Pub Date : 2023-04-15DOI: 10.1142/s2737416523500291
J. Shen, Meiyuan Chen, Jianqin Chen, Jiangang Wu, Yan Shen, Yumei Chen, Z. Wang
{"title":"Hydrocarbon Stapling-improved Coupled Folding-upon-Binding of Peptide-mediated Interaction between the Nucleocapsid and Phosphoprotein of Human Orthopneumovirus","authors":"J. Shen, Meiyuan Chen, Jianqin Chen, Jiangang Wu, Yan Shen, Yumei Chen, Z. Wang","doi":"10.1142/s2737416523500291","DOIUrl":"https://doi.org/10.1142/s2737416523500291","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49033574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-04-15DOI: 10.1142/s273741652350031x
Ekrem Yaşar, M. Yaşar, Segun Dogru, N. Yaraş, E. Eroglu
{"title":"Effects of Angiotensin 1-7 Binding on the Dynamics of Human MAS Proto-oncogene, GPCR: A Molecular Dynamics Study","authors":"Ekrem Yaşar, M. Yaşar, Segun Dogru, N. Yaraş, E. Eroglu","doi":"10.1142/s273741652350031x","DOIUrl":"https://doi.org/10.1142/s273741652350031x","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41434707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-04-06DOI: 10.1142/s273741652350028x
{"title":"LSDDB: Lysosomal Storage Disorder DataBase for lysosomal proteins and their single amino acid substitutions","authors":"","doi":"10.1142/s273741652350028x","DOIUrl":"https://doi.org/10.1142/s273741652350028x","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42151076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-10DOI: 10.1142/s2737416523500266
M. Rezaei-Sameti, H. Torabi
{"title":"Assessment of the capability and potential of pristine, Sc, Ti and Ni-doped C24 nanocage to delivery and sensor property of Prothionamide drug: Insight of DFT, TD-DFT computational methods","authors":"M. Rezaei-Sameti, H. Torabi","doi":"10.1142/s2737416523500266","DOIUrl":"https://doi.org/10.1142/s2737416523500266","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45320469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-10DOI: 10.1142/s2737416523500254
Pedro M. S. Suzano, Inês D. S. Pires, Tomás F D Silva, Nuno F. B. Oliveira, Pedro B. P. S. Reis, M. Machuqueiro
{"title":"MembIT - a tool to calculate solute membrane insertions and deformations in molecular dynamics simulations","authors":"Pedro M. S. Suzano, Inês D. S. Pires, Tomás F D Silva, Nuno F. B. Oliveira, Pedro B. P. S. Reis, M. Machuqueiro","doi":"10.1142/s2737416523500254","DOIUrl":"https://doi.org/10.1142/s2737416523500254","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42176708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-10DOI: 10.1142/s2737416523500242
N. M. Tam, L. Tran, Q. Vo, Minh Quan Pham, H. Phung
The COVID-19 pandemic raised an unprecedented race in biotechnology in search for effective therapies and a preventive vaccine. Scientists worldwide have been attempting to stop the viral infection by interfering with the biological function of the SARS-CoV-2 main protease (Mpro), a critical protein required for viral transcription and replication during infection. In this study, we employed an effective approach integrating deep learning model calculations and steered molecular dynamic simulations to generate highly promising inhibitors of SARS-CoV-2 Mpro. First, using deep learning calculations, a natural molecule that was identified as a potential inhibitor of SARS-CoV-2 Mpro was chemically altered to boost its ligand-binding affinity to the Mpro protease. The proposed compounds were then verified using steered molecular dynamic simulations to estimate their binding free energies to SARS-CoV-2 Mpro. The procedure was repeated until the binding free energies of the proposed compounds did not improve further. Overall, one proposed compound was shown to have a high nanomolar affinity, and two others were estimated to possess nanomolar affinities for SARS-CoV-2 Mpro, indicating that they are highly promising inhibitors of the protease. Absorption, distribution, metabolism, and excretion and toxicity analysis show that all three chemicals are drug-like compounds following the MACCS-II Drug Data Report database, orally absorbed, tightly attached to the plasma membrane, and noncarcinogenic in rats. The results obtained potentially support COVID-19 treatment. [ FROM AUTHOR] Copyright of Journal of Computational Biophysics & Chemistry is the property of World Scientific Publishing Company and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)
{"title":"Designing Potential Inhibitors of SARS-CoV-2 Mpro Using Deep-Learning and Steered-Molecular Dynamic Simulations","authors":"N. M. Tam, L. Tran, Q. Vo, Minh Quan Pham, H. Phung","doi":"10.1142/s2737416523500242","DOIUrl":"https://doi.org/10.1142/s2737416523500242","url":null,"abstract":"The COVID-19 pandemic raised an unprecedented race in biotechnology in search for effective therapies and a preventive vaccine. Scientists worldwide have been attempting to stop the viral infection by interfering with the biological function of the SARS-CoV-2 main protease (Mpro), a critical protein required for viral transcription and replication during infection. In this study, we employed an effective approach integrating deep learning model calculations and steered molecular dynamic simulations to generate highly promising inhibitors of SARS-CoV-2 Mpro. First, using deep learning calculations, a natural molecule that was identified as a potential inhibitor of SARS-CoV-2 Mpro was chemically altered to boost its ligand-binding affinity to the Mpro protease. The proposed compounds were then verified using steered molecular dynamic simulations to estimate their binding free energies to SARS-CoV-2 Mpro. The procedure was repeated until the binding free energies of the proposed compounds did not improve further. Overall, one proposed compound was shown to have a high nanomolar affinity, and two others were estimated to possess nanomolar affinities for SARS-CoV-2 Mpro, indicating that they are highly promising inhibitors of the protease. Absorption, distribution, metabolism, and excretion and toxicity analysis show that all three chemicals are drug-like compounds following the MACCS-II Drug Data Report database, orally absorbed, tightly attached to the plasma membrane, and noncarcinogenic in rats. The results obtained potentially support COVID-19 treatment. [ FROM AUTHOR] Copyright of Journal of Computational Biophysics & Chemistry is the property of World Scientific Publishing Company and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44111262","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-03-08DOI: 10.1142/s2737416523410016
Yeman Zhou, Hanlin Li, De'en Yu, Cheng Zhang, Heng Yang, Chunping Wang, Youhua Zhang, W. Deng, Bo Li, Shihua Zhang
{"title":"Developing high-resolution metastasis signatures for improved cancer prognosis and drug sensitivity prediction using single-cell RNA sequencing data: A case study in lung adenocarcinoma","authors":"Yeman Zhou, Hanlin Li, De'en Yu, Cheng Zhang, Heng Yang, Chunping Wang, Youhua Zhang, W. Deng, Bo Li, Shihua Zhang","doi":"10.1142/s2737416523410016","DOIUrl":"https://doi.org/10.1142/s2737416523410016","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45185314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-02-16DOI: 10.1142/s2737416523500229
Jian Liu, Dong Chen, Feng Pan, Jie Wu
{"title":"Neighborhood Path Complex for the Quantitative Analysis of the Structure and Stability of Carboranes","authors":"Jian Liu, Dong Chen, Feng Pan, Jie Wu","doi":"10.1142/s2737416523500229","DOIUrl":"https://doi.org/10.1142/s2737416523500229","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47254449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-01-19DOI: 10.1142/s2737416523500205
N. Panahi, N. Razzaghi-Asl
{"title":"In silico Identification of Triclosan Derivatives as Potential Inhibitors of Mutant Mycobacterium tuberculosis InhA","authors":"N. Panahi, N. Razzaghi-Asl","doi":"10.1142/s2737416523500205","DOIUrl":"https://doi.org/10.1142/s2737416523500205","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46414554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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