dynamics (MD) simulations was performed to consider the different protonation/deprotonation during 250 ns, verifying the structural stability of Mpro at different pHs. (3) Results: The present findings demonstrate that active site residues and residues that allow Mpro dimerisation was not affected by pH changes. However, Mpro substrate-binding residues were altered at low pHs, allowing the increased pocket volume. Additionally, the results of the solvent distribution around Sγ, Hγ, Nδ1 and Hδ1 atoms of the catalytic residues Cys145 and His41 showed a low and high-water affinity at acidic pH, respectively. It which could be crucial in the catalytic mechanism of SARS-CoV-2 Mpro at low pHs. Moreover, we analysed the docking interactions of PF-00835231 from Pfizer in the preclinical phase, which shows excellent affinity with the Mpro at different pHs. (4) Conclusion: Overall, these findings indicate that SARS-CoV-2 Mpro is highly stable at acidic pH conditions, and this inhibitor could have a desirable function at this condition.
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Affiliation(s)
- Haruna Luz Barazorda-Ccahuana
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08028 Barcelona, Spain;
- Vicerrectorado de Investigación, Universidad Católica de Santa María, Arequipa 04000, Peru
| | - Miroslava Nedyalkova
- Department of Inorganic Chemistry, University of Sofia “St. Kl. Okhridski”, 1164 Sofia, Bulgaria;
| | - Francesc Mas
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08028 Barcelona, Spain;
| | - Sergio Madurga
- Materials Science and Physical Chemistry Department & Research Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08028 Barcelona, Spain;
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Azad I, Khan T, Maurya AK, Irfan Azad M, Mishra N, Alanazi AM. Identification of Severe Acute Respiratory Syndrome Coronavirus-2 inhibitors through in silico structure-based virtual screening and molecular interaction studies. J Mol Recognit 2021; 34:e2918. [PMID: 34132436 PMCID: PMC8420533 DOI: 10.1002/jmr.2918] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 01/10/2023]
Abstract
The novel coronavirus Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) or COVID-19 has caused a worldwide pandemic. The fatal virus has affected the health of human beings as well as the socio-economic situation all over the world. To date, no concrete medicinal solution has been proposed to combat the viral infection, calling for an urgent, strategic, and cost-effective drug development approach that may be achievable by applying targeted computational and virtual screening protocols. Immunity is the body's natural defense against disease-causing pathogens, which can be boosted by consuming plant-based or natural food products. Active constituents derived from natural sources also scavenge the free radicals and have anti-inflammatory activities. Herbs and spices have been used for various medicinal purposes. In this study, 2,96 365 natural and synthetic derivatives (ligands) belonging to 102 classes of compounds were obtained from PubChem and assessed on Lipinski's parameters for their potential bioavailability. Out of all the derivatives, 3254 obeyed Lipinski's rule and were virtually screened. The 115 top derivatives were docked against SARS-CoV-2, SARS-CoV, MERS-CoV, and HCoV-HKV1 main proteases (Mpro s) as receptors using AutoDock Vina, AutoDock, and iGEMDOCK 2.1. The lowest binding energy was exhibited by ligands 2 and 6 against all the four Mpro s. The molecular dynamic simulation was also performed with ligand 6 using the GROMACS package. Good bioactivity scores, absorption, distribution, metabolism, excretion, and toxicity profile and drug-like pharmacokinetic parameters were also obtained. Hydroxychloroquine was used as the control drug.
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Affiliation(s)
- Iqbal Azad
- Department of ChemistryIntegral UniversityLucknowIndia
| | - Tahmeena Khan
- Department of ChemistryIntegral UniversityLucknowIndia
| | - Akhilesh Kumar Maurya
- Department of Applied SciencesIndian Institute of Information Technology AllahabadPrayagrajIndia
| | | | - Nidhi Mishra
- Department of Applied SciencesIndian Institute of Information Technology AllahabadPrayagrajIndia
| | - Amer M. Alanazi
- Department of Pharmaceutical ChemistryCollege of Pharmacy, King Saud UniversityRiyadhSaudi Arabia
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Thirumalaisamy R, Aroulmoji V, Iqbal MN, Deepa M, Sivasankar C, Khan R, Selvankumar T. Molecular insights of hyaluronic acid-hydroxychloroquine conjugate as a promising drug in targeting SARS-CoV-2 viral proteins. J Mol Struct 2021; 1238:130457. [PMID: 33867575 PMCID: PMC8041731 DOI: 10.1016/j.molstruc.2021.130457] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 12/16/2022]
Abstract
In-silico anti-viral activity of Hydroxychloroquine (HCQ) and its Hyaluronic Acid-derivative (HA-HCQ) towards different SARS-CoV-2 protein molecular targets were studied. Four different SARS-CoV-2 proteins molecular target i.e., three different main proteases and one helicase were chosen for In-silico anti-viral analysis. The HA-HCQ conjugates exhibited superior binding affinity and interactions with all the screened SAR-CoV-2 molecular target proteins with the exception of a few targets. The study also revealed that the HA-HCQ conjugate has multiple advantages of efficient drug delivery to its CD44 variant isoform receptors of the lower respiratory tract, highest interactive binding affinity with SARS-CoV-2 protein target. Moreover, the HA-HCQ drug conjugate possesses added advantages of good biodegradability, biocompatibility, non-toxicity and non-immunogenicity. The prominent binding ability of HA-HCQ conjugate towards Mpro (PDB ID 5R82) and Helicase (PDB ID 6ZSL) target protein as compared with HCQ alone was proven through MD simulation analysis. In conclusion, our study suggested that further in-vitro and in-vivo examination of HA-HCQ drug conjugate will be useful to establish a promising early stage antiviral drug for the novel treatment of COVID-19.
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Affiliation(s)
- R. Thirumalaisamy
- Department of Biotechnology, Mahendra Arts & Science College (Autonomous), Namakkal (Dt.) - 637 501, Tamil Nadu, India,Department of Biotechnology, Sona College of Arts and Science, Salem (Dt.) -636 005, Tamil Nadu, India
| | - V. Aroulmoji
- Centre for Research & Development, Mahendra Engineering College (Autonomous), Mallasamudram, Namakkal (Dt.) - 637 503, Tamil Nadu, India,Corresponding author
| | - Muhammad Nasir Iqbal
- Department of Biosciences, COMSATS University, Islamabad Campus, Islamabad, Pakistan
| | - M. Deepa
- Postgraduate and Research Department of Chemistry, Muthurangam Govt. Arts College, Vellore, India
| | - C. Sivasankar
- Catalysis and Energy Laboratory, Department of Chemistry, Pondicherry University, R.V.Nagar, Kalapet, Pondicherry, 605014, India
| | - Riaz Khan
- Rumsey, Old Bath Road, Sonning, Berkshire, RG4 6TA, England, United Kingdom
| | - T. Selvankumar
- Department of Biotechnology, Mahendra Arts & Science College (Autonomous), Namakkal (Dt.) - 637 501, Tamil Nadu, India
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Rahnama S, Azimzadeh Irani M, Amininasab M, Ejtehadi MR. S494 O-glycosylation site on the SARS-CoV-2 RBD affects the virus affinity to ACE2 and its infectivity; a molecular dynamics study. Sci Rep 2021; 11:15162. [PMID: 34312429 PMCID: PMC8313699 DOI: 10.1038/s41598-021-94602-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 07/13/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is a strain of Coronavirus family that caused the ongoing pandemic of COVID-19. Several studies showed that the glycosylation of virus spike (S) protein and the Angiotensin-Converting Enzyme 2 (ACE2) receptor on the host cell is critical for the virus infectivity. Molecular Dynamics (MD) simulations were used to explore the role of a novel mutated O-glycosylation site (D494S) on the Receptor Binding Domain (RBD) of S protein. This site was suggested as a key mediator of virus-host interaction. By exploring the dynamics of three O-glycosylated models and the control systems of unglcosylated S4944 and S494D complexes, it was shown that the decoration of S494 with elongated O-glycans results in stabilized interactions on the direct RBD-ACE2. Calculation of the distances between RBD and two major H1, H2 helices of ACE2 and the interacting pairs of amino acids in the interface showed that the elongated O-glycan maintains these interactions by forming several polar contacts with the neighbouring residues while it would not interfere in the direct binding interface. Relative binding free energy of RBD-ACE2 is also more favorable in the O-glycosylated models with longer glycans. The increase of RBD binding affinity to ACE2 depends on the size of attached O-glycan. By increasing the size of O-glycan, the RBD-ACE2 binding affinity will increase. Hence, this crucial factor must be taken into account for any further inhibitory approaches towards RBD-ACE2 interaction.
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Affiliation(s)
- Shadi Rahnama
- Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, 14588, Iran
| | | | - Mehriar Amininasab
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
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Discovery of ( E)- N-(4-cyanobenzylidene)- 6-fluoro- 3-hydroxypyrazine-2 -carboxamide (cyanorona-20): the first potent and specific anti-COVID-19 drug. CHEMICAL PAPERS 2021; 75:4669-4685. [PMID: 34025012 PMCID: PMC8126404 DOI: 10.1007/s11696-021-01640-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/02/2021] [Indexed: 01/18/2023]
Abstract
Abstract Specific inhibition of the viral RNA-dependent RNA polymerase (RdRp) of the newly-emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a very promising strategy for developing highly potent medicines for coronavirus disease 2019 (COVID-19). However, almost all of the reported viral RdRp inhibitors (either repurposed drugs or new antiviral agents) lack selectivity against the SARS-CoV-2 RdRp. Herein, I discovered a new favipiravir derivative, (E)-N-(4-cyanobenzylidene)-6-fluoro-3-hydroxypyrazine-2-carboxamide (cyanorona-20), as the first potent SARS-CoV-2 inhibitor with very high selectivity (209- and 45-fold more potent than favipiravir and remdesivir, respectively). Based on the significant reduction in the in vitro SARS-CoV-2 replication/copies, strong computational cyanorona-20 ligand-RdRp protein interactions, and anti-RdRp activity of the parent favipiravir drug, SARS-CoV-2 inhibition is thought to be mediated through the coronaviral-2 RdRp inhibition. This promising selective anti-COVID-19 compound is also, to the best of our knowledge, the first bioactive derivative of favipiravir, the known antiinfluenza and antiviral drug. This new nucleoside analog was designed, synthesized, characterized, computationally studied (through pharmacokinetic calculations along with computational molecular modeling and prediction), and biologically evaluated for its anti-COVID-19 activities (through a validated in vitro anti-COVID-19 assay). The results of the biological assay showed that cyanorona-20 surprisingly exhibited very significant anti-COVID-19 activity (anti-SARS-CoV-2 EC50 = 0.45 μM), and, in addition, it could be also a very promising lead compound for the design of new anti-COVID-19 agents. Cyanorona-20 is a new favipiravir derivative with promise for the treatment of SARS-CoV-2 infection. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s11696-021-01640-9.
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Mengist HM, Dilnessa T, Jin T. Structural Basis of Potential Inhibitors Targeting SARS-CoV-2 Main Protease. Front Chem 2021; 9:622898. [PMID: 33889562 PMCID: PMC8056153 DOI: 10.3389/fchem.2021.622898] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/04/2021] [Indexed: 12/23/2022] Open
Abstract
The Coronavirus disease-19 (COVID-19) pandemic is still devastating the world causing significant social, economic, and political chaos. Corresponding to the absence of globally approved antiviral drugs for treatment and vaccines for controlling the pandemic, the number of cases and/or mortalities are still rising. Current patient management relies on supportive treatment and the use of repurposed drugs as an indispensable option. Of a crucial role in the viral life cycle, ongoing studies are looking for potential inhibitors to the main protease (Mpro) of severe acute respiratory syndrome Coronavirus -2 (SARS-CoV-2) to tackle the pandemic. Although promising results have been achieved in searching for drugs inhibiting the Mpro, work remains to be done on designing structure-based improved drugs. This review discusses the structural basis of potential inhibitors targeting SARS-CoV-2 Mpro, identifies gaps, and provides future directions. Further, compounds with potential Mpro based antiviral activity are highlighted.
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Affiliation(s)
- Hylemariam Mihiretie Mengist
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of innate immunity and chronic disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Department of Medical Laboratory Science, College of Health Science, Debre Markos University, Debre Markos, Ethiopia
| | - Tebelay Dilnessa
- Department of Medical Laboratory Science, College of Health Science, Debre Markos University, Debre Markos, Ethiopia
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of innate immunity and chronic disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Science, Shanghai, China
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Chugh H, Awasthi A, Agarwal Y, Gaur RK, Dhawan G, Chandra R. A comprehensive review on potential therapeutics interventions for COVID-19. Eur J Pharmacol 2021; 890:173741. [PMID: 33227287 PMCID: PMC7677683 DOI: 10.1016/j.ejphar.2020.173741] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/15/2022]
Abstract
COVID-19 is an infectious respiratory disease caused by SARS-CoV-2, a new beta coronavirus that emerged in Wuhan, China. Being primarily a respiratory disease, it is highly transmissible through both direct and indirect contacts. It displays a range of symptoms in different individuals and thus has been grouped into mild, moderate, and severe diseases. The virus utilizes spike proteins present on its surface to recognize ACE-2 receptors present on the host cells to enter the cell cytoplasm and replicate. The viral invasion of cells induces damage response, pyroptosis, infiltration of immune cells, expression of pro-inflammatory cytokines (cytokine storm), and activation of the adaptive immune system. Depending on viral load and host factors like age and underlying medical conditions, the immune responses mounted against SARS-CoV-2 may cause acute respiratory distress syndrome (ARDS), multiple organ failure, and death. In this review, we specify and justify both viral and host therapeutic targets that can be modulated to relieve the symptoms and treat the disease. Furthermore, we discuss vaccine development in the time of pandemic and the most promising vaccine candidates by far, according to WHO database. Finally, we discuss the conventional re-purposed drugs and potential alternative treatments as adjuvants.
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Affiliation(s)
- Heerak Chugh
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Amardeep Awasthi
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Yashi Agarwal
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Rajesh K Gaur
- Division of Medical Oncology, University of Southern California, CA 90033, USA
| | - Gagan Dhawan
- Department of Biomedical Sciences, Acharya Narendra Dev College, University of Delhi, India
| | - Ramesh Chandra
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India; Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India.
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Chugh H, Awasthi A, Agarwal Y, Gaur RK, Dhawan G, Chandra R. A comprehensive review on potential therapeutics interventions for COVID-19. Eur J Pharmacol 2021. [PMID: 33227287 DOI: 10.1016/j.ejphar.2020.17374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
COVID-19 is an infectious respiratory disease caused by SARS-CoV-2, a new beta coronavirus that emerged in Wuhan, China. Being primarily a respiratory disease, it is highly transmissible through both direct and indirect contacts. It displays a range of symptoms in different individuals and thus has been grouped into mild, moderate, and severe diseases. The virus utilizes spike proteins present on its surface to recognize ACE-2 receptors present on the host cells to enter the cell cytoplasm and replicate. The viral invasion of cells induces damage response, pyroptosis, infiltration of immune cells, expression of pro-inflammatory cytokines (cytokine storm), and activation of the adaptive immune system. Depending on viral load and host factors like age and underlying medical conditions, the immune responses mounted against SARS-CoV-2 may cause acute respiratory distress syndrome (ARDS), multiple organ failure, and death. In this review, we specify and justify both viral and host therapeutic targets that can be modulated to relieve the symptoms and treat the disease. Furthermore, we discuss vaccine development in the time of pandemic and the most promising vaccine candidates by far, according to WHO database. Finally, we discuss the conventional re-purposed drugs and potential alternative treatments as adjuvants.
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Affiliation(s)
- Heerak Chugh
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Amardeep Awasthi
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Yashi Agarwal
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Rajesh K Gaur
- Division of Medical Oncology, University of Southern California, CA 90033, USA
| | - Gagan Dhawan
- Department of Biomedical Sciences, Acharya Narendra Dev College, University of Delhi, India
| | - Ramesh Chandra
- Drug Discovery & Development Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India; Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India.
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Click triazole as a linker for drug repurposing against SARs-CoV-2: A greener approach in race to find COVID-19 therapeutic. CURRENT RESEARCH IN GREEN AND SUSTAINABLE CHEMISTRY 2021; 4. [PMCID: PMC7874918 DOI: 10.1016/j.crgsc.2021.100064] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
WHO holding the hands of the scientific commune and trying to repurpose the drugs against the SARS-CoV-2. The robust scientific data has illustrated the probable mechanistic path of SARS-CoV-2 entry and action in damaging the cells. Which further has demonstrated Hydroxychloroquine (HCQ; antimalarial drug) as promising drug therapeutic; apart from certain setbacks to be an excellent agent in treating COVID-19. In the present study, we have explored the derivatives of HCQ, conjugated with bioactive agents by the virtue of sustainably modified clicked triazole approach as potential Mpro enzyme inhibitors. In results, we found the chloroquinetrithaizone has strong binding affinity for the Mpro enzyme of SARS CoV-2. We also found the stable binding of CQ-TrOne conjugate with Mpro by MD simulation studies through RMSD, RMSF and Rg calculations. Moreover, in conjunction with critical reaction coordinate outcomes, binding MMGB/PB energy profile depicted the efficient binding affinity towards Mpro. Also, DFT analyses illustrated the stability of the repurposed drug under study. These significant outcomes have shown high potency of compounds and can be further assessed through in vitro and in vivo assays to develop the effective drug against COVID-19.
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Rajapaksha H, Perera BT, Meepage J, Perera RT, Dissanayake C. Mitigate the cytokine storm due to the severe COVID-19: A computational investigation of possible allosteric inhibitory actions on IL-6R and IL-1R using selected phytochemicals. ACTA ACUST UNITED AC 2020. [DOI: 10.5155/eurjchem.11.4.351-363.2043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The novel corona virus 2019 (COVID 19) is growing at an increasing rate with high mortality. Meanwhile, the cytokine storm is the most dangerous and potentially life-threatening event related to COVID 19. Phyto-compounds found in existing Ayurveda drugs have the ability to inhibit the Interleukin 6 (IL-6R) and Interleukin 1 (IL-1R) receptors. IL-6R and IL-1R receptors involve in cytokine storm and recognition of phytochemicals with proven safety profiles could open a pathway to the development of the most effective drugs against cytokine storm. In this study, we intend to perform an in silico investigation of effective phyto compounds, which can be isolated from selected medicinal herbs to avoid cytokine storm, inhibiting the IL-6 and IL-1 receptor binding process. An extensive literature survey followed by virtual screening was carried out to identify phytochemicals with potential anti-hyper-inflammatory action. Flexible docking was conducted for validated models of IL-1R and IL-6R-α with the most promising phytochemicals at possible allosteric sites using AutoDock Vina. Molecular dynamics (MD) studies were conducted for selected protein-ligand complexes using LARMD server and conformational changes were evaluated. According to the results, taepeenin J had Gibbs energy (ΔG) of -10.85 kcal/mol towards IL-1R but had limited oral bioavailability. MD analysis revealed that taepeenin J can cause significant conformational movements in IL-1R. Nortaepeenin B showed a ΔG of -8.5 kcal/mol towards IL-6R-α with an excellent oral bioavailability. MD analysis predicted that it can cause significant conformational movements in IL-6R-α. Hence, the evaluated phytochemicals are potential candidates for further in vitro studies for the development of medicine against cytokine storm on behalf of SARS-COV-2 infected patients.
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Affiliation(s)
- Harindu Rajapaksha
- Department of Chemistry, Faculty of Science, University of Kelaniya, Dalugama, 11 300, Sri Lanka
| | - Bingun Tharusha Perera
- Department of Chemistry, Faculty of Science, University of Kelaniya, Dalugama, 11 300, Sri Lanka
| | - Jeewani Meepage
- Department of Chemistry, Faculty of Science, University of Kelaniya, Dalugama, 11 300, Sri Lanka
| | - Ruwan Tharanga Perera
- Graduate Studies Division, Gampaha Wickramarachchi Ayurveda Institute, University of Kelaniya, Yakkala, 11870, Sri Lanka
| | - Chithramala Dissanayake
- Department of Cikitsa, Gampaha Wickramarachchi Ayurveda Institute, University of Kelaniya, Yakkala, 11870, Sri Lanka
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