Abstract COVID‐19 is an infectious disease caused by SARS‐CoV‐2 that is spreading in many countries around the world. In attempts to discover compounds that have an effect on SARS‐CoV‐2, many important molecular targets have been identified, involved in viral infection and replication including spike protein, main protease, capthesin L, helicase, 2‐O‐methyltransferase, endoRNAse. In this study, we would like to identify pot ential flavonoids that could simultaneously inhibit 3CLP, capthesin L, endoRNAse, 2‐O‐methyltransferase, and PLP from a 4389‐flavonoid database using molecular docking, molecular dynamics simulation, pharmacokinetic and toxicity prediction. Out of 4389 compounds, 79 potential flavonoids that could simultaneously inhibit five COVID‐19 molecular targets were identified. Pharmacokinetic and toxicity prediction showed that these compounds were well absorbed from the gastrointestinal tract and safe for human use. These potential compounds were noteworthy during drug research and development for SARS‐CoV‐2 treatment.
{"title":"Flavonoids as potential agents for development of multi‐target drugs for covid‐19 treatment: An in silico study","authors":"Nguyễn Thị Thu Hằng, N. Van Phuong","doi":"10.1002/vjch.202100108","DOIUrl":"https://doi.org/10.1002/vjch.202100108","url":null,"abstract":"Abstract COVID‐19 is an infectious disease caused by SARS‐CoV‐2 that is spreading in many countries around the world. In attempts to discover compounds that have an effect on SARS‐CoV‐2, many important molecular targets have been identified, involved in viral infection and replication including spike protein, main protease, capthesin L, helicase, 2‐O‐methyltransferase, endoRNAse. In this study, we would like to identify pot ential flavonoids that could simultaneously inhibit 3CLP, capthesin L, endoRNAse, 2‐O‐methyltransferase, and PLP from a 4389‐flavonoid database using molecular docking, molecular dynamics simulation, pharmacokinetic and toxicity prediction. Out of 4389 compounds, 79 potential flavonoids that could simultaneously inhibit five COVID‐19 molecular targets were identified. Pharmacokinetic and toxicity prediction showed that these compounds were well absorbed from the gastrointestinal tract and safe for human use. These potential compounds were noteworthy during drug research and development for SARS‐CoV‐2 treatment.","PeriodicalId":23525,"journal":{"name":"Vietnam Journal of Chemistry","volume":"23 1","pages":"281 - 296"},"PeriodicalIF":0.9,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83295802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Thanh Q. Bui, Nguyen Thi Thanh Hai, Tran Thi Ai My, Nguyen Ho Vu Phong, N. Nhan, P. Quy, N. D. Nguyen, N. Nhung
Abstract Baloxavir marboxil (D1), Baricitinib (D2), Galidesivir (D3), Nitazoxanide (D4), and Oseltamivir (D5) are well‐known performing broad‐spectrum activity against a variety of viruses, thus holding high potentiality towards SARS‐CoV‐2. Quantum properties were examined using density functional theory (DFT). The inhibitability of the drugs towards Angiotensin‐converting enzyme 2 (ACE2) and SARS‐CoV‐2 main protease (6LU7) was evaluated by molecular docking simulation, while their bio‐compatibility was justified by physicochemical properties obtained from QSARIS‐based analysis in reference to Lipinski's rule of five. Quantum analysis suggests that the compounds are highly favourable for intermolecular interaction towards protein structures. Given ligand‐ACE2 systems, the inhibitory effectiveness follows the order D3‐ACE2 > D4‐ACE2 > D2‐ACE2 > D5‐ACE2 > D1‐ACE2; and the corresponding order for ligand‐6LU7 systems is D2‐6LU7 > D4‐6LU7 > D3‐6LU7 > D5‐6LU7 > D1‐6LU7. Galidesivir is predicted as the most effective inhibitor towards both targeted protein structures (DSaverage ‐13.1 kcal.mol‐1) and the most bio‐compatible molecule (Mass 264.9 amu; LogP ‐0.9; Polarisability 26.8 Å3). The theoretical screening suggests all drugs, especially Galidesivir (D3), promising for treatment of SARS‐CoV‐2 infection and encourages in‐related clinical trials.
{"title":"An in silico study on inhibitability of Baloxavir marboxil, Baricitinib, Galidesivir, Nitazoxanide, and Oseltamivir against SARS‐CoV‐2","authors":"Thanh Q. Bui, Nguyen Thi Thanh Hai, Tran Thi Ai My, Nguyen Ho Vu Phong, N. Nhan, P. Quy, N. D. Nguyen, N. Nhung","doi":"10.1002/vjch.202100145","DOIUrl":"https://doi.org/10.1002/vjch.202100145","url":null,"abstract":"Abstract Baloxavir marboxil (D1), Baricitinib (D2), Galidesivir (D3), Nitazoxanide (D4), and Oseltamivir (D5) are well‐known performing broad‐spectrum activity against a variety of viruses, thus holding high potentiality towards SARS‐CoV‐2. Quantum properties were examined using density functional theory (DFT). The inhibitability of the drugs towards Angiotensin‐converting enzyme 2 (ACE2) and SARS‐CoV‐2 main protease (6LU7) was evaluated by molecular docking simulation, while their bio‐compatibility was justified by physicochemical properties obtained from QSARIS‐based analysis in reference to Lipinski's rule of five. Quantum analysis suggests that the compounds are highly favourable for intermolecular interaction towards protein structures. Given ligand‐ACE2 systems, the inhibitory effectiveness follows the order D3‐ACE2 > D4‐ACE2 > D2‐ACE2 > D5‐ACE2 > D1‐ACE2; and the corresponding order for ligand‐6LU7 systems is D2‐6LU7 > D4‐6LU7 > D3‐6LU7 > D5‐6LU7 > D1‐6LU7. Galidesivir is predicted as the most effective inhibitor towards both targeted protein structures (DSaverage ‐13.1 kcal.mol‐1) and the most bio‐compatible molecule (Mass 264.9 amu; LogP ‐0.9; Polarisability 26.8 Å3). The theoretical screening suggests all drugs, especially Galidesivir (D3), promising for treatment of SARS‐CoV‐2 infection and encourages in‐related clinical trials.","PeriodicalId":23525,"journal":{"name":"Vietnam Journal of Chemistry","volume":"73 1","pages":"333 - 345"},"PeriodicalIF":0.9,"publicationDate":"2022-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85817632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Thanh Q. Bui, Nguyen Thi Thanh Hai, Tran Van Chen, P. Quy, Ly Nguyen Hai Du, T. Cuong, Nguyen Thanh Triet, Nguyen Thi Thu Thuy, N. Nhung
Abstract Berberine (V1), lycorine (V2), hemanthamine (V3), aloperin (V4), dendrobine (V5) possess structural frameworks resembling known anti‐influenza and anti‐SARS‐CoV‐2 drugs, thus subjected for a computational screening. Their quantum properties were examined using density functional theory (DFT); the ligand‐protein inhibitability was evaluated using molecular docking simulation; physicochemical properties were obtained from QSARIS‐based analysis in reference to Lipinski's rule of five; pharmacokinetic parameters were assessed by ADMET‐based analysis. DFT calculations indicate that there are no abnormal bonding constraints observed; NBO analysis suggests all possessing favorable electric configurations for intermolecular inhibition. Regarding ligand‐2VIU, the order for static inhibitability is V3‐2VIU > V2‐2VIU > V1‐2VIU > V5‐2VIU > V4‐2VIU; Regarding ligand‐6LU7, the corresponding order follows: V2‐6LU7 > V3‐6LU7 > V1‐6LU7 > V5‐6LU7 > V4‐6LU7. An exceptional hydrophilic bonding (π‐cation) with the associated Gibbs free energy of ‐10.9 kcal.mol‐1 is detected in inhibitory complex V1‐2VIU. QSARIS‐based analysis reveals that all the candidates are highly bio‐compatible. ADMET‐based analysis specifies V2 and V3 as being safe and suitable for the use as orally administrated drugs. The results encourage further investigations for more in‐depth mechanisms and experimental validations, such as molecular dynamics simulation and in vitro enzyme assays.
{"title":"Theoretical study on inhibitability of some natural alkaloids against influenza virus hemagglutinin and SARS‐CoV‐2 main protease","authors":"Thanh Q. Bui, Nguyen Thi Thanh Hai, Tran Van Chen, P. Quy, Ly Nguyen Hai Du, T. Cuong, Nguyen Thanh Triet, Nguyen Thi Thu Thuy, N. Nhung","doi":"10.1002/vjch.202100175","DOIUrl":"https://doi.org/10.1002/vjch.202100175","url":null,"abstract":"Abstract Berberine (V1), lycorine (V2), hemanthamine (V3), aloperin (V4), dendrobine (V5) possess structural frameworks resembling known anti‐influenza and anti‐SARS‐CoV‐2 drugs, thus subjected for a computational screening. Their quantum properties were examined using density functional theory (DFT); the ligand‐protein inhibitability was evaluated using molecular docking simulation; physicochemical properties were obtained from QSARIS‐based analysis in reference to Lipinski's rule of five; pharmacokinetic parameters were assessed by ADMET‐based analysis. DFT calculations indicate that there are no abnormal bonding constraints observed; NBO analysis suggests all possessing favorable electric configurations for intermolecular inhibition. Regarding ligand‐2VIU, the order for static inhibitability is V3‐2VIU > V2‐2VIU > V1‐2VIU > V5‐2VIU > V4‐2VIU; Regarding ligand‐6LU7, the corresponding order follows: V2‐6LU7 > V3‐6LU7 > V1‐6LU7 > V5‐6LU7 > V4‐6LU7. An exceptional hydrophilic bonding (π‐cation) with the associated Gibbs free energy of ‐10.9 kcal.mol‐1 is detected in inhibitory complex V1‐2VIU. QSARIS‐based analysis reveals that all the candidates are highly bio‐compatible. ADMET‐based analysis specifies V2 and V3 as being safe and suitable for the use as orally administrated drugs. The results encourage further investigations for more in‐depth mechanisms and experimental validations, such as molecular dynamics simulation and in vitro enzyme assays.","PeriodicalId":23525,"journal":{"name":"Vietnam Journal of Chemistry","volume":"9 1","pages":"502 - 517"},"PeriodicalIF":0.9,"publicationDate":"2022-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90137613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Coronavirus infectious disease 2019 (COVID‐19) is an infectious disease of the human respiratory tract caused by the SARS‐CoV‐2 virus. Spike protein is a class I glycoprotein trimeric TM involved in viral entry and infection. Four major targets to inhibit the SARS‐CoV‐2 virus are spike protein, angiotensin‐converting enzyme 2 (ACE2), main protease and the enzyme RNA‐dependent RNA polymerase (RdRp). In this study, we evaluated the inhibitory potential of natural antiviral compounds against spike protein, ACE2, main protease, RdRp targets by molecular docking and molecular dynamics simulations. Lipinski Rule of Five was used to evaluate the drug‐like properties of these compounds. The pkCSM tool was used to assess the pharmacokinetic parameters of prospective substances. Based on the ChemFaces database, we have collected 273 natural antiviral compounds. The results showed that the 7/273 compounds with the most potential to inhibit SARS‐CoV‐2 were: hinokiflavone, sotetsuflavone, mulberroside C, daphnoretin, morellic acid, digitoxin, and hypericin. Among them, sotetsuflavone is the most potent compound that inhibits four targets, with drug‐like properties, good intestinal absorption, and low toxicity. The molecular dynamics simulation results of the complexes are also relatively stable. As a results, in vitro and in vivo test should be carried out to verify the potential for COVID‐19 treatment of this compound.
{"title":"In silico screening of natural antivirals as potential inhibitors of SARS‐CoV‐2 virus","authors":"T. Hằng, Do Thi Hong Khanh, B. Tùng","doi":"10.1002/vjch.202100187","DOIUrl":"https://doi.org/10.1002/vjch.202100187","url":null,"abstract":"Abstract Coronavirus infectious disease 2019 (COVID‐19) is an infectious disease of the human respiratory tract caused by the SARS‐CoV‐2 virus. Spike protein is a class I glycoprotein trimeric TM involved in viral entry and infection. Four major targets to inhibit the SARS‐CoV‐2 virus are spike protein, angiotensin‐converting enzyme 2 (ACE2), main protease and the enzyme RNA‐dependent RNA polymerase (RdRp). In this study, we evaluated the inhibitory potential of natural antiviral compounds against spike protein, ACE2, main protease, RdRp targets by molecular docking and molecular dynamics simulations. Lipinski Rule of Five was used to evaluate the drug‐like properties of these compounds. The pkCSM tool was used to assess the pharmacokinetic parameters of prospective substances. Based on the ChemFaces database, we have collected 273 natural antiviral compounds. The results showed that the 7/273 compounds with the most potential to inhibit SARS‐CoV‐2 were: hinokiflavone, sotetsuflavone, mulberroside C, daphnoretin, morellic acid, digitoxin, and hypericin. Among them, sotetsuflavone is the most potent compound that inhibits four targets, with drug‐like properties, good intestinal absorption, and low toxicity. The molecular dynamics simulation results of the complexes are also relatively stable. As a results, in vitro and in vivo test should be carried out to verify the potential for COVID‐19 treatment of this compound.","PeriodicalId":23525,"journal":{"name":"Vietnam Journal of Chemistry","volume":"6 1","pages":"211 - 222"},"PeriodicalIF":0.9,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84443870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Mg2+ embedded MIL-101(Cr)-NH2 framework for improved CO2 adsorption and CO2/N2 selectivity","authors":"Duong Tuan Quang","doi":"10.1002/VJCH.202100035","DOIUrl":"https://doi.org/10.1002/VJCH.202100035","url":null,"abstract":"","PeriodicalId":23525,"journal":{"name":"Vietnam Journal of Chemistry","volume":"3 1","pages":"667-675"},"PeriodicalIF":0.9,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84184951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
V. A. Adole, R. More, R. Shinde, Sunil L. Dhonnar, Bapusonu Jagdale, S. Shinde, A. V. Patil, T. B. Pawar
{"title":"Spectroscopic (FTIR and UV), quantum Chemical, antifungal and antioxidant investigations of (E)-7-(4-(trifluoromethyl)benzylidene)-1,2,6,7-tetrahydro-8H-indeno[5,4-b]furan-8-one: A combined experimental and theoretical study","authors":"V. A. Adole, R. More, R. Shinde, Sunil L. Dhonnar, Bapusonu Jagdale, S. Shinde, A. V. Patil, T. B. Pawar","doi":"10.1002/VJCH.202100034","DOIUrl":"https://doi.org/10.1002/VJCH.202100034","url":null,"abstract":"","PeriodicalId":23525,"journal":{"name":"Vietnam Journal of Chemistry","volume":"72 1","pages":"689-700"},"PeriodicalIF":0.9,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74058355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
T. Quang, Le Ngoc Anh, T. H. Hanh, N. X. Cuong, N. Ngan, N. Q. Trung, N. H. Nam
{"title":"Cytotoxic and antimicrobial benzodiazepine and phenolic metabolites from Aspergillus ostianus IMBC-NMTP03","authors":"T. Quang, Le Ngoc Anh, T. H. Hanh, N. X. Cuong, N. Ngan, N. Q. Trung, N. H. Nam","doi":"10.1002/VJCH.202100032","DOIUrl":"https://doi.org/10.1002/VJCH.202100032","url":null,"abstract":"","PeriodicalId":23525,"journal":{"name":"Vietnam Journal of Chemistry","volume":"3 1","pages":"660-666"},"PeriodicalIF":0.9,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81396453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lê Tín Thanh, Dang Xuan Hai, N. Hien, Lê Thị Hồng Hải, Lê Thanh Thanh, D. Tung
{"title":"Synthesis of 1,1’-diphenyl-2-thienyl-2’-(4-substituted-styryl)ethenes via oxidative Heck coupling reaction and photophysical studies","authors":"Lê Tín Thanh, Dang Xuan Hai, N. Hien, Lê Thị Hồng Hải, Lê Thanh Thanh, D. Tung","doi":"10.1002/VJCH.202000197","DOIUrl":"https://doi.org/10.1002/VJCH.202000197","url":null,"abstract":"","PeriodicalId":23525,"journal":{"name":"Vietnam Journal of Chemistry","volume":"1 1","pages":"585-589"},"PeriodicalIF":0.9,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75580204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
S. K. Gupta, Abhishek Gupta, R. Yadav, Ajeet Singh, B. Yadav
{"title":"Highly efficient in-situ sulfur doped graphitic carbon nitride nanoplates as an artificial photosynthetic system for NADH regeneration","authors":"S. K. Gupta, Abhishek Gupta, R. Yadav, Ajeet Singh, B. Yadav","doi":"10.1002/VJCH.202000220","DOIUrl":"https://doi.org/10.1002/VJCH.202000220","url":null,"abstract":"","PeriodicalId":23525,"journal":{"name":"Vietnam Journal of Chemistry","volume":"93 1","pages":"590-598"},"PeriodicalIF":0.9,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79018245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Modified bis-tetrahydrofuran inhibitors toward improved binding to HIV-1 proteases","authors":"J. Paulin, Francisco C. Franco","doi":"10.1002/VJCH.202000179","DOIUrl":"https://doi.org/10.1002/VJCH.202000179","url":null,"abstract":"","PeriodicalId":23525,"journal":{"name":"Vietnam Journal of Chemistry","volume":"176 1","pages":"563-579"},"PeriodicalIF":0.9,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76872314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：