Pub Date : 2021-01-01DOI: 10.1504/ijcbdd.2021.10045829
S. Mukherjee, Santanu Paul
Introduction: Concerning the current pandemic situation, the world is facing due to the highly infectious coronavirus (SARS-CoV2), we aim to gain some insight into the pre-existing drugs and compounds for curing the disease. Method: Here, we have studied the interaction of 10 drug molecules by in silico study against three targets, Angiotensin Convertase Enzyme-2 receptor (ACE-2), main protease (Mpro) and RNA dependent RNA polymerase (RDRP) and further analysed the interaction of the best docked compound against spike mutants. Results: By analysing the protein-ligand interactions by docking, and molecular dynamics simulation, it proves that RO 28-2653 can be a potent candidate drug for future COVID treatment even against the mutant strains. Conclusion: The used drugs have been implicated in asthma, hypertension, etc., so repurposing these drugs can have a beneficial role on COVID-19, keeping in mind that any drug should be used in a certain prescribed dosage.
{"title":"In silico study identifies RO 28-2653 as a novel drug against SARS-CoV2 mutant strains","authors":"S. Mukherjee, Santanu Paul","doi":"10.1504/ijcbdd.2021.10045829","DOIUrl":"https://doi.org/10.1504/ijcbdd.2021.10045829","url":null,"abstract":"Introduction: Concerning the current pandemic situation, the world is facing due to the highly infectious coronavirus (SARS-CoV2), we aim to gain some insight into the pre-existing drugs and compounds for curing the disease. Method: Here, we have studied the interaction of 10 drug molecules by in silico study against three targets, Angiotensin Convertase Enzyme-2 receptor (ACE-2), main protease (Mpro) and RNA dependent RNA polymerase (RDRP) and further analysed the interaction of the best docked compound against spike mutants. Results: By analysing the protein-ligand interactions by docking, and molecular dynamics simulation, it proves that RO 28-2653 can be a potent candidate drug for future COVID treatment even against the mutant strains. Conclusion: The used drugs have been implicated in asthma, hypertension, etc., so repurposing these drugs can have a beneficial role on COVID-19, keeping in mind that any drug should be used in a certain prescribed dosage.","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"1 1","pages":"457-480"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88869540","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}
Pub Date : 2021-01-01DOI: 10.1504/ijcbdd.2021.10045802
Jennifer Fowler, J. Stubblefield, J. Causey, J. Qualls, Wei Dong, Hongmei Jiang, K. Walker, Y. Guan, Xiuzhen Huang
{"title":"Identify differentially expressed genes with large background samples","authors":"Jennifer Fowler, J. Stubblefield, J. Causey, J. Qualls, Wei Dong, Hongmei Jiang, K. Walker, Y. Guan, Xiuzhen Huang","doi":"10.1504/ijcbdd.2021.10045802","DOIUrl":"https://doi.org/10.1504/ijcbdd.2021.10045802","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"17 1","pages":"411-428"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74804303","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}
Pub Date : 2021-01-01DOI: 10.1504/ijcbdd.2021.10040277
S. Dabravolski, Y. Kavalionak
{"title":"In silico characterisation and phylogenetic analysis of Arabidopsis homologues of the human antiretroviral SERINC proteins","authors":"S. Dabravolski, Y. Kavalionak","doi":"10.1504/ijcbdd.2021.10040277","DOIUrl":"https://doi.org/10.1504/ijcbdd.2021.10040277","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"1 1","pages":"217-236"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72731007","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}
Pub Date : 2021-01-01DOI: 10.1504/IJCBDD.2021.114092
S. Jibril, H. Sirat, N. Basar, R. A. Wahab, N. Mahat, W. Salleh
{"title":"Ultrasonic-assisted rapid extraction of Cassia sieberiana D.C.: a Box-Behnken design process optimisation","authors":"S. Jibril, H. Sirat, N. Basar, R. A. Wahab, N. Mahat, W. Salleh","doi":"10.1504/IJCBDD.2021.114092","DOIUrl":"https://doi.org/10.1504/IJCBDD.2021.114092","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"11 1","pages":"15-31"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75990520","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}
Pub Date : 2021-01-01DOI: 10.1504/IJCBDD.2021.114098
P. Jayaraj, K. M. Mithun, G. Gopakumar, U. Jaleel
{"title":"A GPU based virtual screening tool using SOM","authors":"P. Jayaraj, K. M. Mithun, G. Gopakumar, U. Jaleel","doi":"10.1504/IJCBDD.2021.114098","DOIUrl":"https://doi.org/10.1504/IJCBDD.2021.114098","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"1 1","pages":"64-80"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74450170","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}
Pub Date : 2021-01-01DOI: 10.1504/IJCBDD.2021.115674
Amie Jobe, Bincy Baby, Amanat Ali, Ranjit Vijayan
{"title":"Identification of potential anti-obesity drug scaffolds using molecular modelling","authors":"Amie Jobe, Bincy Baby, Amanat Ali, Ranjit Vijayan","doi":"10.1504/IJCBDD.2021.115674","DOIUrl":"https://doi.org/10.1504/IJCBDD.2021.115674","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"7 1","pages":"103-129"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78949597","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}
Pub Date : 2021-01-01DOI: 10.1504/ijcbdd.2021.10042392
S. Sahoo
Upon a viral outbreak of novel coronavirus (2019-nCoV), it is very important to understand the molecular characteristics of the SARS-CoV-2 genome to detect the causative agent of the deadly viral infection. In the present study, we comprehensively analysed the codon usage pattern of SARS-CoV-2 to gain an insight into the viral pathogenesis as well as the evolutionary process of the newly emerging coronavirus. The correspondence analysis (CA), the effective number of codons versus GC3(NC-plot), and the relationship between GC12 versus GC3 show that a low codon usage bias exists in SARS-CoV-2. Both mutation and natural selection pressure have contributed to this low codon usage bias, with the former being the main determining factor. Lastly, the relationship of codon usage index (CUI), codon adaptation index (CAI), and the gene expression profile of SARS-CoV-2 genes have been discussed in reference to codon bias score (CBS) for further study on the virus-host relationship and their evolutionary phenomenon.
{"title":"Analysis of the codon usage pattern in 2019-nCoV","authors":"S. Sahoo","doi":"10.1504/ijcbdd.2021.10042392","DOIUrl":"https://doi.org/10.1504/ijcbdd.2021.10042392","url":null,"abstract":"Upon a viral outbreak of novel coronavirus (2019-nCoV), it is very important to understand the molecular characteristics of the SARS-CoV-2 genome to detect the causative agent of the deadly viral infection. In the present study, we comprehensively analysed the codon usage pattern of SARS-CoV-2 to gain an insight into the viral pathogenesis as well as the evolutionary process of the newly emerging coronavirus. The correspondence analysis (CA), the effective number of codons versus GC3(NC-plot), and the relationship between GC12 versus GC3 show that a low codon usage bias exists in SARS-CoV-2. Both mutation and natural selection pressure have contributed to this low codon usage bias, with the former being the main determining factor. Lastly, the relationship of codon usage index (CUI), codon adaptation index (CAI), and the gene expression profile of SARS-CoV-2 genes have been discussed in reference to codon bias score (CBS) for further study on the virus-host relationship and their evolutionary phenomenon.","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"84 1","pages":"273-296"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74042322","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}
Pub Date : 2021-01-01DOI: 10.1504/IJCBDD.2021.115678
A. Joy, S. Balaji, Md. Afroz Alam
{"title":"Interaction network of insulin resistance proteins with organophosphorus and chlorine pesticides","authors":"A. Joy, S. Balaji, Md. Afroz Alam","doi":"10.1504/IJCBDD.2021.115678","DOIUrl":"https://doi.org/10.1504/IJCBDD.2021.115678","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"26 1","pages":"138-157"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85852804","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}
Pub Date : 2021-01-01DOI: 10.1504/ijcbdd.2021.10042525
S. Thota, Naresh Krishna Narasimha
{"title":"Screening for novel lead compounds targeting benzodiazepine allosteric binding site of wild-type and H129Y variant of GABAA receptor: an in-silico molecular docking study","authors":"S. Thota, Naresh Krishna Narasimha","doi":"10.1504/ijcbdd.2021.10042525","DOIUrl":"https://doi.org/10.1504/ijcbdd.2021.10042525","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"117 1","pages":"377-409"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80452125","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}
Pub Date : 2021-01-01DOI: 10.1504/ijcbdd.2021.10040272
A. Karami, A. F. Movaghar
{"title":"A new edge effect correction for sequence alignment","authors":"A. Karami, A. F. Movaghar","doi":"10.1504/ijcbdd.2021.10040272","DOIUrl":"https://doi.org/10.1504/ijcbdd.2021.10040272","url":null,"abstract":"","PeriodicalId":13612,"journal":{"name":"Int. J. Comput. Biol. Drug Des.","volume":"64 1","pages":"159-165"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79347843","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：