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Jangra J, Bajad NG, Singh R, Kumar A, Singh SK. Identification of novel potential cathepsin-B inhibitors through pharmacophore-based virtual screening, molecular docking, and dynamics simulation studies for the treatment of Alzheimer's disease. Mol Divers 2024:10.1007/s11030-024-10821-z. [PMID: 38517648 DOI: 10.1007/s11030-024-10821-z] [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: 11/28/2023] [Accepted: 02/03/2024] [Indexed: 03/24/2024]
Abstract
Cathepsin B is a cysteine protease lysosomal enzyme involved in several physiological functions. Overexpression of the enzyme enhances its proteolytic activity and causes the breakdown of amyloid precursor protein (APP) into neurotoxic amyloid β (Aβ), a characteristic hallmark of Alzheimer's disease (AD). Therefore, inhibition of the enzyme is a crucial therapeutic aspect for treating the disease. Combined structure and ligand-based drug design strategies were employed in the current study to identify the novel potential cathepsin B inhibitors. Five different pharmacophore models were developed and used for the screening of the ZINC-15 database. The obtained hits were analyzed for the presence of duplicates, interfering PAINS moieties, and structural similarities based on Tanimoto's coefficient. The molecular docking study was performed to screen hits with better target binding affinity. The top seven hits were selected and were further evaluated based on their predicted ADME properties. The resulting best hits, ZINC827855702, ZINC123282431, and ZINC95386847, were finally subjected to molecular dynamics simulation studies to determine the stability of the protein-ligand complex during the run. ZINC123282431 was obtained as the virtual lead compound for cathepsin B inhibition and may be a promising novel anti-Alzheimer agent.
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Affiliation(s)
- Jatin Jangra
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Nilesh Gajanan Bajad
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Ravi Singh
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Ashok Kumar
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Sushil Kumar Singh
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India.
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Jawarkar RD, Zaki MEA, Al-Hussain SA, Al-Mutairi AA, Samad A, Mukerjee N, Ghosh A, Masand VH, Ming LC, Rashid S. QSAR modeling approaches to identify a novel ACE2 inhibitor that selectively bind with the C and N terminals of the ectodomain. J Biomol Struct Dyn 2024; 42:2550-2569. [PMID: 37144753 DOI: 10.1080/07391102.2023.2205948] [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: 01/25/2023] [Accepted: 04/17/2023] [Indexed: 05/06/2023]
Abstract
Due to the high rates of drug development failure and the massive expenses associated with drug discovery, repurposing existing drugs has become more popular. As a result, we have used QSAR modelling on a large and varied dataset of 657 compounds in an effort to discover both explicit and subtle structural features requisite for ACE2 inhibitory activity, with the goal of identifying novel hit molecules. The QSAR modelling yielded a statistically robust QSAR model with high predictivity (R2tr=0.84, R2ex=0.79), previously undisclosed features, and novel mechanistic interpretations. The developed QSAR model predicted the ACE2 inhibitory activity (PIC50) of 1615 ZINC FDA compounds. This led to the detection of a PIC50 of 8.604 M for the hit molecule (ZINC000027990463). The hit molecule's docking score is -9.67 kcal/mol (RMSD 1.4). The hit molecule revealed 25 interactions with the residue ASP40, which defines the N and C termini of the ectodomain of ACE2. The HIT molecule conducted more than thirty contacts with water molecules and exhibited polar interaction with the ARG522 residue coupled with the second chloride ion, which is 10.4 nm away from the zinc ion. Both molecular docking and QSAR produced comparable findings. Moreover, MD simulation and MMGBSA studies verified docking analysis. The MD simulation showed that the hit molecule-ACE2 receptor complex is stable for 400 ns, suggesting that repurposed hit molecule 3 is a viable ACE2 inhibitor.
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Affiliation(s)
- Rahul D Jawarkar
- Department of Medicinal Chemistry and Drug Discovery, Dr Rajendra Gode Institute of Pharmacy, Amravati, Maharashtra, India
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Sami A Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Aamal A Al-Mutairi
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdul Samad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Nobendu Mukerjee
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, Kolkata, India
| | - Arabinda Ghosh
- Microbiology Division, Department of Botany, Gauhati University, Guwahati, India
| | - Vijay H Masand
- Department of Chemistry, Vidyabharati Mahavidyalalya, Amravati, Maharashtra, India
| | - Long Chiau Ming
- School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia
| | - Summya Rashid
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
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Cyril AC, Ali NM, Nelliyulla Parambath A, Vazhappilly CG, Jan RK, Karuvantevida N, Aburamadan H, Lozon Y, Radhakrishnan R. Nigella sativa and its chemical constituents: pre-clinical and clinical evidence for their potential anti-SARS-CoV-2 effects. Inflammopharmacology 2024; 32:273-285. [PMID: 37966624 DOI: 10.1007/s10787-023-01385-9] [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: 05/01/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused over 500 million reported cases of COVID-19 worldwide with relatively high morbidity and mortality. Although global vaccination drive has helped control the pandemic, the newer variant of the virus still holds the world in ransom. Several medicinal herbs with antiviral properties have been reported, and one such promising herb is Nigella sativa (NS). Recent molecular docking, pre-clinical, and clinical studies have shown that NS extracts may have the potential to prevent the entry of coronaviruses into the host cell as well as to treat and manage COVID-19 symptoms. Several active compounds from NS, such as nigelledine, α-hederin, dithymoquinone (DTQ), and thymoquinone (TQ), have been proposed as excellent ligands to target angiotensin-converting enzyme 2 (ACE2 receptors) and other targets on host cells as well as the spike protein (S protein) on SARS-CoV-2. By binding to these target proteins, these ligands could potentially prevent the binding between ACE2 and S protein. Though several articles have been published on the promising therapeutic role of NS and its constituents against SARS-CoV-2 infection, in this review, we consolidate the published information on NS and SARS-CoV-2, focusing on pre-clinical in silico studies as well as clinical trials reported between 2012 and 2023.
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Affiliation(s)
- Asha Caroline Cyril
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
| | - Najma Mohamed Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Anagha Nelliyulla Parambath
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Cijo George Vazhappilly
- Department of Biotechnology, American University of Ras Al Khaimah, Ras Al Khaimah, United Arab Emirates
| | - Reem Kais Jan
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Haneen Aburamadan
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Yosra Lozon
- Dubai Pharmacy College for Girls, Dubai, United Arab Emirates
| | - Rajan Radhakrishnan
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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4
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Okamoto C, Ando K. Molecular dynamics simulation analysis of structural dynamic cross correlation induced by odorant hydrogen-bonding in mouse eugenol ol- factory receptor. Biophys Physicobiol 2024; 21:e210007. [PMID: 38803338 PMCID: PMC11128758 DOI: 10.2142/biophysico.bppb-v21.0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/16/2024] [Indexed: 05/29/2024] Open
Abstract
Structural fluctuations and dynamic cross-correlations in the mouse eugenol olfactory receptor (Olfr73) were studied by molecular dynamics (MD) simulation to characterize the dynamic response of the protein upon ligand binding. The initial structure was generated by the artificial intelligence tool AlphaFold2 due to the current lack of experimental data. We focused on the hydrogen (H) bond of the odorant eugenol to Ser113, Asn207, and Tyr260 of the receptor protein, the importance of which has been suggested by previous experimental studies. The H-bond was not observed in docking simulations, but in subsequent MD simulations the H-bond to Ser113 was formed in 2-4 ns. The lifetime of the H-bond was in the range of 1-20 ns. On the trajectory with the most stable (20 ns) H-bond, the structural fluctuation of the α-carbon atoms of the receptor main chain was studied by calculating the root mean square fluctuations, the dynamic cross-correlation map, and the time-dependent dynamic cross-correlation. The analysis suggested a correlation transfer pathway Ser113 → Phe182 → (Leu259 or Tyr260) → Tyr291 induced by the ligand binding with a time scale of 4-6 ns.
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Affiliation(s)
- Chisato Okamoto
- Department of Information and Sciences, Tokyo Woman’s Christian University, Tokyo 167-8585, Japan
| | - Koji Ando
- Department of Information and Sciences, Tokyo Woman’s Christian University, Tokyo 167-8585, Japan
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Dhanasekaran S, Pushparaj Selvadoss P, Sundar Manoharan S, Jeyabalan S, Devi Rajeswari V. Revealing anti-fungal potential of plant-derived bioactive therapeutics in targeting secreted aspartyl proteinase (SAP) of Candida albicans: a molecular dynamics approach. J Biomol Struct Dyn 2024; 42:710-724. [PMID: 37021476 DOI: 10.1080/07391102.2023.2196703] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/17/2023] [Indexed: 04/07/2023]
Abstract
Candida species have established themselves as a major source of nosocomial infections. Increased expression of secreted aspartyl proteinases (SAP5) plays a crucial role in the pathogenesis of Candida species. Phytotherapeutics continue to serve as a viable resource for discovering novel antifungal agents. Hence the main aim of the present investigation is to explore the possible inhibitory role of the selected bioactive molecules against the SAP5 enzyme of C. albicans using in silico approach. Molecular docking and dynamic simulations were utilized to predict the binding affinity of the lead molecules using the AutoDock and Gromacs in-silico screening tools. Results of preliminary docking simulations show that the compounds hesperidin, vitexin, berberine, adhatodine, piperine, and chlorogenic acid exhibit significant interactions with the core catalytic residues of the target protein. The best binding ligands (hesperidin, vitexin, fluconazole) were subjected to molecular dynamics (MD) and essential dynamics of the trajectories. Results of the MD simulation confirm that the ligand-protein complexes became more stable from 20 ns until 100 ns. The calculated residue-level contributions to the interaction energy along a steady simulation trajectory of all three hits (hesperidin (-132.720 kJ/mol), vitexin (-83.963 kJ/mol) and fluconazole (-98.864 kJ/mol)) ensure greater stability of the leads near the catalytic region. Essential dynamics of PCA and DCCM analysis signifies that the binding of hesperidin and vitexin created a more structurally stable environment in the protein target. The overall outcomes of this study clearly emphasize that the bioactive therapeutics found in medicinal herbs may have remarkable scope in managing Candida infection.
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Affiliation(s)
| | | | | | - Srikanth Jeyabalan
- Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, India
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6
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Prabha S, Chauhan P, Warkare S, Pandey KM. A computational investigation of potential plant-based bioactive compounds against drug-resistant Staphylococcus aureus of multiple target proteins. J Biomol Struct Dyn 2023:1-19. [PMID: 38133950 DOI: 10.1080/07391102.2023.2297009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023]
Abstract
Drug-resistant Staphylococcus aureus (DRSA) poses a significant global health threat, like bacteremia, endocarditis, skin, soft tissue, bone, and joint infections. Nowadays, the resistance against conventional drugs has been a prompt and focused medical concern. The present study aimed to explore the inhibitory potential of plant-based bioactive compounds (PBBCs) against effective target proteins using a computational approach. We retrieved and verified 22 target proteins associated with DRSA and conducted a screening process that involved testing 87 PBBCs. Molecular docking was performed between screened PBBCs and reference drugs with selected target proteins via AutoDock. Subsequently, we filtered the target proteins and top PBBCs based on their binding affinity scores. Furthermore, molecular dynamic simulation was carried out through GROMACS for a duration of 100 ns, and the binding free energy was calculated using the gmx_MMPBSA. The result showed consistent hydrogen bonding interactions among the amino acid residues Ser 149, Arg 151, Thr 165, Thr 216, Glu 239, Ser 240, Ile 14, as well as Asn 18, Gln 19, Lys 45, Thr 46, Tyr 109, with their respective target proteins of the penicillin-binding protein and dihydrofolate reductase complex. Additionally, we assessed the pharmacokinetic properties of screened PBBCs via SwissADME and AdmetSAR. The findings suggest that β-amyrin, oleanolic acid, kaempferol, quercetin, and friedelin have the potential to inhibit the selected target proteins. In future research, both in vitro and in vivo, experiments will be needed to establish these PBBCs as potent antimicrobial drugs for DRSA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sarit Prabha
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | | | - Sudeesh Warkare
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Khushhali M Pandey
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, India
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7
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Ramzan A, Yousaf MA, Rashid MU, Basheera S, Malkani N. In-silico prediction of TGF-β1 non-synonymous variants and their impact on binding affinity to Fresolimumab. J Biomol Struct Dyn 2023:1-14. [PMID: 37817532 DOI: 10.1080/07391102.2023.2268198] [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: 05/02/2023] [Accepted: 10/03/2023] [Indexed: 10/12/2023]
Abstract
TGF-β1 is a potent immunoregulatory cytokine that plays diverse roles in development, bone healing, fibrosis, and cancer. However, characterizing TGF-β1 gene variants is challenging because the structural and functional consequences of these variants are still undetermined. In this study, we aimed to perform an in-silico analysis of TGF-β1 non-synonymous variants and their pathogenic effects on the TGF-β1 protein. A total of 10,252 TGF-β1 SNPs were collected from the NCBI dbSNP database and in-silico tools (SIFT, PROVEAN, Mutation Taster, ClinVar, PolyPhen-2, CScape, MutPred, and ConSurf) were used. The in-silico predicted potential variants were further investigated for their binding to the TGF-β1 targeting drug "Fresolimumab". Molecular docking was performed using HADDOCK and confirmed by PRODIGY and PDBsum. The in-silico analysis predicted four potential TGF-β1 nsSNPs: E47G in the LAP domain of the propeptide and I22T, L28F, and E35D in the mature TGF-β1 peptide. HADDOCK and molecular dynamics simulations revealed that the I22T and E35D variants have higher binding affinity for Fresolimumab as compared to the wild type and L28F variants. Molecular dynamics simulations (100 ns) and principal component analysis showed that TGF-β1 variants influenced the protein structure and caused variations in the internal dynamics of protein complexes with the antibody. Among them, the E35D variant significantly destabilized the TGF-β1 protein structure, resulting in rearrangement in the binding site and affecting the interactions with the Fresolimumab. This study identified four variants that can affect the TGF-β1 protein structure and result in functional consequences such as impaired response to Fresolimumab.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ammara Ramzan
- Department of Zoology, GC University, Lahore, Pakistan
| | - Muhammad Abrar Yousaf
- Section of Biology and Genetics, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Muhammad Usman Rashid
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, Pakistan
| | - Shefin Basheera
- Department of Biotechnology and Bioinformatics, Thiruvananthapuram, India
| | - Naila Malkani
- Department of Zoology, GC University, Lahore, Pakistan
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Alguridi HI, Alzahrani F, Almalki S, Zamzami MA, Altayb HN. Identification and molecular docking of novel chikungunya virus NSP4 inhibitory peptides from camel milk proteins. J Biomol Struct Dyn 2023:1-16. [PMID: 37668009 DOI: 10.1080/07391102.2023.2254398] [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: 03/27/2023] [Accepted: 08/28/2023] [Indexed: 09/06/2023]
Abstract
The chikungunya (CHIK) virus is an arbovirus belonging to the alphavirus (Togaviridae family). Around 85% of infected individuals suffer from symptoms such as high fever and severe joint pain; about 30 to 40% will develop a chronic joint illness. The Nsp4 protease is the most conserved protein in the alphavirus family and serves as an RNA-dependent RNA polymerase (RdRp). Targeting this enzyme might inhibit the CHIKV replication cycle. This work aims to in silico study the CHIKV RdRp inhibitory effect of peptides derived from camel milk protein as antiviral peptides. Various bioinformatics tools were recruited to identify, screen, predict and assess peptides obtained from camel milk as antiviral peptides (AVPs). During this study, CHIKV Nsp4 (polymerase) was used as a target to be inhibited by interaction with peptides derived from camel milk protein. Among 91 putative bioactive peptides, the best predicted 5 were further evaluated. Molecular docking showed that the top 5 AVPs generated better docking scores and interacted well with active sites of Nsp4 by the formation of different hydrogen bonds as well as other bonds. AVP63 and AVP20 showed the best Molecular docking and MD simulation results. The residue 315ASP of the GDD motif (catalytic core) exhibited a favorable interaction with the AVPs. The findings of this study suggest that the AVP20 derived from camel milk protein can be a potential novel CHIKV polymerase inhibitor.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hassan I Alguridi
- Molecular Biology Department, Jeddah Regional Laboratory, Ministry of Health, Jeddah, Saudi Arabia
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University Jeddah, Saudi Arabia
- Research Unit, Jeddah Regional Laboratory, Ministry of Health, Jeddah, Saudi Arabia
| | - Faisal Alzahrani
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University Jeddah, Saudi Arabia
- Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- King Fahd Medical Research Center, Embryonic Stem Cells Unit, King Abdulaziz University Jeddah, Saudi Arabia
| | - Safar Almalki
- Molecular Biology Department, Jeddah Regional Laboratory, Ministry of Health, Jeddah, Saudi Arabia
- Laboratories and Blood Banks Administration, Ministry of Health, Jeddah, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University Jeddah, Saudi Arabia
- Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hisham N Altayb
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University Jeddah, Saudi Arabia
- Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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Molecular modeling and simulations of some antiviral drugs, benzylisoquinoline alkaloid, and coumarin molecules to investigate the effects on Mpro main viral protease inhibition. Biochem Biophys Rep 2023; 34:101459. [PMID: 36987522 PMCID: PMC10037929 DOI: 10.1016/j.bbrep.2023.101459] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/26/2023] Open
Abstract
Background SARS-CoV-2 is a deadly viral disease and uncounted deaths occurs since its first appearance in the year 2019. The antiviral drugs, benzylisoquinoline alkaloids, and coumarin molecules were searched using different online engines for drug repurposing with SARS-CoV-2 and to investigate the effects on main viral protease (Mpro) upon their bindings. Methods A database composed of antiviral drugs, benzylisoquinoline alkaloids, and Coumarin molecules was screened through a molecular docking strategy to uncover the interactions of collected molecules with SARS-CoV-2 Mpro. Further, molecular dynamics simulations (MDS) were implemented for 100 ns to calculate the stability of the best complexed molecular scaffold with Mpro. The conformations of the simulated complexes were investigated by using principal component analysis (PCA) and Gibbs energy landscape (FEL) and DSSP together. Next, free binding energy (ΔGbind) was calculated using the mmpbsa method. Results Molecular docking simulations demonstrate 17 molecules exhibited better binding affinity out of 99 molecules present in the database with the viral protease Mpro, followed ADMET properties and were documented. The Coumarin-EM04 molecular scaffold exhibited interactions with catalytical dyad HIS41, CYS145, and neighboring amino acids SER165 and GLN189 in the catalytical site. The crucial factor RMSD was calculated to determine the orientations of Coumarin-EM04. The Coumarin-EM04 complexed with Mpro was found stable in the binding site during MDS. Furthermore, the free energy binding ΔGbind of Coumarin-EM04 was found to be −187.471 ± 2.230 kJ/mol, and for Remdesivir ΔGbind was −171.926 ± 2.237 kJ/mol with SARS-CoV-2 Mpro. Conclusion In this study, we identify potent molecules that exhibit interactions with catalytical dyad HIS41 and CYS145 amino acids and unravel Coumarin-EM04 exhibited ΔGbind higher than Remdesivir against Mpro and thus may serve better antiviral agent against SARS-CoV-2.
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Rafiq A, Jabeen T, Aslam S, Ahmad M, Ashfaq UA, Mohsin NUA, Zaki MEA, Al-Hussain SA. A Comprehensive Update of Various Attempts by Medicinal Chemists to Combat COVID-19 through Natural Products. Molecules 2023; 28:4860. [PMID: 37375415 DOI: 10.3390/molecules28124860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The ongoing COVID-19 pandemic has resulted in a global panic because of its continual evolution and recurring spikes. This serious malignancy is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the outbreak, millions of people have been affected from December 2019 till now, which has led to a great surge in finding treatments. Despite trying to handle the pandemic with the repurposing of some drugs, such as chloroquine, hydroxychloroquine, remdesivir, lopinavir, ivermectin, etc., against COVID-19, the SARS-CoV-2 virus continues its out-of-control spread. There is a dire need to identify a new regimen of natural products to combat the deadly viral disease. This article deals with the literature reports to date of natural products showing inhibitory activity towards SARS-CoV-2 through different approaches, such as in vivo, in vitro, and in silico studies. Natural compounds targeting the proteins of SARS-CoV-2-the main protease (Mpro), papain-like protease (PLpro), spike proteins, RNA-dependent RNA polymerase (RdRp), endoribonuclease, exoribonuclease, helicase, nucleocapsid, methyltransferase, adeno diphosphate (ADP) phosphatase, other nonstructural proteins, and envelope proteins-were extracted mainly from plants, and some were isolated from bacteria, algae, fungi, and a few marine organisms.
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Affiliation(s)
- Ayesha Rafiq
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Tooba Jabeen
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Sana Aslam
- Department of Chemistry, Government College Women University, Faisalabad 38000, Pakistan
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan
| | - Noor Ul Amin Mohsin
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Government College University, Faisalabad 38000, Pakistan
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Sami A Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
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11
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Ramli S, Wu YS, Batumalaie K, Guad RM, Choy KW, Kumar A, Gopinath SCB, Rahman Sarker MM, Subramaniyan V, Sekar M, Fuloria NK, Fuloria S, Chinni SV, Ramachawolran G. Phytochemicals of Withania somnifera as a Future Promising Drug against SARS-CoV-2: Pharmacological Role, Molecular Mechanism, Molecular Docking Evaluation, and Efficient Delivery. Microorganisms 2023; 11:microorganisms11041000. [PMID: 37110423 PMCID: PMC10142625 DOI: 10.3390/microorganisms11041000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/02/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Coronavirus disease (COVID-19) has killed millions of people since first reported in Wuhan, China, in December 2019. Intriguingly, Withania somnifera (WS) has shown promising antiviral effects against numerous viral infections, including SARS-CoV and SARS-CoV-2, which are contributed by its phytochemicals. This review focused on the updated testing of therapeutic efficacy and associated molecular mechanisms of WS extracts and their phytochemicals against SARS-CoV-2 infection in preclinical and clinical studies with the aim to develop a long-term solution against COVID-19. It also deciphered the current use of the in silico molecular docking approach in developing potential inhibitors from WS targeting SARS-CoV-2 and host cell receptors that may aid the development of targeted therapy against SARS-CoV-2 ranging from prior to viral entry until acute respiratory distress syndrome (ARDS). This review also discussed nanoformulations or nanocarriers in achieving effective WS delivery to enhance its bioavailability and therapeutic efficacy, consequently preventing the emergence of drug resistance, and eventually therapeutic failure.
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Affiliation(s)
- Suaidah Ramli
- Department of Pharmacy, Hospital Sultanah Nur Zahirah, Kuala Terengganu 20400, Malaysia
| | - Yuan Seng Wu
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, Subang Jaya 47500, Malaysia
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Subang Jaya 47500, Malaysia
| | - Kalaivani Batumalaie
- Department of Biomedical Sciences, Faculty of Health Sciences, Asia Metropolitan University, Johor Bahru 81750, Malaysia
| | - Rhanye Mac Guad
- Department of Biomedical Science and Therapeutics, Faculty of Medicine and Health Science, Universiti Malaysia Sabah, Kota Kinabalu 88400, Malaysia
| | - Ker Woon Choy
- Department of Anatomy, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh 47000, Malaysia
| | - Ashok Kumar
- Department of Internal Medicine, Division of Pulmonary, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Subash C B Gopinath
- Centre of Excellence (CoE), Faculty of Chemical Engineering & Technology & Micro System Technology, Universiti Malaysia Perlis (UniMAP), Arau 02600, Malaysia
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis (UniMAP), Kangar 01000, Malaysia
| | - Md Moklesur Rahman Sarker
- Department of Pharmacy, State University of Bangladesh, 77 Satmasjid Road, Dhanmondi, Dhaka 1205, Bangladesh
- Health Med Science Research Network, 3/1, Block F, Lalmatia, Dhaka 1207, Bangladesh
| | - Vetriselvan Subramaniyan
- Pharmacology Unit, Jeffrey Cheah School of Medicine and Health Sciences, MONASH University, Jalan Lagoon Selatan, Bandar Sunway, Subang Jaya 47500, Malaysia
- Department of Pharmacology, School of Medicine, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Subang Jaya 42610, Malaysia
| | - Mahendran Sekar
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Subang Jaya 47500, Malaysia
| | - Neeraj Kumar Fuloria
- Centre of Excellence for Biomaterials Engineering & Faculty of Pharmacy, AIMST University, Bedong 08100, Malaysia
- Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College and Hospitals, Saveetha University, Chennai 600077, India
| | - Shivkanya Fuloria
- Faculty of Pharmacy, AIMST University, Semeling, Bedong 08100, Malaysia
| | - Suresh V Chinni
- Department of Biochemistry, Faculty of Medicine, Bioscience, and Nursing, MAHSA University, Jenjarom 42610, Malaysia
- Department of Periodontics, Saveetha Institute of Medical and Technical Sciences, Saveetha Dental College and Hospitals, Chennai 600077, India
| | - Gobinath Ramachawolran
- Department of Foundation, RCSI & UCD Malaysia Campus, No 4, Jalan Sepoy Lines, Georgetown 10450, Malaysia
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12
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Identification of medicinal plant-based phytochemicals as a potential inhibitor for SARS-CoV-2 main protease (M pro) using molecular docking and deep learning methods. Comput Biol Med 2023; 157:106785. [PMID: 36931201 PMCID: PMC10008098 DOI: 10.1016/j.compbiomed.2023.106785] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/15/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023]
Abstract
Highly transmissive and rapidly evolving Coronavirus disease-2019 (COVID-19), a viral disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), triggered a global pandemic, which is one of the most researched viruses in the academia. Effective drugs to treat people with COVID-19 have yet to be developed to reduce mortality and transmission. Studies on the SARS-CoV-2 virus identified that its main protease (Mpro) might be a potential therapeutic target for drug development, as this enzyme plays a key role in viral replication. In search of potential inhibitors of Mpro, we developed a phytochemical library consisting of 2431 phytochemicals from 104 Korean medicinal plants that exhibited medicinal and antioxidant properties. The library was screened by molecular docking, followed by revalidation by re-screening with a deep learning method. Recurrent Neural Networks (RNN) computing system was used to develop an inhibitory predictive model using SARS coronavirus Mpro dataset. It was deployed to screen the top 12 compounds based on their docked binding affinity that ranged from -8.0 to -8.9 kcal/mol. The top two lead compounds, Catechin gallate and Quercetin 3-O-malonylglucoside, were selected depending on inhibitory potency against Mpro. Interactions with the target protein active sites, including His41, Met49, Cys145, Met165, and Thr190 were also examined. Molecular dynamics simulation was performed to analyze root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (RG), solvent accessible surface area (SASA), and number of hydrogen bonds. Results confirmed the inflexible nature of the docked complexes. Absorption, distribution, metabolism, excretion, and toxicity (ADMET), as well as bioactivity prediction confirmed the pharmaceutical activities of the lead compound. Findings of this research might help scientists to optimize compatible drugs for the treatment of COVID-19 patients.
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13
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Liu HT, Weng CY, Zhou L, Xu HB, Liao ZY, Hong HY, Ye YF, Li SF, Wang YJ, Zheng YG. Coevolving stability and activity of LsCR by a single point mutation and constructing neat substrate bioreaction system. Biotechnol Bioeng 2023; 120:1521-1530. [PMID: 36799475 DOI: 10.1002/bit.28357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/29/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023]
Abstract
Carbonyl reductase (CR)-catalyzed bioreduction in the organic phase and the neat substrate reaction system is a lasting challenge, placing higher requirements on the performance of enzymes. Protein engineering is an effective method to enhance the properties of enzymes for industrial applications. In the present work, a single point mutation E145A on our previously constructed CR mutant LsCRM3 , coevolved thermostability, and activity. Compared with LsCRM3 , the catalytic efficiency kcat /KM of LsCRM3 -E145A (LsCRM4 ) was increased from 6.6 to 21.9 s-1 mM-1 . Moreover, E145A prolonged the half-life t1/2 at 40°C from 4.1 to 117 h, T m ${T}_{m}$ was increased by 5°C, T 50 30 ${T}_{50}^{30}$ was increased by 14.6°C, and Topt was increased by 15°C. Only 1 g/L of lyophilized Escherichia coli cells expressing LsCRM4 completely reduced up to 600 g/L 2-chloro-1-(3,4-difluorophenyl)ethanone (CFPO) within 13 h at 45°C, yielding the corresponding (1S)-2-chloro-1-(3,4-difluorophenyl)ethanol ((S)-CFPL) in 99.5% eeP , with a space-time yield of 1.0 kg/L d, the substrate to catalyst ratios (S/C) of 600 g/g. Compared with LsCRM3 , the substrate loading was increased by 50%, with the S/C increased by 14 times. Compared with LsCRWT , the substrate loading was increased by 6.5 times. In contrast, LsCRM4 completely converted 600 g/L CFPO within 12 h in the neat substrate bioreaction system.
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Affiliation(s)
- Hua-Tao Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Chun-Yue Weng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Lei Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Hao-Bo Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Zhen-Yu Liao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Han-Yue Hong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yuan-Fan Ye
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Shu-Fang Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, China
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14
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Kadiri HE, Ossai HU. Ameliorative potential of Acalypha wilkesiana leaf extract (subsp. macrophylla) on cyanide-induced renal damaged Wister rats. SCIENTIFIC AFRICAN 2023. [DOI: 10.1016/j.sciaf.2023.e01568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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15
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Choudhary P, Gupta S, Shukla R, Gupta A, Pahal S, Singh S. Regulation of neuronal repair and regeneration through inhibition of oligodendrocyte myelin glycoprotein (OMgp). J Biomol Struct Dyn 2022; 40:13936-13952. [PMID: 34787055 DOI: 10.1080/07391102.2021.1997820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The inability of neural cells to regenerate themselves after an injury represents the major difference between neural cells and other cells of the body. Various factors are responsible for this, as the expression of myelin-derived inhibitors of axonal outgrowth such as neurite outgrowth inhibitor (Nogo), myelin-associated growth factor, and oligodendrocyte-myelin glycoprotein (OMgp) hinder the central nervous system (CNS) axons to recover properly and inhibit the neuron regeneration. The patient with spinal cord injury can even permanently lose their function due to the inability of axons to regenerate. However, their role in neural regeneration in vivo is not known completely. During the study, we found that once CNS gets injured, the axon growth inhibitor OMgp binds to the Nogo-66 Receptor 1 (NgR1) which in turn restricts the normal functioning of CNS. Considering the OMgp as the target protein, two flavonoid libraries (curcumin and piperine) were screened against it to get potential inhibitors. The effectiveness of the ligands was first screened by three-tier structure-based virtual screening by Glide, Schrödinger. Based on the docking score, the best-docked compounds were taken for absorption, distribution, metabolism, and excretion analysis and the top two complexes from each library were chosen for simulation studies. Flavonoid ligands showed a much better binding affinity when compared with already known inhibitors Riluzole and Minocycline. To date, no natural inhibitors are known for OMgp. Hence, this study can provide novel insight for upcoming research in this area. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Princy Choudhary
- Applied Science Department, Indian Institute of Information Technology, Allahabad, UP, India
| | - Shivani Gupta
- Applied Science Department, Indian Institute of Information Technology, Allahabad, UP, India
| | - Richa Shukla
- Applied Science Department, Indian Institute of Information Technology, Allahabad, UP, India
| | - Ayushi Gupta
- Applied Science Department, Indian Institute of Information Technology, Allahabad, UP, India
| | - Sonu Pahal
- Applied Science Department, Indian Institute of Information Technology, Allahabad, UP, India
| | - Sangeeta Singh
- Applied Science Department, Indian Institute of Information Technology, Allahabad, UP, India
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16
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Liu Z, Huang H, Yu Y, Jia Y, Dang X, Wang Y, Huang L. Exploring the Potential Mechanism of Danshen in the Treatment of Concurrent Ischemic Heart Disease and Depression Using Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221143637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Objective: This study aimed to explore the potential targets and mechanism of action of Danshen in treating concurrent ischemic heart disease (IHD) and depression using network pharmacology, molecular docking, and molecular dynamics simulation (MDS). Methods: The Traditional Chinese Medicine Systems Pharmacology (TCMSP) database was used to obtain active ingredients and targets of Danshen. Candidate targets for IHD and depression were obtained from the Genecards and DisGeNet databases. The protein–protein interaction (PPI) network was constructed using the STRING database and the Cytoscape 3.8.2 software. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using the Metascape database and the GlueGO package of the Cytoscape 3.8.2 software. Molecular docking was performed using Autodock 1.5.6 and Vina, and the MDS was completed using GROMACS 5.1.2. Results: We obtained 65 active ingredients of Danshen with 131 candidate targets and 39 intersection targets of the active ingredients and diseases. Luteolin, tanshinone IIA, and salviolone were the core active ingredients, and AKT1, TNF, IL-6, MMP9, CASP3, IL-10, PTGS2, STAT3, PPARG, IL-4, EGFR, MAPK14, NOS3, and EDN1 were the core targets. The GO and KEGG pathway enrichment analyses revealed that the intersection targets were mainly enriched in positive regulation of protein phosphorylation, blood circulation, IL-17 signaling pathway, VEGF signaling pathway, and JAK/STAT signaling pathway. The molecular docking revealed that the core active ingredients had a good affinity for the core targets. The results of MDS revealed that the protein-ligand complexes were stable. Conclusions: This study used network pharmacology to analyze the potential mechanism of action of Danshen in the treatment of concurrent IHD and depression. Additionally, the study provided a theoretical basis for further studying the pharmacological mechanisms and targets of Danshen.
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Affiliation(s)
- Zhiyao Liu
- College of Rehabilitation Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Hailiang Huang
- College of Rehabilitation Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ying Yu
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yuqi Jia
- College of Rehabilitation Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiaowen Dang
- College of Rehabilitation Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yajie Wang
- College of Rehabilitation Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lei Huang
- College of Rehabilitation Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
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17
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Identification of natural inhibitor against L1 β-lactamase present in Stenotrophomonas maltophilia. J Mol Model 2022; 28:342. [PMID: 36197525 PMCID: PMC9533269 DOI: 10.1007/s00894-022-05336-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/28/2022] [Indexed: 11/21/2022]
Abstract
Antibiotic resistance is threatening the medical industry in treating microbial infections. Many organisms are acquiring antibiotic resistance because of the continuous use of the same drug. Gram-negative organisms are developing multi-drug resistance properties (MDR) due to chromosomal level changes that occurred as a part of evolution or some intrinsic factors already present in the organism. Stenotrophomonas maltophilia falls under the category of multidrug-resistant organism. WHO has also urged to evaluate the scenario and develop new strategies for making this organism susceptible to otherwise resistant antibiotics. Using novel compounds as drugs can ameliorate the issue to some extent. The β-lactamase enzyme in the bacteria is responsible for inhibiting several drugs currently being used for treatment. This enzyme can be targeted to find an inhibitor that can inhibit the enzyme activity and make the organism susceptible to β-lactam antibiotics. Plants produce several secondary metabolites for their survival in adverse environments. Several phytoconstituents have antimicrobial properties and have been used in traditional medicine for a long time. The computational technologies can be exploited to find the best compound from many compounds. Virtual screening, molecular docking, and dynamic simulation methods are followed to get the best inhibitor for L1 β-lactamase. IMPPAT database is screened, and the top hit compounds are studied for ADMET properties. Finally, four compounds are selected to set for molecular dynamics simulation. After all the computational calculations, withanolide R is found to have a better binding and forms a stable complex with the protein. This compound can act as a potent natural inhibitor for L1 β-lactamase.
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18
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Mahaboob Ali AA, Bugarcic A, Naumovski N, Ghildyal R. Ayurvedic formulations: Potential COVID-19 therapeutics? PHYTOMEDICINE PLUS : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 2:100286. [PMID: 35474908 PMCID: PMC9020642 DOI: 10.1016/j.phyplu.2022.100286] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]
Abstract
BACKGROUND While Molnupiravir and Paxlovid have recently been approved for use in some countries, there are no widely available treatments for COVID-19, the disease caused by SARS-CoV-2 infection. Herbal extracts have been used to treat respiratory clinical indications by Ayurvedic medicine practitioners with minimal adverse reactions and intense research efforts are currently under way to develop some of these formulations for COVID-19 treatment. METHODS Literature search for in silico, in vitro, in vivo, and clinical studies on the topic of Ayurvedic formulations for potential COVID-19 treatment, in order to present the current state of current knowledge by integrating information across all systems. RESULTS The search yielded 20 peer reviewed articles on in silico studies examining the interaction of phytoconstituents of popular Ayurvedic formulations with SARS-CoV-2 components and its receptors; five articles on preclinical investigations of the ability of selected Ayurvedic formulations to inhibit functions of SARS-CoV-2 proteins; and 51 completed clinical trials on the efficacy of using Ayurvedic formulations for treatment of mild to moderate COVID-19. Clinical data was available from 17 of the 51 trials. There was a considerable overlap between formulations used in the in silico studies and the clinical trials. This finding was unexpected as there is no clearly stated alignment between studies and the traditional pathway to drug discovery- basic discovery leading to in vitro and in vivo proof of concept, followed by validation in clinical trials. This was further demonstrated in the majority of the in silico studies where focus was on potential antiviral mechanisms, while the clinical trials were focused on patient recovery using oral treatments. In all 17 clinical trials where data was available, Ayurvedic treatments lead to a shorter period to recovery in participants with COVID-19. CONCLUSION The most commonly used Ayurvedic treatments for management of respiratory symptoms associated with SARS-CoV-2 infection appear to have prophylactic and/or therapeutic properties. It would be of particular interest to assess synergistic and concomitant systemic effects and antiviral activities of individual phytoconstituents and their combinations in the Ayurvedic treatments.
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Affiliation(s)
- Anees Ahmed Mahaboob Ali
- Centre for Research in Therapeutic Solutions, Faculty of Science and Technology, University of Canberra, Canberra, Australia
| | - Andrea Bugarcic
- National Centre for Naturopathic Medicine, Southern Cross University, Lismore, New South Wales, Australia
| | - Nenad Naumovski
- Functional Foods and Nutrition Research Laboratory, Faculty of Health, University of Canberra, Canberra, Ngunnawal Country, Australia
- Department of Nutrition-Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Reena Ghildyal
- Centre for Research in Therapeutic Solutions, Faculty of Science and Technology, University of Canberra, Canberra, Australia
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19
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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20
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Wylie MR, Merrell DS. The Antimicrobial Potential of the Neem Tree Azadirachta indica. Front Pharmacol 2022; 13:891535. [PMID: 35712721 PMCID: PMC9195866 DOI: 10.3389/fphar.2022.891535] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/09/2022] [Indexed: 12/24/2022] Open
Abstract
Azadirachta indica (A. Juss), also known as the neem tree, has been used for millennia as a traditional remedy for a multitude of human ailments. Also recognized around the world as a broad-spectrum pesticide and fertilizer, neem has applications in agriculture and beyond. Currently, the extensive antimicrobial activities of A. indica are being explored through research in the fields of dentistry, food safety, bacteriology, mycology, virology, and parasitology. Herein, some of the most recent studies that demonstrate the potential of neem as a previously untapped source of novel therapeutics are summarized as they relate to the aforementioned research topics. Additionally, the capacity of neem extracts and compounds to act against drug-resistant and biofilm-forming organisms, both of which represent large groups of pathogens for which there are limited treatment options, are highlighted. Updated information on the phytochemistry and safety of neem-derived products are discussed as well. Although there is a growing body of exciting evidence that supports the use of A. indica as an antimicrobial, additional studies are clearly needed to determine the specific mechanisms of action, clinical efficacy, and in vivo safety of neem as a treatment for human pathogens of interest. Moreover, the various ongoing studies and the diverse properties of neem discussed herein may serve as a guide for the discovery of new antimicrobials that may exist in other herbal panaceas across the globe.
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Affiliation(s)
- Marina R Wylie
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - D Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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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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Pathak S, Agrawal N, Goyal A. A Comprehensive Review on in silico Predicted Potential Phytochemicals against SARS-CoV-2: Food for Thought to Researchers. LETT ORG CHEM 2022. [DOI: 10.2174/1570178619666220309160557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract:
The battle against the novel coronavirus disease (COVID-19) emerged in December 2019. It is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is still existent all over the world. Researchers worldwide are continuously conducting in silico studies or virtual screening on various phytochemicals and reporting potential candidates that can be developed against COVID-19 after in vitro and in vivo validation. Antiviral effects of several phytochemicals have been demonstrated against different kinds of coronavirus, including SARS-CoV. Using drug repurposing techniques, a number of phytochemicals have shown substantial antiviral efficacy against COVID 19. This article reviews the efficacy of lead phytochemicals in computational studies on different important targets of SARS-CoV-2 like main protease, ACE-2, papain-like protease, spike protein, nsp-1, nsp-15, RdRp, MTase, helicase, cathepsin, TMPRSS-2. This review carries vision for the potential application of these phytochemicals, which can guide medicinal chemists to choose phytochemicals to proceed with further in vitro and in vivo testing for SARS-CoV-2, which may eventually lead to an effective therapeutic agent and thus can be used to control the current ongoing pandemic.
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Affiliation(s)
- Shilpi Pathak
- Institute of Pharmaceutical Research, GLA University Mathura, India
| | - Neetu Agrawal
- Institute of Pharmaceutical Research, GLA University Mathura, India
| | - Ahsas Goyal
- Institute of Pharmaceutical Research, GLA University Mathura, India
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Pagano E. Phytocompounds and COVID-19: Two years of knowledge. Phytother Res 2022; 36:2267-2271. [PMID: 35170093 PMCID: PMC9111037 DOI: 10.1002/ptr.7420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 01/30/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Ester Pagano
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Naples, Italy
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Basak HK, Saha S, Ghosh J, Paswan U, Karmakar S, Pal A, Chatterjee A. Sequence Analysis, Structure Prediction of Receptor Proteins and In Silico
Study of Potential Inhibitors for Management of Life Threatening
COVID-19. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666210804141613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Treatment of the Covid-19 pandemic caused by the highly contagious and
pathogenic SARS-CoV-2 is a global menace. Day by day, this pandemic is getting worse. Doctors,
scientists and researchers across the world are urgently scrambling for a cure for novel corona virus
and continuously working at break neck speed to develop vaccines or drugs. But to date, there
are no specific drugs or vaccines available in the market to cope up with the virus.
Objective:
The present study helps us to elucidate 3D structures of SARS-CoV-2 proteins and also
to identify natural compounds as potential inhibitors against COVID-19.
Methods:
The 3D structures of the proteins were constructed using Modeller 9.16 modeling tool.
Modelled proteins were validated with PROCHECK by Ramachandran plot analysis. In this study,
a small library of natural compounds (fifty compounds) was docked to the hACE2 binding site of
the modelled surface glycoprotein of SARS-CoV-2 using AutoDock Vina to repurpose these inhibitors
against SARS-CoV-2. Conceptual density functional theory calculations of the best eight
compounds had been performed by Gaussian-09. Geometry optimizations for these molecules were
done at M06-2X/ def2-TZVP level of theory. ADME parameters, pharmacokinetic properties and
drug likeness of the compounds were analyzed using swissADME website.
Results:
In this study, we analysed the sequences of surface glycoprotein, nucleocapsid phosphoprotein
and envelope protein obtained from different parts of the globe. We modelled all the different
sequences of surface glycoprotein and envelop protein in order to derive 3D structure of a molecular
target, which is essential for the development of therapeutics. Different electronic properties
of the inhibitors have been calculated using DFT through M06-2X functional with def2-TZVP
basis set. Docking result at the hACE2 binding site of all modelled surface glycoproteins of SARSCoV-
2 showed that all the eight inhibitors (actinomycin D, avellanin C, ichangin, kanglemycin A,
obacunone, ursolic acid, ansamiotocin P-3 and isomitomycin A) studied here were many folds
better compared to hydroxychloroquine which has been found to be effective to treat patients suffering
from COVID-19. All the inhibitors meet most of the criteria of drug likeness assessment.
Conclusion:
We expect that eight compounds (actinomycin D, avellanin C, ichangin, kanglemycin
A, obacunone, ursolic acid, ansamiotocin P-3 and isomitomycin A) can be used as potential inhibitors
against SARS-CoV-2.
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Affiliation(s)
- Hriday Kumar Basak
- In silico Chemical Laboratory, Department of Chemistry, Raiganj University, Raiganj, West Bengal, India
| | - Soumen Saha
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Joydeep Ghosh
- In silico Chemical Laboratory, Department of Chemistry, Raiganj University, Raiganj, West Bengal, India
| | - Uttam Paswan
- In silico Chemical Laboratory, Department of Chemistry, Raiganj University, Raiganj, West Bengal, India
| | - Sujoy Karmakar
- In silico Chemical Laboratory, Department of Chemistry, Raiganj University, Raiganj, West Bengal, India
| | - Ayon Pal
- Microbiology & Computational
Biology Laboratory, Department of Botany, Raiganj University, Raiganj, West Bengal, India
| | - Abhik Chatterjee
- In silico Chemical Laboratory, Department of Chemistry, Raiganj University, Raiganj, West Bengal, India
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Abstract
Covering: March 2010 to December 2020. Previous review: Nat. Prod. Rep., 2011, 28, 705This review summarizes the latest progress and perspectives on the structural classification, biological activities and mechanisms, metabolism and pharmacokinetic investigations, biosynthesis, chemical synthesis and structural modifications, as well as future research directions of the promising natural withanolides. The literature from March 2010 to December 2020 is reviewed, and 287 references are cited.
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Affiliation(s)
- Gui-Yang Xia
- School of Chinese Materia Medica, State Key Laboratory of Component-Based Chinese Medicine, Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China. .,Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Shi-Jie Cao
- School of Chinese Materia Medica, State Key Laboratory of Component-Based Chinese Medicine, Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China.
| | - Li-Xia Chen
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Feng Qiu
- School of Chinese Materia Medica, State Key Laboratory of Component-Based Chinese Medicine, Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin, 301617, China.
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Paul D, Mahanta S, Tag H, Das SK, Das Gupta D, Tanti B, Ananthan R, Das R, Jambhulkar S, Hui PK. Identification of tyrosine kinase inhibitors from Panax bipinnatifidus and Panax pseudoginseng for RTK-HER2 and VEGFR2 receptors, by in silico approach. Mol Divers 2021; 26:1933-1955. [PMID: 34554395 DOI: 10.1007/s11030-021-10304-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/24/2021] [Indexed: 11/26/2022]
Abstract
Breast and stomach cancer is reported as a leading cause for human mortality across the world. The overexpression of receptor tyrosine kinase (RTK) proteins, namely the human epidermal growth factor receptor2 (HER2) and the vascular endothelial growth factor receptor2 (VEGFR2), is reported to be responsible for development and metastasis of breast and stomach cancer. Although several synthetic tyrosine kinase inhibitors (TKIs) as drug candidates targeting RTK-HER2 and VEGFR2 are currently available in the market, these are expensive with the reported side effects. This confers an opportunity for development of alternative novel tyrosine kinase inhibitors (TKIs) for RTK-HER2 and VEGFR2 receptors from the botanical sources. In the present study, we characterized 47 bioactive phytocompounds from the methanol extracts of the rhizomes of Asiatic traditional medicinal herbs-Panax bipinnatifidus and Panax pseudoginseng, of Indian Himalayan landraces using HPLC, GC-MS and high-sensitivity LC-MS tools. We performed molecular docking and molecular dynamics simulation analysis using Schrödinger suite 2020-3 to confirm the TKI phytocompounds showing the best binding affinity towards RTK-HER2 and VEGFR2 receptors. The results of molecular docking studies confirmed that the phytocompound (ligand) luteolin 7-O-glucoside (IHP15) showed the highest binding affinity towards receptor HER2 (PDB ID: 3PP0) with docking score and Glide g score (G-Score) of - 13.272, while chlorogenic acid (IHP12) showed the highest binding affinity towards receptor VEGFR2 (PDB ID: 4AGC) with docking score and Glide g score (G-Score) of - 10.673. Molecular dynamics (MD) simulation analysis carried out for 100 ns has confirmed strong binding interaction between the ligand and receptor complex [luteolin 7-O-glucoside (IHP15) and HER2 (PDB ID: 3PP0)] and is found to be stabilized within 40 to 100 ns of MD simulation, whereas ligand-receptor complex [chlorogenic acid (IPH12) and VEGFR2 (PDB ID: 4AGC)] also showed strong binding interaction and is found to be stabilized within 18-30 ns but slightly deviated during 100 ns of MD simulation. In silico ADME-Tox study using SwissADME revealed that the ligands luteolin 7-O-glucoside (IHP15) and chlorogenic acid (IHP12) have passed majority parameters of the common drug discovery rules. The present study has confirmed luteolin 7-O-glucoside (IHP15) and chlorogenic acid (IHP12) as potential tyrosine kinase inhibitors (TKIs) which were found to inhibit RTKs-HER2 and VEGFR2 receptor proteins, and thus paving the way for development of alternative potential TKIs (drug molecules) for treatment of HER2- and VEGFR2-positive breast and stomach cancer.
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Affiliation(s)
- Dipayan Paul
- Department of Biotechnology, National Institute of Technology Arunachal Pradesh, Yupia, Papum Pare, Arunachal Pradesh, 791112, India
| | - Saurov Mahanta
- National Institute of Electronics and Information Technology, Guwahati, Assam, 781008, India
| | - Hui Tag
- Pharmacognosy and Phytochemistry Research Laboratory, Department of Botany, Rajiv Gandhi University, Rono Hills, Doimukh, Arunachal Pradesh, 791112, India.
| | - Sanjib Kumar Das
- Department of Biotechnology, National Institute of Technology Arunachal Pradesh, Yupia, Papum Pare, Arunachal Pradesh, 791112, India
| | - Debmalya Das Gupta
- Department of Biotechnology, National Institute of Technology Arunachal Pradesh, Yupia, Papum Pare, Arunachal Pradesh, 791112, India
| | - Bhaben Tanti
- Department of Botany, Gauhati University, Guwahati, Assam, 781014, India
| | - Rajendran Ananthan
- Food Chemistry Division, ICMR National Institute of Nutrition, Jamai-Osmania PO, Hyderabad, Telangana, 500007, India
| | - Ranjan Das
- Department of Crop Physiology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Sanjay Jambhulkar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra, 400085, India
| | - Pallabi Kalita Hui
- Department of Biotechnology, National Institute of Technology Arunachal Pradesh, Yupia, Papum Pare, Arunachal Pradesh, 791112, India.
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Singh R, Bhardwaj VK, Sharma J, Kumar D, Purohit R. Identification of potential plant bioactive as SARS-CoV-2 Spike protein and human ACE2 fusion inhibitors. Comput Biol Med 2021; 136:104631. [PMID: 34273770 PMCID: PMC8264305 DOI: 10.1016/j.compbiomed.2021.104631] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 01/14/2023]
Abstract
The Spike receptor binding domain (S-RBD) from SARS-CoV-2, a crucial protein for the entrance of the virus into target cells is known to cause infection by binding to a cell surface protein. Hence, reckoning therapeutics for the S-RBD of SARS-CoV-2 may address a significant way to target viral entry into the host cells. Herein, through in-silico approaches (Molecular docking, molecular dynamics (MD) simulations, and end-state thermodynamics), we aimed to screen natural molecules from different plants for their ability to inhibit S-RBD of SARS-CoV-2. We prioritized the best interacting molecules (Diacetylcurcumin and Dicaffeoylquinic acid) by analysis of protein-ligand interactions and subjected them for long-term MD simulations. We found that Dicaffeoylquinic acid interacted prominently with essential residues (Lys417, Gln493, Tyr489, Phe456, Tyr473, and Glu484) of S-RBD. These residues are involved in interactions between S-RBD and ACE2 and could inhibit the viral entry into the host cells. The in-silico analyses indicated that Dicaffeoylquinic acid and Diacetylcurcumin might have the potential to act as inhibitors of SARS-CoV-2 S-RBD. The present study warrants further in-vitro and in-vivo studies of Dicaffeoylquinic acid and Diacetylcurcumin for validation and acceptance of their inhibitory potential against S-RBD of SARS-CoV-2.
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Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
| | - Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jatin Sharma
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
| | - Dinesh Kumar
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Post Box No. 6, Palampur, 176061, Himachal Pradesh, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Koulgi S, Jani V, Uppuladinne V. N. M, Sonavane U, Joshi R. Natural plant products as potential inhibitors of RNA dependent RNA polymerase of Severe Acute Respiratory Syndrome Coronavirus-2. PLoS One 2021; 16:e0251801. [PMID: 33984041 PMCID: PMC8118514 DOI: 10.1371/journal.pone.0251801] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 05/03/2021] [Indexed: 01/18/2023] Open
Abstract
Drug repurposing studies targeting inhibition of RNA dependent RNA polymerase (RdRP) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) have exhibited the potential effect of small molecules. In the present work a detailed interaction study between the phytochemicals from Indian medicinal plants and the RdRP of SARS-CoV-2 has been performed. The top four phytochemicals obtained through molecular docking were, swertiapuniside, cordifolide A, sitoindoside IX, and amarogentin belonging to Swertia chirayita, Tinospora cordifolia and Withania somnifera. These ligands bound to the RdRP were further studied using molecular dynamics simulations. The principal component analysis of these systems showed significant conformational changes in the finger and thumb subdomain of the RdRP. Hydrogen bonding, salt-bridge and water mediated interactions supported by MM-GBSA free energy of binding revealed strong binding of cordifolide A and sitoindoside IX to RdRP. The ligand-interacting residues belonged to either of the seven conserved motifs of the RdRP. These residues were polar and charged amino acids, namely, ARG 553, ARG 555, ASP 618, ASP 760, ASP 761, GLU 811, and SER 814. The glycosidic moieties of the phytochemicals were observed to form favourable interactions with these residues. Hence, these phytochemicals may hold the potential to act as RdRP inhibitors owing to their stability in binding to the druggable site.
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Affiliation(s)
- Shruti Koulgi
- High Performance Computing—Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Pune, India
| | - Vinod Jani
- High Performance Computing—Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Pune, India
| | | | - Uddhavesh Sonavane
- High Performance Computing—Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Pune, India
| | - Rajendra Joshi
- High Performance Computing—Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Pune, India
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Identification of phytocompounds from Houttuynia cordata Thunb. as potential inhibitors for SARS-CoV-2 replication proteins through GC-MS/LC-MS characterization, molecular docking and molecular dynamics simulation. Mol Divers 2021; 26:365-388. [PMID: 33961167 PMCID: PMC8103070 DOI: 10.1007/s11030-021-10226-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/22/2021] [Indexed: 02/07/2023]
Abstract
The COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a massive viral disease outbreak of international concerns. The present study is mainly intended to identify the bioactive phytocompounds from traditional antiviral herb Houttuynia cordata Thunb. as potential inhibitors for three main replication proteins of SARS-CoV-2, namely Main protease (Mpro), Papain-Like protease (PLpro) and ADP ribose phosphatase (ADRP) which control the replication process. A total of 177 phytocompounds were characterized from H. cordata using GC–MS/LC–MS and they were docked against three SARS-CoV-2 proteins (receptors), namely Mpro, PLpro and ADRP using Epic, LigPrep and Glide module of Schrödinger suite 2020-3. During docking studies, phytocompounds (ligand) 6-Hydroxyondansetron (A104) have demonstrated strong binding affinity toward receptors Mpro (PDB ID 6LU7) and PLpro (PDB ID 7JRN) with G-score of − 7.274 and − 5.672, respectively, while Quercitrin (A166) also showed strong binding affinity toward ADRP (PDB ID 6W02) with G-score -6.788. Molecular Dynamics Simulation (MDS) performed using Desmond module of Schrödinger suite 2020–3 has demonstrated better stability in the ligand–receptor complexes A104-6LU7 and A166-6W02 within 100 ns than the A104-7JRN complex. The ADME-Tox study performed using SwissADMEserver for pharmacokinetics of the selected phytocompounds 6-Hydroxyondansetron (A104) and Quercitrin (A166) demonstrated that 6-Hydroxyondansetron passes all the required drug discovery rules which can potentially inhibit Mpro and PLpro of SARS-CoV-2 without causing toxicity while Quercitrin demonstrated less drug-like properties but also demonstrated as potential inhibitor for ADRP. Present findings confer opportunities for 6-Hydroxyondansetron and Quercitrin to be developed as new therapeutic drug against COVID-19.
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Saggam A, Limgaokar K, Borse S, Chavan-Gautam P, Dixit S, Tillu G, Patwardhan B. Withania somnifera (L.) Dunal: Opportunity for Clinical Repurposing in COVID-19 Management. Front Pharmacol 2021; 12:623795. [PMID: 34012390 PMCID: PMC8126694 DOI: 10.3389/fphar.2021.623795] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/30/2021] [Indexed: 12/13/2022] Open
Abstract
As the COVID-19 pandemic is progressing, the therapeutic gaps in conventional management have highlighted the need for the integration of traditional knowledge systems with modern medicine. Ayurvedic medicines, especially Ashwagandha (Withania somnifera (L.) Dunal, WS), may be beneficial in the management of COVID-19. WS is a widely prescribed Ayurvedic botanical known as an immunomodulatory, antiviral, anti-inflammatory, and adaptogenic agent. The chemical profile and pharmacological activities of WS have been extensively reported. Several clinical studies have reported its safety for use in humans. This review presents a research synthesis of in silico, in vitro, in vivo, and clinical studies on Withania somnifera (L.) Dunal (WS) and discusses its potential for prophylaxis and management of COVID-19. We have collated the data from studies on WS that focused on viral infections (HIV, HSV, H1N1 influenza, etc.) and noncommunicable diseases (hypertension, diabetes, cancer, etc.). The experimental literature indicates that WS has the potential for 1) maintaining immune homeostasis, 2) regulating inflammation, 3) suppressing pro-inflammatory cytokines, 4) organ protection (nervous system, heart, lung, liver, and kidney), and 5) anti-stress, antihypertensive, and antidiabetic activities. Using these trends, the review presents a triangulation of Ayurveda wisdom, pharmacological properties, and COVID-19 pathophysiology ranging from viral entry to end-stage acute respiratory distress syndrome (ARDS). The review proposes WS as a potential therapeutic adjuvant for various stages of COVID-19 management. WS may also have beneficial effects on comorbidities associated with the COVID-19. However, systematic studies are needed to realize the potential of WS for improving clinical outcome of patients with COVID-19.
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Affiliation(s)
- Akash Saggam
- AYUSH Center of Excellence, Center for Complementary and Integrative Health, Interdisciplinary School of Health Sciences, Savitribai Phule Pune University, Pune, India
| | - Kirti Limgaokar
- Division of Biochemistry, Department of Chemistry, Fergusson College (Autonomous), Pune, India
| | - Swapnil Borse
- AYUSH Center of Excellence, Center for Complementary and Integrative Health, Interdisciplinary School of Health Sciences, Savitribai Phule Pune University, Pune, India
| | - Preeti Chavan-Gautam
- AYUSH Center of Excellence, Center for Complementary and Integrative Health, Interdisciplinary School of Health Sciences, Savitribai Phule Pune University, Pune, India
| | | | - Girish Tillu
- AYUSH Center of Excellence, Center for Complementary and Integrative Health, Interdisciplinary School of Health Sciences, Savitribai Phule Pune University, Pune, India
| | - Bhushan Patwardhan
- AYUSH Center of Excellence, Center for Complementary and Integrative Health, Interdisciplinary School of Health Sciences, Savitribai Phule Pune University, Pune, India
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Parida PK, Paul D, Chakravorty D. Nature's therapy for COVID-19: Targeting the vital non-structural proteins (NSP) from SARS-CoV-2 with phytochemicals from Indian medicinal plants. PHYTOMEDICINE PLUS : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 1:100002. [PMID: 35403083 PMCID: PMC7691168 DOI: 10.1016/j.phyplu.2020.100002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/06/2020] [Accepted: 11/24/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Containing COVID-19 is still a global challenge. It has affected the "normal" world by targeting its economy and health sector. The effect is shifting of focus of research from life threatening diseases like cancer. Thus, we need to develop a medical solution at the earliest. The purpose of this present work was to understand the efficacy of 22 rationally screened phytochemicals from Indian medicinal plants obtained from our previous work, following drug-likeness properties, against 6 non-structural-proteins (NSP) from SARS-CoV-2. METHODS 100 ns molecular dynamics simulations were performed, and relative binding free energies were computed by MM/PBSA. Further, principal component analysis, dynamic cross correlation and hydrogen bond occupancy were analyzed to characterize protein-ligand interactions. Biological pathway enrichment analysis was also carried out to elucidate the therapeutic targets of the phytochemicals in comparison to SARS-CoV-2. RESULTS The potential binding modes and favourable molecular interaction profile of 9 phytochemicals, majorly from Withania somnifera with lowest free binding energies, against the SARS-CoV-2 NSP targets were identified. It was understood that phytochemicals and 2 repurposed drugs with steroidal moieties in their chemical structures formed stable interactions with the NSPs. Additionally, human target pathway analysis for SARS-CoV-2 and phytochemicals showed that cytokine mediated pathway and phosphorylation pathways were with the most significant p-value. CONCLUSIONS To summarize this work, we suggest a global approach of targeting multiple proteins of SARS-CoV-2 with phytochemicals as a natural alternative therapy for COVID-19. We also suggest that these phytochemicals need to be tested experimentally to confirm their efficacy.
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Key Words
- ACPYPE, AnteChamberPYthon Parser interface
- ATP, Adenosine tri phosphate
- Binding energy
- COVID-19, Corona Virus Disease 2019
- DCCM, Dynamic Cross Correlation Matrix
- GO, Gene Ontology enrichment
- H-bond, Hydrogen Bond
- HIV, Human Immuno Deficiency Virus
- India
- JAK-STAT, The Janus kinase (JAK)-signal transducer and activator of transcription (STAT)
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MAPK, Mitogen-activated protein kinase
- MD, Molecular dynamics
- MM/PBSA, Molecular Mechanics/Poisson–Boltzmann (Generalized Born) surface area
- Molecular dynamics simulation
- NSP, Non Structural Proteins
- PCA, Principal Component Analysis
- PME, Particle-Mesh-Ewald summation
- Pathway enrichment
- Phytochemicals
- RMSD, Root mean square deviation
- RMSF, Root mean square fluctuations
- RNA, Ribonucleic Acid
- RdRp, RNA-dependent RNA polymerase
- Rg, Radius of gyration (Rg)
- SARS-CoV, Severe acute respiratory syndrome/coronavirus
- SARS-CoV-2
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2
- vdW, van der Waal's energy.
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Affiliation(s)
| | - Dipak Paul
- Noor Enzymes Private Limited, 37-B, Darga Road, Kolkata 700 017, India
| | - Debamitra Chakravorty
- Novel Techsciences (OPC) Private Limited, 37-B, Darga Road, 1st Floor, Kolkata 700 017, India
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Fakhri S, Piri S, Majnooni MB, Farzaei MH, Echeverría J. Targeting Neurological Manifestations of Coronaviruses by Candidate Phytochemicals: A Mechanistic Approach. Front Pharmacol 2021; 11:621099. [PMID: 33708124 PMCID: PMC7941749 DOI: 10.3389/fphar.2020.621099] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 12/08/2020] [Indexed: 01/08/2023] Open
Abstract
The novel coronavirus 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made a wide range of manifestations. In this regard, growing evidence is focusing on COVID-19 neurological associations; however, there is a lack of established pathophysiological mechanisms and related treatments. Accordingly, a comprehensive review was conducted, using electronic databases, including PubMed, Scopus, Web of Science, and Cochrane, along with the author's expertize in COVID-19 associated neuronal signaling pathways. Besides, potential phytochemicals have been provided against neurological signs of COVID-19. Considering a high homology among SARS-CoV, Middle East Respiratory Syndrome and SARS-CoV-2, revealing their precise pathophysiological mechanisms seems to pave the road for the treatment of COVID-19 neural manifestations. There is a complex pathophysiological mechanism behind central manifestations of COVID-19, including pain, hypo/anosmia, delirium, impaired consciousness, pyramidal signs, and ischemic stroke. Among those dysregulated neuronal mechanisms, neuroinflammation, angiotensin-converting enzyme 2 (ACE2)/spike proteins, RNA-dependent RNA polymerase and protease are of special attention. So, employing multi-target therapeutic agents with considerable safety and efficacy seems to show a bright future in fighting COVID-19 neurological manifestations. Nowadays, natural secondary metabolites are highlighted as potential multi-target phytochemicals in combating several complications of COVID-19. In this review, central pathophysiological mechanisms and therapeutic targets of SARS-CoV-2 has been provided. Besides, in terms of pharmacological mechanisms, phytochemicals have been introduced as potential multi-target agents in combating COVID-19 central nervous system complications.
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Affiliation(s)
- Sajad Fakhri
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sana Piri
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | | | - Mohammad Hosein Farzaei
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Javier Echeverría
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
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Parida PK, Paul D, Chakravorty D. The natural way forward: Molecular dynamics simulation analysis of phytochemicals from Indian medicinal plants as potential inhibitors of SARS-CoV-2 targets. Phytother Res 2020; 34:3420-3433. [PMID: 32969524 PMCID: PMC7537166 DOI: 10.1002/ptr.6868] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/19/2020] [Accepted: 08/22/2020] [Indexed: 01/08/2023]
Abstract
The pandemic COVID‐19 has become a global panic‐forcing life towards a compromised “new normal.” Antiviral therapy against SARS‐CoV‐2 is still lacking. Thus, development of natural inhibitors as a prophylactic measure is an attractive strategy. In this context, this work explored phytochemicals as potential inhibitors for SARS‐CoV‐2 by performing all atom molecular dynamics simulations using high performance computing for 8 rationally screened phytochemicals from Withania somnifera and Azadirachta indica and two repurposed drugs docked with the spike glycoprotein and the main protease of SARS‐CoV‐2. These phytochemicals were rationally screened from 55 Indian medicinal plants in our previous work. MM/PBSA, principal component analysis (PCA), dynamic cross correlation matrix (DCCM) plots and biological pathway enrichment analysis were performed to reveal the therapeutic efficacy of these phytochemicals. The results revealed that Withanolide R (−141.96 KJ/mol) and 2,3‐Dihydrowithaferin A (−87.60 KJ/mol) were with the lowest relative free energy of binding for main protease and the spike proteins respectively. It was also observed that the phytochemicals exhibit a remarkable multipotency with the ability to modulate various human biological pathways especially pathways in cancer. Conclusively we suggest that these compounds need further detailed in vivo experimental evaluation and clinical validation to implement them as potent therapeutic agents for combating SARS‐CoV‐2.
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Affiliation(s)
| | - Dipak Paul
- Research Scientist, Noor Enzymes Private Limited, Kolkata, India
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