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Farhadi S, Taghizadeh M, Mousavi-Niri N, Nemati F. Comparative Analysis of Leishmania major Nucleoside Hydrolases Toward Selecting Multi-target Strategy. Acta Parasitol 2024; 69:332-342. [PMID: 38085461 DOI: 10.1007/s11686-023-00748-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 11/06/2023] [Indexed: 05/01/2024]
Abstract
PURPOSE Leishmania causes multiple types of leishmaniasis in different parts of the world. It has a lack of metabolic machine to produce purine bases. Therefore, the parasite produces purine bases through the breakdown of nutritional nucleotides and it makes the nucleoside hydrolases (NHs) good drug targets. They have different substrate-preferring (SP) types. Our objectives were modeling and comparative analysis of these protein structures for Leishmania major. METHOD In this work, available sequences for all SP types of L. major NH enzymes including inosine-uridine preferring NH (IUNH), inosine-guanosine preferring NH (IGNH), and inosine-adenosine-guanosine preferring NH (IAGNH) were used to make 24 structural models via SWISS-MODEL and LOMETS. After evaluating the structural models, three enzyme structures were finalized and used to analyze substrate-binding pockets. RESULTS The three SP types of L. major NH enzymes that can breakdown purine nucleosides were highly different in terms of sequence, structure, and profile of interacting residues within the substrate-binding pockets. In this study, new enzyme structures have been presented for three SP types and they have been compared in different aspects and it indicated that they were very different from each other. CONCLUSION Although, previously indicated that from these three SP types in genera other than Leishmania, the role of IGNH and IAGNH was greater than IUNH in supplying purine bases, till this work, just IUNH has been structurally studied and used in drug-design investigations for Leishmania. Therefore, we are offering to use all three SP types of NHs as multi-target strategy in anti-leishmaniosis drug-design studies.
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Affiliation(s)
- Samaneh Farhadi
- Biotechnology Department, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, 1916893813, Iran
| | - Mohammad Taghizadeh
- Biotechnology Department, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, 1916893813, Iran.
| | - Neda Mousavi-Niri
- Biotechnology Department, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, 1916893813, Iran
| | - Fahimeh Nemati
- Biotechnology Department, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, 1916893813, Iran
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Abdallah AEM, Abdel-Latif SA, Elgemeie GH. Novel Fluorescent Benzothiazolyl-Coumarin Hybrids as Anti-SARS-COVID-2 Agents Supported by Molecular Docking Studies: Design, Synthesis, X-ray Crystal Structures, DFT, and TD-DFT/PCM Calculations. ACS OMEGA 2023; 8:19587-19602. [PMID: 37284548 PMCID: PMC10237303 DOI: 10.1021/acsomega.3c01085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/28/2023] [Indexed: 06/08/2023]
Abstract
This study revealed the design and preparation of new 3-(benzo[d]thiazol-2-yl)-2H-chromen-2-one derivatives 9a-h. The structures of the synthesized products were elucidated by their spectroscopic data and X-ray crystallography for compounds 9a and 9d. The prepared new compounds were measured for their fluorescence, and a good result indicated that the emission efficiency was decreased by increasing the electron-withdrawing groups from the unsubstituted compound 9a to the highly substituted derivative 9h (2 Br heavy atoms). On the other hand, the B3LYP/6-311G** theoretical level of theory was used to optimize the quantum mechanical calculations of the geometrical characteristics and energy of the novel compounds 9a-h under study. The electronic transition was investigated using the TD-DFT/PCM B3LYP approach, which uses time-dependent density functional calculations. Moreover, the compounds exhibited nonlinear optical properties (NLO) and a small HOMO-LUMO energy gap, which makes them easy to polarize. Furthermore, the acquired infrared spectra were compared with the expected harmonic vibrations of the substances 9a-h. On the other hand, binding energy analyses of compounds 9a-h with human corona virus nucleocapsid protein Nl63 (PDB ID: 5epw) were predicted using molecular docking and virtual screening tools. The results showed a promising binding and how these potent compounds were inhibiting the COVID-19 virus. Compound 9h was the most active anti-COVID-19 agent among all the synthesized benzothiazolyl-coumarin derivatives, as it forms five bonds. The presence of the two bromine atoms in its structure was responsible for the potent activity.
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Hanai T. Further quantitative in silico analysis of SARS-CoV-2 S-RBD Omicron BA.4, BA.5, BA.2.75, BQ.1, and BQ.1.1 transmissibility. Talanta 2023; 254:124127. [PMID: 36462284 PMCID: PMC9682881 DOI: 10.1016/j.talanta.2022.124127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022]
Abstract
The Covid-19 variants' transmissibility was further quantitatively analyzed in silico to study the binding strength with ACE-2 and find the binding inhibitors. The molecular interaction energy values of their optimized complex structures (MIFS) demonstrated that Omicron BA.4 and 5's MIFS value (344.6 kcal mol-1) was equivalent to wild-type MIFS (346.1 kcal mol-1), that of Omicron BQ.1 and BQ. 1.1's MIFS value (309.9 and 364.6 kcal mol-1). Furthermore, the MIFS value of Omicron BA.2.75 (515.1 kcal mol-1) was about Delta-plus (511.3 kcal mol-1). The binding strength of Omicron BA.4, BA. 5, and BQ.1.1 may be neglectable, but that of Omicron BA.2.75 was urging. Furthermore, the 79 medicine candidates were analyzed as the binding inhibitors from binding strength with ACE-2. Only carboxy compounds were repulsed from the ACE-2 binding site indicating that further modification of medical treatment candidates may produce an effective binding inhibitor.
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In Silico Study of Coumarins: Wedelolactone as a Potential Inhibitor of the Spike Protein of the SARS-CoV-2 Variants. J Trop Med 2023. [DOI: 10.1155/2023/4771745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Despite the rigorous global efforts to control SARS-CoV-2 transmission, it continues to pose a serious threat to humans with the frequent emergence of new variants. Thus, robust therapeutics to combat the virus are a desperate need. The SARS-CoV-2 spike (S) protein is an important target protein as it mediates the entry of the virus inside the host cells, which is initiated by the binding of the receptor-binding domain (RBD) to its cognate receptor, angiotensin-converting enzyme 2 (ACE-2). Herein, the inhibition potential of several naturally occurring coumarins was investigated against the spike proteins of SARS-CoV-2 variants using computational approaches. Molecular docking studies revealed 26 coumarins with better binding energies than the reference ligands, molnupiravir and ceftazidime, against the S-RBD of the omicron variant. The top 10 best-docked coumarins were further analyzed to understand their binding interactions against the spike proteins of other variants (wild-type, Alpha, Beta, Gamma, and Delta), and these studies also demonstrated decent binding energies. Physicochemical, QSAR, and pharmacokinetics analyses of the coumarins revealed wedelolactone as the best inhibitor of the spike protein with ideal Lipinski’s drug-likeness and optimal ADMET properties. Furthermore, coarse-grained molecular dynamics (MD) simulation studies of spike protein-wedelolactone complexes validated the stable binding of wedelolactone in the respective binding pockets. As an outcome, wedelolactone could be utilized to develop a potent drug candidate against COVID-19 by blocking the viral entry into the host cell.
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Insight into Triglyceride-reducing Potential of Quercetin in Blood Plasma Environment. Process Biochem 2023. [DOI: 10.1016/j.procbio.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Omar RA, Koparir P, Sarac K, Koparir M, Safin DA. A novel coumarin-triazole-thiophene hybrid: synthesis, characterization, ADMET prediction, molecular docking and molecular dynamics studies with a series of SARS-CoV-2 proteins. J CHEM SCI 2023; 135:6. [PMID: 36686402 PMCID: PMC9845830 DOI: 10.1007/s12039-022-02127-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 01/19/2023]
Abstract
Synthesis, characterization and theoretical studies of a novel coumarin-triazole-thiophene hybrid 4-(((4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazol-3-yl)thio)methyl)-6,7-dimethyl-2H-chromen-2-one (1), which was fabricated from 4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazole-3-thiol and 4-(chloromethyl)-6,7-dimethyl-2H-chromen-2-one, are reported. The resulting compound was characterized by microanalysis, IR, 1H, and 13C APT NMR spectroscopy. The DFT calculations examined the structure and electronic properties of 1 in gas phase. Its reactivity descriptors and molecular electrostatic potential revealed the reactivity and the reactive centers of 1. ADMET properties of 1 were evaluated using the respective online tools. It was established that 1 exhibit positive gastrointestinal absorption properties and negative human blood-brain barrier penetration. The Toxicity Model Report revealed that 1 belongs to toxicity class 4. Molecular docking was additionally applied to study the interaction of 1 with some SARS-CoV-2 proteins. It was established that the title compound is active against all the applied proteins with the most efficient interaction with Papain-like protease (PLpro). The interaction of 1 with the applied proteins was also studied using molecular dynamics simulations. Graphical abstract A novel coumarin-triazole-thiophene hybrid 4-(((4-ethyl-5-(thiophen-2-yl)-4H-1,2,4-triazol-3-yl)thio)methyl)-6,7-dimethyl-2H-chromen-2-one (1) is reported. The structure and electronic properties of 1 were examined by the DFT calculations. ADMET properties of 1 were also evaluated. Molecular docking and molecular dynamics simulations were applied to study interactions of 1 with a series of the SARS-CoV-2 proteins. Supplementary Information The online version contains supplementary material available at 10.1007/s12039-022-02127-0.
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Affiliation(s)
- Rebaz Anwar Omar
- Department of Chemistry, Faculty of Science and Health, Koya University, Koya KOY45, Kurdistan Region – F.R. Iraq Iraq
| | - Pelin Koparir
- Department of Chemistry, Institute of Forensics, Firat University, 23169 Elazig, Turkey
| | - Kamuran Sarac
- Department of Chemistry, Faculty of Art and Sciences, Bitlis Eren University, 13000 Bitlis, Turkey
| | - Metin Koparir
- Department of Chemistry, Faculty of Sciences, Firat University, 23000 Elazığ, Turkey
| | - Damir A Safin
- Scientific and Educational and Innovation Center for Chemical and Pharmaceutical Technologies, Ural Federal University named after the First President of Russia B. N. Yeltsin, Ekaterinburg, 620002 Russian Federation ,University of Tyumen, Volodarskogo Str. 6, 625003 Tyumen, Russian Federation
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Taxillus chinensis (DC.) Danser: a comprehensive review on botany, traditional uses, phytochemistry, pharmacology, and toxicology. Chin Med 2022; 17:136. [PMID: 36482376 PMCID: PMC9730624 DOI: 10.1186/s13020-022-00694-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/26/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Taxillus chinensis (DC.) Danser (T. chinensis), known as "Sangjisheng" in Chinese, is a member of the family Loranthaceae, with the traditional functions of "dispelling wind dampness, strengthening bones and muscles, and preventing miscarriage". Since Eastern Han dynasty, it has been used for the treatment of rheumatoid arthritis, arthralgia, threatened abortion, and hypertension. Nowadays, T. chinensis is included in the 2020 Edition of the Chinese Pharmacopoeia as Taxilli Herba. The purpose of this review is to summarize the latest research on T. chinensis in recent years, and make critical comments, so as to provide reference for the clinical application and modern research of T. chinensis. MAIN BODY In this review, we summarize the botany, traditional uses, and research advances in the phytochemistry and pharmacological effects of T. chinensis. Its toxicity has also been discussed. The published literature on current pharmacological and toxicological data has also been assessed. To date, approximately 110 compounds, including flavonoids, phenolic acids, phenylpropanoids, tannins, glycosides, amino acids, and nucleosides, have been identified in T. chinensis. Flavonoids are considered the most vital bioactive ingredients in T. chinensis. Pharmacological studies have demonstrated that T. chinensis possesses anti-inflammatory, antioxidant, anticancer, antimicrobial, antiviral, diuretic, antihypertensive, antihyperglycemic, and other properties. CONCLUSION Currently, research on T. chinensis is in the preliminary stages, and further research is required to understand the active compounds present and mechanisms of action. We hope that this comprehensive review of T. chinensis will serve as a background for further research.
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Mun CS, Hui LY, Sing LC, Karunakaran R, Ravichandran V. Multi-targeted molecular docking, pharmacokinetics, and drug-likeness evaluation of coumarin based compounds targeting proteins involved in development of COVID-19. Saudi J Biol Sci 2022; 29:103458. [PMID: 36187455 PMCID: PMC9512525 DOI: 10.1016/j.sjbs.2022.103458] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/25/2022] Open
Abstract
COVID-19 is a progressing pandemic of coronavirus disease-2019, which had drowned the whole world in a deep sorrow sea. Uncountable deaths were extending the list of deaths every single day. The present research was aimed to study the multi-target interaction of coumarins against COVID-19 using molecular docking analysis. The structure of coumarin compounds was checked for ADME and Lipinski rule of five by using SwissADME, an online tool. SARS-CoV-2 proteins such as RdRp, PLpro, Mpro and spike protein were collected from the Protein Data Bank. The molecular docking study was performed in the PyRx tool, and the molecular interactions were visualised by Discovery Studio Visualizer. All the coumarin compounds used in the study were obeyed Lipinski’s rule of 5 without any violations. All the three designed derivatives of phenprocoumon, hymecromone, and psoralen were showed high binding affinity and prominent interactions with the drug target. The presence of –OH groups in the compound, His41, a catalytic dyad in Mpro, number of and the distance of hydrogen bond interactions with SARS-CoV-2 targets was accountable for the high binding attractions. The modified drug structures possess better binding efficacy towards at least three targets compared to their parent compounds. Further, molecular dynamic studies can be suggested to find the ligand–protein complex stability. The present study outcome reveals that the designed coumarins can be synthesised and examined as a potent inhibitory drug of SARS-CoV-2.
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Affiliation(s)
- Chan Sook Mun
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia
| | - Lok Yong Hui
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia
| | - Lai Cong Sing
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia
| | - Rohini Karunakaran
- Unit of Biochemistry, Faculty of Medicine, AIMST University, Semeling 08100, Kedah, Malaysia.,Centre of Excellence for Biomaterial Science, AIMST University, Semeling 08100, Kedah, Malaysia
| | - Veerasamy Ravichandran
- Pharmaceutical Chemistry Unit, Faculty of Pharmacy, AIMST University, Semeling 08100, Malaysia.,Centre of Excellence for Biomaterial Science, AIMST University, Semeling 08100, Kedah, Malaysia.,Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
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Aslam H, Khan AU, Qazi NG, Ali F, Hassan SSU, Bungau S. Pharmacological basis of bergapten in gastrointestinal diseases focusing on H+/K+ ATPase and voltage-gated calcium channel inhibition: A toxicological evaluation on vital organs. Front Pharmacol 2022; 13:1005154. [DOI: 10.3389/fphar.2022.1005154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022] Open
Abstract
Aim and objectives: This study aimed to establish a pharmacological basis for evaluating the effects of bergapten (5-methoxypsoralen) in gastrointestinal diseases and assessment of its toxicological profile.Methods: The pharmacokinetic profile was evaluated using the SwissADME tool. AUTODOCK and PyRx were used for evaluating the binding affinities. The obtained results were further investigated for a post-dock analysis using Discovery Studio Visualizer 2016. The Desmond software package was used to conduct molecular dynamic simulations of best bound poses. Bergapten was further investigated for antidiarrheal, anti-secretory, charcoal meal transit time, anti-ulcer, anti-H. pylori activity.Results: Bergapten at a dose of 50, 100, and 200 mg/kg was proved effective in reducing diarrheal secretions, intestinal secretions, and distance moved by charcoal meal. Bergapten at the aforementioned doses acts as a gastroprotective agent in the ethanol-induced ulcer model that can be attributed to its effectiveness against H. pylori. Bergapten shows concentration-dependent relaxation of both spontaneous and K+ (80 mM)-induced contractions in the isolated rabbit jejunum model; the Ca2+ concentration–response curves (CRCs) were shifted to the right showing potentiating effect similar to papaverine. For molecular investigation, the H+/K+ ATPase inhibitory assay indicated inhibition of the pump comparable to omeprazole. Oxidative stress markers GST, GSH, and catalase showed increased expression, whereas the expression of LPO (lipid peroxidation) was reduced. Histopathological examination indicated marked improvement in cellular morphology. ELISA and western blot confirmed the reduction in inflammatory mediator expression. RT-PCR reduced the mRNA expression level of H+/K+ ATPase, confirming inhibition of the pump. The toxicological profile of bergapten was evaluated by an acute toxicity assay and evaluated for behavioral analysis, and the vital organs were used to analyze biochemical, hematological, and histopathological examination.Conclusion: Bergapten at the tested doses proved to be an antioxidant, anti-inflammatory, anti-ulcer, and antidiarrheal agent and relatively safe in acute toxicity assay.
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7,8-Dihydroxycoumarin derivatives: In silico molecular docking and in vitro anticholinesterase activity. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Novel Drug Design for Treatment of COVID-19: A Systematic Review of Preclinical Studies. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:2044282. [PMID: 36199815 PMCID: PMC9527439 DOI: 10.1155/2022/2044282] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/23/2022] [Accepted: 08/03/2022] [Indexed: 11/27/2022]
Abstract
Background Since the beginning of the novel coronavirus (SARS-CoV-2) disease outbreak, there has been an increasing interest in discovering potential therapeutic agents for this disease. In this regard, we conducted a systematic review through an overview of drug development (in silico, in vitro, and in vivo) for treating COVID-19. Methods A systematic search was carried out in major databases including PubMed, Web of Science, Scopus, EMBASE, and Google Scholar from December 2019 to March 2021. A combination of the following terms was used: coronavirus, COVID-19, SARS-CoV-2, drug design, drug development, In silico, In vitro, and In vivo. A narrative synthesis was performed as a qualitative method for the data synthesis of each outcome measure. Results A total of 2168 articles were identified through searching databases. Finally, 315 studies (266 in silico, 34 in vitro, and 15 in vivo) were included. In studies with in silico approach, 98 article study repurposed drug and 91 studies evaluated herbal medicine on COVID-19. Among 260 drugs repurposed by the computational method, the best results were observed with saquinavir (n = 9), ritonavir (n = 8), and lopinavir (n = 6). Main protease (n = 154) following spike glycoprotein (n = 62) and other nonstructural protein of virus (n = 45) was among the most studied targets. Doxycycline, chlorpromazine, azithromycin, heparin, bepridil, and glycyrrhizic acid showed both in silico and in vitro inhibitory effects against SARS-CoV-2. Conclusion The preclinical studies of novel drug design for COVID-19 focused on main protease and spike glycoprotein as targets for antiviral development. From evaluated structures, saquinavir, ritonavir, eucalyptus, Tinospora cordifolia, aloe, green tea, curcumin, pyrazole, and triazole derivatives in in silico studies and doxycycline, chlorpromazine, and heparin from in vitro and human monoclonal antibodies from in vivo studies showed promised results regarding efficacy. It seems that due to the nature of COVID-19 disease, finding some drugs with multitarget antiviral actions and anti-inflammatory potential is valuable and some herbal medicines have this potential.
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Alshawaf E, Hammad MM, Marafie SK, Ali H, Al-Mulla F, Abubaker J, Mohammad A. Discovery of natural products to block SARS-CoV-2 S-protein interaction with Neuropilin-1 receptor: A molecular dynamics simulation approach. Microb Pathog 2022; 170:105701. [PMID: 35963279 PMCID: PMC9364730 DOI: 10.1016/j.micpath.2022.105701] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 10/26/2022]
Abstract
Neuropilin-1 (NRP1) is a widely expressed cell surface receptor protein characterized by its pleiotropic function. Recent reports highlighted NRP1 as an additional entry point of the SARS-CoV-2 virus, enhancing viral infectivity by interacting with the S-protein of SARS-CoV-2. The ubiquitous distribution and mechanism of action of NRP1 enable the SARS-CoV-2 virus to attack multiple organs in the body simultaneously. Therefore, blocking NRP1 is a potential therapeutic approach against SARS-CoV-2 infection. The current study screened the South African natural compounds database (SANCDB) for molecules that can disrupt the SARS-CoV-2 S protein-NRP1 interaction as a potential antiviral target for SARS-CoV-2 cellular entry. Following excessive screening and validation analysis 3-O-Methylquercetin and Esculetin were identified as potential compounds to disrupt the S-protein-NRP1 interaction. Furthermore, to understand the conformational stability and dynamic features between NRP1 interaction with the selected natural products, we performed 200 ns molecular dynamics (MD) simulations. In addition, molecular mechanics-generalized Born surface area (MM/GBSA) was utilized to calculate the free binding energies of the natural products interacting with NRP1. 3-O-methylquercetin showed an inhibitory effect with binding energies ΔG of -25.52 ± 0.04 kcal/mol to NRP1, indicating the possible disruption of the NRP1-S-protein interaction. Our analysis demonstrated that 3-O-methylquercetin presents a potential antiviral compound against SARS-CoV-2 infectivity. These results set the path for future functional in-vitro and in-vivo studies in SARS-CoV-2 research.
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Affiliation(s)
- Eman Alshawaf
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait, 15462
| | - Maha M Hammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait, 15462
| | - Sulaiman K Marafie
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait, 15462
| | - Hamad Ali
- Faculty of Department of Medical Laboratory Sciences 2, Faculty of Allied Health Sciences, Health Sciences Center (HSC), Kuwait University, Jabriya, Kuwait University, Kuwait; Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait, 15462
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait, 15462
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait, 15462
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait, 15462.
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Quetglas-Llabrés MM, Quispe C, Herrera-Bravo J, Catarino MD, Pereira OR, Cardoso SM, Dua K, Chellappan DK, Pabreja K, Satija S, Mehta M, Sureda A, Martorell M, Satmbekova D, Yeskaliyeva B, Sharifi-Rad J, Rasool N, Butnariu M, Bagiu IC, Bagiu RV, Calina D, Cho WC. Pharmacological Properties of Bergapten: Mechanistic and Therapeutic Aspects. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8615242. [PMID: 35509838 PMCID: PMC9060977 DOI: 10.1155/2022/8615242] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/01/2021] [Accepted: 03/31/2022] [Indexed: 01/03/2023]
Abstract
Bergapten (BP) or 5-methoxypsoralen (5-MOP) is a furocoumarin compound mainly found in bergamot essential oil but also in other citrus essential oils and grapefruit juice. This compound presents antibacterial, anti-inflammatory, hypolipemic, and anticancer effects and is successfully used as a photosensitizing agent. The present review focuses on the research evidence related to the therapeutic properties of bergapten collected in recent years. Many preclinical and in vitro studies have been evidenced the therapeutic action of BP; however, few clinical trials have been carried out to evaluate its efficacy. These clinical trials with BP are mainly focused on patients suffering from skin disorders such as psoriasis or vitiligo. In these trials, the administration of BP (oral or topical) combined with UV irradiation induces relevant lesion clearance rates. In addition, beneficial effects of bergamot extract were also observed in patients with altered serum lipid profiles and in people with nonalcoholic fatty liver. On the contrary, there are no clinical trials that investigate the possible effects on cancer. Although the bioavailability of BP is lower than that of its 8-methoxypsoralen (8-MOP) isomer, it has fewer side effects allowing higher concentrations to be administered. In conclusion, although the use of BP has therapeutic applications on skin disorders as a sensitizing agent and as components of bergamot extract as hypolipemic therapy, more trials are necessary to define the doses and treatment guidelines and its usefulness against other pathologies such as cancer or bacterial infections.
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Affiliation(s)
- Maria Magdalena Quetglas-Llabrés
- Research Group in Community Nutrition and Oxidative Stress, University of the Balearic Islands and Health Research Institute of Balearic Islands (IdISBa), 07122 Palma de Mallorca, Spain
| | - Cristina Quispe
- Facultad de Ciencias de la Salud, Universidad Arturo Prat, Avda. Arturo Prat 2120, Iquique 1110939, Chile
| | - Jesús Herrera-Bravo
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomas, Chile
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| | - Marcelo D. Catarino
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Olívia R. Pereira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal
| | - Susana M. Cardoso
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo NSW 2007, Australia
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Kuala Lumpur 57000, Malaysia
| | - Kavita Pabreja
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar, Delhi G.T. Road (NH-1), Phagwara, 144411 Punjab, India
| | - Saurabh Satija
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar, Delhi G.T. Road (NH-1), Phagwara, 144411 Punjab, India
| | - Meenu Mehta
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar, Delhi G.T. Road (NH-1), Phagwara, 144411 Punjab, India
| | - Antoni Sureda
- Research Group in Community Nutrition and Oxidative Stress, University of the Balearic Islands and Health Research Institute of Balearic Islands (IdISBa), 07122 Palma de Mallorca, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Miquel Martorell
- Department of Nutrition and Dietetics, Faculty of Pharmacy, And Centre for Healthy Living, University of Concepción, 4070386 Concepción, Chile
| | - Dinara Satmbekova
- High School of Medicine, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Balakyz Yeskaliyeva
- Faculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | | | - Naeem Rasool
- Department Pharmacology and Toxicology, University of Veterinary and Animals Science, Lahore, Pakistan
| | - Monica Butnariu
- Banat's University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania” from Timisoara, Timisoara, Romania
| | - Iulia Cristina Bagiu
- Victor Babes University of Medicine and Pharmacy of Timisoara Department of Microbiology, Timisoara, Romania
- Multidisciplinary Research Center on Antimicrobial Resistance, Timisoara, Romania
| | - Radu Vasile Bagiu
- Victor Babes University of Medicine and Pharmacy of Timisoara Department of Microbiology, Timisoara, Romania
- Preventive Medicine Study Center, Timisoara, Romania
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
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14
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Suleimen YM, Jose RA, Suleimen RN, Ishmuratova MY, Toppet S, Dehaen W, Alsfouk AA, Elkaeed EB, Eissa IH, Metwaly AM. Isolation and In Silico SARS-CoV-2 Main Protease Inhibition Potential of Jusan Coumarin, a New Dicoumarin from Artemisia glauca. Molecules 2022; 27:2281. [PMID: 35408682 PMCID: PMC9000794 DOI: 10.3390/molecules27072281] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 12/31/2022] Open
Abstract
A new dicoumarin, jusan coumarin, (1), has been isolated from Artemisia glauca aerial parts. The chemical structure of jusan coumarin was estimated, by 1D, 2D NMR as well as HR-Ms spectroscopic methods, to be 7-hydroxy-6-methoxy-3-[(2-oxo-2H-chromen-6-yl)oxy]-2H-chromen-2-one. As the first time to be introduced in nature, its potential against SARS-CoV-2 has been estimated using various in silico methods. Molecular similarity and fingerprints experiments have been utilized for 1 against nine co-crystallized ligands of COVID-19 vital proteins. The results declared a great similarity between Jusan Coumarin and X77, the ligand of COVID-19 main protease (PDB ID: 6W63), Mpro. To authenticate the obtained outputs, a DFT experiment was achieved to confirm the similarity of X77 and 1. Consequently, 1 was docked against Mpro. The results clarified that 1 bonded in a correct way inside Mpro active site, with a binding energy of -18.45 kcal/mol. Furthermore, the ADMET and toxicity profiles of 1 were evaluated and showed the safety of 1 and its likeness to be a drug. Finally, to confirm the binding and understand the thermodynamic characters between 1 and Mpro, several molecular dynamics (MD) simulations studies have been administered. Additionally, the known coumarin derivative, 7-isopentenyloxycoumarin (2), has been isolated as well as β-sitosterol (3).
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Affiliation(s)
- Yerlan M. Suleimen
- The International Centre for Interdisciplinary Solutions on Antibiotics and Secondary Metabolites, Republican Collection of Microorganisms, Nur-Sultan 010000, Kazakhstan;
- The Laboratory of Engineering Profile of NMR Spectroscopy, Sh. Ualikhanov Kokshetau University, Kokshetau 020000, Kazakhstan
| | - Rani A. Jose
- Molecular Design & Synthesis, Department of Chemistry, Catholic University of Leuven, B-3001 Leuven, Belgium; (R.A.J.); (S.T.); (W.D.)
- Department of Chemistry, St. Dominic’s College, Mahatma Gandhi University, Kanjirappally 686512, India
| | - Raigul N. Suleimen
- Department of Technical Physics, Faculty of Physics and Technology, L.N. Gumilyov Eurasian National University, Nur-Sultan 010010, Kazakhstan
| | | | - Suzanne Toppet
- Molecular Design & Synthesis, Department of Chemistry, Catholic University of Leuven, B-3001 Leuven, Belgium; (R.A.J.); (S.T.); (W.D.)
| | - Wim Dehaen
- Molecular Design & Synthesis, Department of Chemistry, Catholic University of Leuven, B-3001 Leuven, Belgium; (R.A.J.); (S.T.); (W.D.)
| | - Aisha A. Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh 13713, Saudi Arabia;
| | - Ibrahim H. Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt;
| | - Ahmed M. Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
- Biopharmaceutical Product Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, Alexandria 21934, Egypt
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15
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Isika DK, Özkömeç FN, Çeşme M, Sadik OA. Synthesis, biological and computational studies of flavonoid acetamide derivatives. RSC Adv 2022; 12:10037-10050. [PMID: 35424949 PMCID: PMC8966662 DOI: 10.1039/d2ra01375d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/23/2022] [Indexed: 12/14/2022] Open
Abstract
This study reports the synthesis and characterization of a novel class of flavonoid acetamide derivatives (FA) of quercetin, apigenin, fisetin, kaempferol, and luteolin. Flavonoids display numerous biological properties but are limited by aqueous insolubility, enzymatic degradation, instability, and low bioavailability. FAs were synthesized, with 80–82% yields, through the sequential modification of the flavonoid hydroxyl groups into the acetamide moieties. Bioavailability, antioxidant, and ADMET are structure–activity-dependent properties that vary across different classes of flavonoids and dictate the prevalent biological applications of the flavonoids. Thus, the FAs were evaluated for their bioavailability, antioxidant, and ADMET toxicity properties versus the unmodified flavonoids (UFs). In vitro bioavailability analysis shows that the UFs have bio-availabilities in the range of 10.78–19.29% against that of the FAs in the range of 20.70–34.87%. The antioxidant capacity was measured using the 2,2-diphenyl-1-picrylhydrazyl (DPPH·) assay with recorded IC50 values of 2.19–13.03 μM for the UFs. Conversely, the FAs had high DPPH IC50 values ranging from 33.83 to 67.10 μM and corresponding to lower antioxidant activity. The FAs showed favorable ADMET properties. The modification of flavonoids into FAs significantly improves the bioavailability and the ADMET toxicity properties, albeit with decreased antioxidant activity. This work highlights the effect of the global modification of the flavonoids with the acetamide groups on the bioavailability, antioxidant, and ADMET toxicity properties which are critical determinants in the biological applications of the flavonoids. This study reports the synthesis and characterization of a novel class of flavonoid acetamide derivatives (FA) of quercetin, apigenin, fisetin, kaempferol, and luteolin.![]()
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Affiliation(s)
- Daniel K Isika
- Department of Chemistry and Environmental Science, BioSensor Materials for Advanced Research & Technology (BioSMART Center), New Jersey Institute of Technology, University Heights 161 Warren Street Newark NJ 07102 USA
| | - Fatma Nur Özkömeç
- Department of Biology, Faculty of Art and Sciences, Kahramanmaras Sutcu Imam University 46040 Kahramanmaras Turkey
| | - Mustafa Çeşme
- Department of Chemistry, Faculty of Art and Sciences, Kahramanmaras Sutcu Imam University 46040 Kahramanmaras Turkey
| | - Omowunmi A Sadik
- Department of Chemistry and Environmental Science, BioSensor Materials for Advanced Research & Technology (BioSMART Center), New Jersey Institute of Technology, University Heights 161 Warren Street Newark NJ 07102 USA
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16
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Keri RS, Budagumpi S, Balappa Somappa S. Synthetic and natural coumarins as potent anticonvulsant agents: A review with structure-activity relationship. J Clin Pharm Ther 2022; 47:915-931. [PMID: 35288962 DOI: 10.1111/jcpt.13644] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/09/2022] [Accepted: 02/24/2022] [Indexed: 12/25/2022]
Abstract
WHAT IS KNOWN AND OBJECTIVE The main objective of this review is to highlight the most relevant studies since 1990 (to date) in the area of medicinal chemistry aspects to provide a panoramic view to the biologists/medicinal chemists working in this area and would assist them in their efforts to design, synthesize and extract (from natural source) coumarin-based anticonvulsant agents. Also, the structure-activity relationship (SAR) studies are also discussed for further rational design of this kind of derivatives. It is hoped that this review will be helpful for new thoughts in the quest for rational designs of more active and less toxic coumarin-based antiepileptic agents. METHODS A literature review emphasizing the application of coumarin core as antiepileptic agents identify articles related to the topic; we performed a standardized search from 1990 to November 2021, using search engines like Scifinder, web of Science, Pubmed and Scopus. RESULTS AND DISCUSSION This review gives an overview of attempts to shed light and compile published reports on coumarin derivatives along with some opinions on different approaches to help the medicinal chemists in designing future generation potent yet safer anticonvulsant agents. The possible structure-activity relationships (SARs) will also be discussed to indicate the direction for the rational design of more effective candidates. WHAT IS NEW AND CONCLUSION The findings from this review provide new indications or directions for the discovery of new and better drugs from synthetic and naturally occurring coumarins as antiepileptic agents. In our review, we have tried to depict the recent researches which made in the design and development of novel anticonvulsant compounds with coumarin nucleus. Also, SAR of expressed derivatives indicated that the choice of a fitting substitution containing electron-withdrawing/donating groups to coumarin or with some heterocyclic moieties joined to parent coumarin skeleton assumes an essential role in changing the anticonvulsant activity of synthesized derivatives. These findings encourage the scientific community towards the optimization of the pharmacological profile of this structural moiety as an important scaffold for the treatment of epilepsy.
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Affiliation(s)
- Rangappa S Keri
- Centre for Nano and Material Sciences, Jain University, Bangalore, India
| | | | - Sasidhar Balappa Somappa
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.,Organic Chemistry Section, Chemical Sciences and Technology Division, Council of Scientific and Industrial Research (CSIR)-National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram, India
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17
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Shoman ME, Abd El-Hafeez AA, Khobrani M, Assiri AA, Al Thagfan SS, Othman EM, Ibrahim ARN. Molecular docking and dynamic simulations study for repurposing of multitarget coumarins against SARS-CoV-2 main protease, papain-like protease and RNA-dependent RNA polymerase. PHARMACIA 2022. [DOI: 10.3897/pharmacia.69.e77021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Proteases and RNA-Dependent RNA polymerase, major enzymes which are essential targets involved in the life and replication of SARS-CoV-2. This study aims at in silico examination of the potential ability of coumarins and their derivatives to inhibit the replication of SARS-Cov-2 through multiple targets, including the main protease, papain-like protease and RNA-Dependent RNA polymerase. Several coumarins as biologically active compounds were studied, including coumarin antibiotics and some naturally reported antiviral coumarins. Aminocoumarin antibiotics, especially coumermycin, showed a high potential to bind to the enzymes’ active site, causing possible inhibition and termination of viral life. They demonstrate the ability to bind to residues essential for triggering the crucial cascades within the viral cell. Molecular dynamics simulations for 50 ns supported these data pointing out the formation of rigid, stable Coumermycin/enzyme complexes. These findings strongly suggest the possible use of Coumermycin, Clorobiocin or Novobiocin in the fight against COVID-19, but biological evidence is still required to support such suggestions.
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18
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Kittakoop P, Darshana D, Sangsuwan R, Mahidol C. Alkaloids and Alkaloid-Like Compounds are Potential Scaffolds of Antiviral Agents against SARS-CoV-2 (COVID-19) Virus. HETEROCYCLES 2022. [DOI: 10.3987/rev-22-sr(r)3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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19
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Mohamed NM, Eltelbany RFA. Synthetic Coumarin Derivatives as SARS‐CoV‐2 Major Protease Inhibitors: Design, Synthesis, Bioevaluation and Molecular Docking. ChemistrySelect 2021. [DOI: 10.1002/slct.202103658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Nada M. Mohamed
- Pharmaceutical Chemistry Department Faculty of Pharmacy Modern University for Technology and Information (MTI) Cairo 11585 Egypt
| | - Rania F. A. Eltelbany
- Biochemistry Department Faculty of Pharmacy Modern University for Technology and Information (MTI) Cairo 11585 Egypt
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20
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Lochab A, Thareja R, Gadre SD, Saxena R. Potential Protein and Enzyme Targets for In‐silico Development and Repurposing of Drug Against Coronaviruses. ChemistrySelect 2021. [DOI: 10.1002/slct.202103350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amit Lochab
- Department of Chemistry Kirori Mal College University of Delhi Delhi India
| | - Rakhi Thareja
- Department of Chemistry St. Stephens College University of Delhi Delhi India
| | - Sangeeta D. Gadre
- Department of Physics Kirori Mal College University of Delhi Delhi India
| | - Reena Saxena
- Department of Chemistry Kirori Mal College University of Delhi Delhi India
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21
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Myrtsi ED, Angelis A, Koulocheri SD, Mitakou S, Haroutounian SA. Retrieval of High Added Value Natural Bioactive Coumarins from Mandarin Juice-Making Industrial Byproduct. Molecules 2021; 26:7527. [PMID: 34946609 PMCID: PMC8708529 DOI: 10.3390/molecules26247527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 01/02/2023] Open
Abstract
Cold pressed essential oil (CPEO) of mandarin (Citrus reticulata Blanco), a by-product of the juice-making industrial process known to contain large amounts of polymethoxyflavones, was exploited for its content in high added value natural coumarins. The study herein afforded a method referring to the evaporation of CPEO volatile fraction under mild conditions (reduced pressure and temperature below 35 °C) as azeotrope with isopropanol. This allowed the isolation of high added value coumarins from the non-volatile fragment using preparative High Performance Liquid Chromatography (HPLC). Pilot-scale application of this procedure afforded for each kg of CPEO processed the following natural bioactive coumarins in chemically pure forms: heraclenol (38-55 mg), 8-gerayloxypsoralen (35-51 mg), auraptene (22-33 mg), and bergamottin (14-19 mg). The structures of coumarins were verified by Nuclear Magnetic Resonance (NMR) spectroscopy and HPLC co-injection with authentic standards. Thus, the low market value mandarin CPEO with current value of 17 to 22 EUR/kg can be valorized through the production of four highly bioactive natural compounds worth 3479 to 5057 EUR/kg, indicating the great potentials of this methodology in the terms of the circular economy.
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Affiliation(s)
- Eleni D. Myrtsi
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.D.M.); (S.D.K.)
| | - Apostolis Angelis
- Division of Pharmacognosy and Chemistry of Natural Products, Faculty of Pharmacy, University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (A.A.); (S.M.)
| | - Sofia D. Koulocheri
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.D.M.); (S.D.K.)
| | - Sofia Mitakou
- Division of Pharmacognosy and Chemistry of Natural Products, Faculty of Pharmacy, University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (A.A.); (S.M.)
| | - Serkos A. Haroutounian
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.D.M.); (S.D.K.)
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22
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Saha P, Bose S, Srivastava AK, Chaudhary AA, Lall R, Prasad S. Jeopardy of COVID-19: Rechecking the Perks of Phytotherapeutic Interventions. Molecules 2021; 26:6783. [PMID: 34833873 PMCID: PMC8621307 DOI: 10.3390/molecules26226783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 01/31/2023] Open
Abstract
The novel coronavirus disease (COVID-19), the reason for worldwide pandemic, has already masked around 220 countries globally. This disease is induced by Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). Arising environmental stress, increase in the oxidative stress level, weak immunity and lack of nutrition deteriorates the clinical status of the infected patients. Though several researches are at its peak for understanding and bringing forward effective therapeutics, yet there is no promising solution treating this disease directly. Medicinal plants and their active metabolites have always been promising in treating many clinical complications since time immemorial. Mother nature provides vivid chemical structures, which act multi-dimensionally all alone or synergistically in mitigating several diseases. Their unique antioxidant and anti-inflammatory activity with least side effects have made them more effective candidate for pharmacological studies. These medicinal plants inhibit attachment, encapsulation and replication of COVID-19 viruses by targeting various signaling molecules such as angiotensin converting enzyme-2, transmembrane serine protease 2, spike glycoprotein, main protease etc. This property is re-examined and its potency is now used to improve the existing global health crisis. This review is an attempt to focus various antiviral activities of various noteworthy medicinal plants. Moreover, its implications as prophylactic or preventive in various secondary complications including neurological, cardiovascular, acute kidney disease, liver disease are also pinpointed in the present review. This knowledge will help emphasis on the therapeutic developments for this novel coronavirus where it can be used as alone or in combination with the repositioned drugs to combat COVID-19.
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Affiliation(s)
- Priyanka Saha
- Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, WB, India; (P.S.); (S.B.); (A.K.S.)
| | - Subhankar Bose
- Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, WB, India; (P.S.); (S.B.); (A.K.S.)
| | - Amit Kumar Srivastava
- Cancer Biology & Inflammatory Disorder Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, WB, India; (P.S.); (S.B.); (A.K.S.)
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSUI), Riyadh 11623, Saudi Arabia;
| | - Rajiv Lall
- Noble Pharma, LLC, 4602 Domain Drive, Menomonie, WI 54751, USA;
| | - Sahdeo Prasad
- Noble Pharma, LLC, 4602 Domain Drive, Menomonie, WI 54751, USA;
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23
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An Overview of COVID-19 and the Potential Plant Harboured Secondary Metabolites against SARS-CoV-2: A Review. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.3.52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The SARS-CoV-2 virus causes COVID-19, a pandemic disease, and it is called the novel coronavirus. It belongs to the Coronaviridae family and has been plagued the world since the end of 2019. Viral infection to the lungs causes fluid filling and breathing difficulties, which leads to pneumonia. Pneumonia progresses to ARDS (Acute Respiratory Distress Syndrome), in which fluid fills the air sac and seeps from the pulmonary veins. In the current scenario, several vaccines have been used to control the pandemic worldwide. Even though vaccines are available and their effectiveness is short, it may be helpful to curb the pandemic, but long-term protection is inevitable when we look for other options. Plants have diversified components such as primary and secondary metabolites. These molecules show several activities such as anti-microbial, anti-cancer, anti-helminthic. In addition, these molecules have good binding ability to the SARS-CoV-2 virus proteins such as RdRp (RNA-dependent RNA polymerase), Mpro (Main Protease), etc. Therefore, these herbal molecules could probably be used to control the COVID-19. However, pre-requisite tests, such as cytotoxicity, in vivo, and human experimental studies, are required before plant molecules can be used as potent drugs. Plant metabolites such as alkaloids, isoquinoline ß-carboline, and quinoline alkaloids such as skimmianine, quinine, cinchonine, and dictamine are present in plants and used in a traditional medicinal system.
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24
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Malekmohammad K, Rafieian-Kopaei M. Mechanistic Aspects of Medicinal Plants and Secondary Metabolites against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Curr Pharm Des 2021; 27:3996-4007. [PMID: 34225607 DOI: 10.2174/1381612827666210705160130] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 06/01/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND OBJECTIVE The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), a highly pathogenic virus, is responsible for a respiratory disease termed coronavirus disease 2019 (COVID-19). SARS-CoV-2 genome encodes various structural and non-structural proteins, which are necessary for viral entry and replication. Among these proteins, papain-like protease (PLpro), 3C-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), helicase, a serine protease, and spike protein are potential targets of herbal remedies and phytocompounds for inhibition of viral infection and replication. There is at present no confirmed cure for the COVID-19. Various plants and their components have been introduced against SARS-Co-2. A number of review articles have also been published on them. This article is focusing on the mechanistic aspects of these plants and their derivatives on SARS-CV-2. METHOD The material in this review article was prepared from significant scientific databases, including Web of Science, PubMed, Science Direct, Scopus and Google Scholar. RESULTS Different medicinal plants and their phytocompounds interact with important structural and non-structural of SARS-CoV-2 proteins. Natural compounds form strong bonds with the active site of SARS-CoV-2 protease and make large conformational changes. These phytochemicals are potential inhibitors of structural and non-structural of SARS-CoV-2 proteins such as Spike protein, PLpro, and 3CLpro. Some important anti-SARS-CoV-2 actions of medicinal plants and their metabolites are inhibition of the virus replication or entry, blocking the angiotensin-converting enzyme 2 (ACE-2) receptor and "Transmembrane protease, serine 2 (TMPRSS2)" regulation of inflammatory mediators, inhibition of endothelial activation, toll-like receptors (TLRs) and activation of the nuclear factor erythroid-derived 2-related factor 2 (Nrf2). Some of these important natural immune boosters that are helpful for prevention and curing various symptoms related to COVID-19 include Allium sativum, Nigella sativa, Glycyrrhiza glabra Zingiber officinalis, Ocimum sanctum, Withania somnifera, Tinospora cordifolia, and Scutellaria baicalensis. Also, Kaempferol, Quercetin, Baicalin, Scutellarin, Glycyrrhizin, Curcumin, Apigenin, Ursolic acid, and Chloroquine are the best candidates for treating the symptoms associated with SARS-CoV-2 infection. CONCLUSION Medicinal plants and/or their bioactive compounds with inhibitory effects against SARS-CoV-2 support the human immune system and help in fighting against COVID-19 and rejuvenating the immune system.
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Affiliation(s)
| | - Mahmoud Rafieian-Kopaei
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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25
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Cárdenas-Rodríguez N, Bandala C, Vanoye-Carlo A, Ignacio-Mejía I, Gómez-Manzo S, Hernández-Cruz EY, Pedraza-Chaverri J, Carmona-Aparicio L, Hernández-Ochoa B. Use of Antioxidants for the Neuro-Therapeutic Management of COVID-19. Antioxidants (Basel) 2021; 10:971. [PMID: 34204362 PMCID: PMC8235474 DOI: 10.3390/antiox10060971] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 02/07/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is an emergent infectious disease that has caused millions of deaths throughout the world. COVID-19 infection's main symptoms are fever, cough, fatigue, and neurological manifestations such as headache, myalgias, anosmia, ageusia, impaired consciousness, seizures, and even neuromuscular junctions' disorders. In addition, it is known that this disease causes a series of systemic complications such as adverse respiratory distress syndrome, cardiac injury, acute kidney injury, and liver dysfunction. Due to the neurological symptoms associated with COVID-19, damage in the central nervous system has been suggested as well as the neuroinvasive potential of SARS-CoV-2. It is known that CoV infections are associated with an inflammation process related to the imbalance of the antioxidant system; cellular changes caused by oxidative stress contribute to brain tissue damage. Although anti-COVID-19 vaccines are under development, there is no specific treatment for COVID-19 and its clinical manifestations and complications; only supportive treatments with immunomodulators, anti-vascular endothelial growth factors, modulating drugs, statins, or nutritional supplements have been used. In the present work, we analyzed the potential of antioxidants as adjuvants for the treatment of COVID-19 and specifically their possible role in preventing or decreasing the neurological manifestations and neurological complications present in the disease.
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Affiliation(s)
- Noemí Cárdenas-Rodríguez
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secreatría de Salud, Ciudad de México 04530, Mexico; (A.V.-C.); (L.C.-A.)
| | - Cindy Bandala
- Division de Neurociencias, Instituto Nacional de Rehabilitación, Secretaría de Salud, Ciudad de México 14389, Mexico;
- Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
| | - América Vanoye-Carlo
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secreatría de Salud, Ciudad de México 04530, Mexico; (A.V.-C.); (L.C.-A.)
| | - Iván Ignacio-Mejía
- Laboratorio de Medicina Traslacional, Escuela Militar de Graduados de Sanidad, SEDENA, Ciudad de México 11200, Mexico;
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Ciudad de México 04530, Mexico;
| | | | - José Pedraza-Chaverri
- Departamento de Biología, Facultad de Química, UNAM, Ciudad de México 04150, Mexico; (E.Y.H.-C.); (J.P.-C.)
| | - Liliana Carmona-Aparicio
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secreatría de Salud, Ciudad de México 04530, Mexico; (A.V.-C.); (L.C.-A.)
| | - Beatriz Hernández-Ochoa
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Ciudad de México 06720, Mexico;
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26
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Merarchi M, Dudha N, Das BC, Garg M. Natural products and phytochemicals as potential anti-SARS-CoV-2 drugs. Phytother Res 2021; 35:5384-5396. [PMID: 34132421 PMCID: PMC8441929 DOI: 10.1002/ptr.7151] [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: 12/24/2020] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 12/12/2022]
Abstract
The current pandemic responsible for the crippling of the health care system is caused by the novel SARS‐CoV‐2 in 2019 and leading to coronavirus disease 2019 (COVID‐19). The virus enters into humans by attachment of its Spike protein (S) to the ACE receptor present on the lung epithelial cell surface followed by cleavage of S protein by the cellular transmembrane serine protease (TMPRSS2). After entry, the SARS‐CoV‐2 RNA genome is released into the cytosol, where it highjacks host replication machinery for viral replication, assemblage, as well as the release of new viral particles. The major drug targets that have been identified for SARS‐CoV‐2 through host‐virus interaction studies include 3CLpro, PLpro, RNA‐dependent RNA polymerase, and S proteins. Several reports of natural compounds along with synthetic products have displayed promising results and some of them are Tripterygium wilfordii, Pudilan Xiaoyan Oral Liquid, Saponin derivates, Artemisia annua, Glycyrrhiza glabra L., Jinhua Qinggan granules, Xuebijing, and Propolis. This review attempts to disclose the natural products identified as anti‐SARS‐CoV‐2 based on in silico prediction and the effect of a variety of phytochemicals either alone and/or in combination with conventional treatments along with their possible molecular mechanisms involved for both prevention and treatment of the SARS‐CoV‐2 disease.
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Affiliation(s)
- Myriam Merarchi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Namrata Dudha
- Department of Biotechnology and Microbiology, School of Sciences, Noida International University, Gautam Budh Nagar, India
| | - Bhudev C Das
- Amity Institute of Molecular Medicine and Stem cell Research (AIMMSCR), Amity University Uttar Pradesh, Noida, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem cell Research (AIMMSCR), Amity University Uttar Pradesh, Noida, India
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27
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Fakhri S, Nouri Z, Moradi SZ, Akkol EK, Piri S, Sobarzo-Sánchez E, Farzaei MH, Echeverría J. Targeting Multiple Signal Transduction Pathways of SARS-CoV-2: Approaches to COVID-19 Therapeutic Candidates. Molecules 2021; 26:2917. [PMID: 34068970 PMCID: PMC8156180 DOI: 10.3390/molecules26102917] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/30/2021] [Accepted: 05/11/2021] [Indexed: 02/06/2023] Open
Abstract
Due to the complicated pathogenic pathways of coronavirus disease 2019 (COVID-19), related medicinal therapies have remained a clinical challenge. COVID-19 highlights the urgent need to develop mechanistic pathogenic pathways and effective agents for preventing/treating future epidemics. As a result, the destructive pathways of COVID-19 are in the line with clinical symptoms induced by severe acute coronary syndrome (SARS), including lung failure and pneumonia. Accordingly, revealing the exact signaling pathways, including inflammation, oxidative stress, apoptosis, and autophagy, as well as relative representative mediators such as tumor necrosis factor-α (TNF-α), nuclear factor erythroid 2-related factor 2 (Nrf2), Bax/caspases, and Beclin/LC3, respectively, will pave the road for combating COVID-19. Prevailing host factors and multiple steps of SARS-CoV-2 attachment/entry, replication, and assembly/release would be hopeful strategies against COVID-19. This is a comprehensive review of the destructive signaling pathways and host-pathogen interaction of SARS-CoV-2, as well as related therapeutic targets and treatment strategies, including potential natural products-based candidates.
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Affiliation(s)
- Sajad Fakhri
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah 6734667149, Iran; (S.F.); (S.Z.M.); (S.P.)
| | - Zeinab Nouri
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah 6714415153, Iran;
| | - Seyed Zachariah Moradi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah 6734667149, Iran; (S.F.); (S.Z.M.); (S.P.)
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah 6734667149, Iran
| | - Esra Küpeli Akkol
- Department of Pharmacognosy, Faculty of Pharmacy, Gazi University, Etiler, Ankara 06330, Turkey;
| | - Sana Piri
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah 6734667149, Iran; (S.F.); (S.Z.M.); (S.P.)
| | - Eduardo Sobarzo-Sánchez
- Instituto de Investigación y Postgrado, Facultad de Ciencias de la Salud, Universidad Central de Chile, Santiago 8330507, Chile
- Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Mohammad Hosein Farzaei
- Medical Technology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah 6734667149, Iran
| | - Javier Echeverría
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170022, Chile
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28
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Noorbakhsh A, Askandar RH, Alhagh MS, Farshadfar C, Seyedi SH, Ahmadizad M, Rahimi A, Ardalan N, Koushki EH. Prevention of SARS-CoV-2 Proliferation with a Novel and Potent Main Protease Inhibitor by Docking, ADMET, MM-PBSA, and Molecular Dynamics Simulation. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416521500149] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
COVID-19 is the last disease caused by SARS-CoV-2 associated with a severe immune response and lung damage. The main protease (Mpro) has a vital role in SARS-CoV-2 proliferation. Moreover, humans lack homologous Mpro, which makes the Mpro a suitable drug target for the development of SARS-CoV-2 drugs. The purchasable L5000 library (Selleckchem Inc) includes 99,040 compounds that were used for virtual screening. After molecular docking and ADME studies, we selected a compound (WAY-604395) with a potent binding affinity to the Mpro active site and acceptable ADME properties compared to the reference drug (nelfinavir). Molecular dynamics (MD) simulation outcomes have proved that the Mpro-WAY604395 complex possesses a considerable value of flexibility, stability, compactness and binding energy. Our Molecular Mechanics Poisson–Boltzmann Surface Area (MM-PBSA) calculation demonstrates that WAY-604395 is more potent ([Formula: see text]272.19[Formula: see text]kcal mol[Formula: see text]) in comparison with nelfinavir ([Formula: see text]173.39[Formula: see text]kcal[Formula: see text]mol[Formula: see text]) against SARS-CoV-2 Mpro. In conclusion, we suggest that WAY-604395 has the potential for the treatment of SARS-CoV-2 by inhibition of the Mpro.
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Affiliation(s)
- Akbar Noorbakhsh
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | | | - Mohammad Shakib Alhagh
- School of Life Science, University of Nottingham, Biodiscovery Institute, Nottingham, UK
| | - Chiako Farshadfar
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Seyed Hamid Seyedi
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Mehran Ahmadizad
- Department of Biochemistry, Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Arian Rahimi
- Young Researchers and Elite Club, East Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Noeman Ardalan
- Department of Microbiology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Elnaz Hosseininezhadian Koushki
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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29
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Joshi G, Sindhu J, Thakur S, Rana A, Sharma G, Mayank, Poduri R. Recent efforts for drug identification from phytochemicals against SARS-CoV-2: Exploration of the chemical space to identify druggable leads. Food Chem Toxicol 2021; 152:112160. [PMID: 33823228 PMCID: PMC8018909 DOI: 10.1016/j.fct.2021.112160] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023]
Abstract
Nature, which remains a central drug discovery pool, is always looked upon to find a putative druggable lead. The natural products and phytochemical derived from plants are essential during a global health crisis. This class represents one of the most practical and promising approaches to decrease pandemic's intensity owing to their therapeutic potential. The present manuscript is therefore kept forth to give the researchers updated information on undergoing research in allied areas of natural product-based drug discovery, particularly for Covid-19 disease. The study briefly shreds evidence from in vitro and in silico researches done so far to find a lead molecule against Covid-19. Following this, we exhaustively explored the concept of chemical space and molecular similarity parameters for the drug discovery about the lead(s) generated from in silico-based studies. The comparison was drawn using FDA-approved anti-infective agents during 2015–2020 using key descriptors to evaluate druglike properties. The outcomes of results were further corroborated using Molecular Dynamics studies which suggested the outcomes in alignment with chemical space ranking. In a nutshell, current research work aims to provide a holistic strategic approach to drug design, keeping in view the identified phytochemicals against Covid-19.
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Affiliation(s)
- Gaurav Joshi
- Department of Pharmaceutical Sciences and Natural Products, School of Health Sciences, Central University of Punjab, Bathinda, 151 401, India; School of Pharmacy, Graphic Era Hill University, Dehradun, 248171, India.
| | - Jayant Sindhu
- Department of Chemistry, COBS & H, CCS Haryana Agricultural University, Hisar, 125 004 India
| | - Shikha Thakur
- Department of Pharmaceutical Sciences and Natural Products, School of Health Sciences, Central University of Punjab, Bathinda, 151 401, India
| | - Abhilash Rana
- Amity Institute of Biotechnology, Amity University, Sector 125 Noida, Uttar Pradesh, India
| | - Geetika Sharma
- Amity Institute of Biotechnology, Amity University, Sector 125 Noida, Uttar Pradesh, India
| | - Mayank
- Shobhaben Pratapbhai Patel - School of Pharmacy & Technology Management, SVKM's NMIMS University, Vile Parle, Mumbai, 400056, India.
| | - Ramarao Poduri
- Department of Pharmaceutical Sciences and Natural Products, School of Health Sciences, Central University of Punjab, Bathinda, 151 401, India.
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30
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Molecular Docking Study on Several Benzoic Acid Derivatives against SARS-CoV-2. Molecules 2020; 25:molecules25245828. [PMID: 33321862 PMCID: PMC7770597 DOI: 10.3390/molecules25245828] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/20/2022] Open
Abstract
Several derivatives of benzoic acid and semisynthetic alkyl gallates were investigated by an in silico approach to evaluate their potential antiviral activity against SARS-CoV-2 main protease. Molecular docking studies were used to predict their binding affinity and interactions with amino acids residues from the active binding site of SARS-CoV-2 main protease, compared to boceprevir. Deep structural insights and quantum chemical reactivity analysis according to Koopmans’ theorem, as a result of density functional theory (DFT) computations, are reported. Additionally, drug-likeness assessment in terms of Lipinski’s and Weber’s rules for pharmaceutical candidates, is provided. The outcomes of docking and key molecular descriptors and properties were forward analyzed by the statistical approach of principal component analysis (PCA) to identify the degree of their correlation. The obtained results suggest two promising candidates for future drug development to fight against the coronavirus infection.
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