Pub Date : 2022-12-16DOI: 10.1142/s2737416523400082
M. Hussain, M. Ashraf, Q. A. Ranjha, M. Inc., S. Jahan
{"title":"Exploration of Newtonian heating, viscous dissipation effects on MHD mixed convection flow of Williamson fluid against radially stretched penetrable wedge: A numerical study","authors":"M. Hussain, M. Ashraf, Q. A. Ranjha, M. Inc., S. Jahan","doi":"10.1142/s2737416523400082","DOIUrl":"https://doi.org/10.1142/s2737416523400082","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45364253","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 : 2022-12-14DOI: 10.1142/s2737416523500163
Mingsong Shi, Jiang Liu, Su-Hong Fu, Heying Pei, Bin Peng, Y. Wen, Haoche Wei, Xiaoping Zhou, Lijuan Chen, Dingguo Xu
{"title":"Structural Insights into the Interactions of Belumosudil with Rho-associated Coiled-coil Containing Protein Kinases 1 and 2 based on Molecular Docking, Molecular Dynamics Simulations, and Free Energy Calculations","authors":"Mingsong Shi, Jiang Liu, Su-Hong Fu, Heying Pei, Bin Peng, Y. Wen, Haoche Wei, Xiaoping Zhou, Lijuan Chen, Dingguo Xu","doi":"10.1142/s2737416523500163","DOIUrl":"https://doi.org/10.1142/s2737416523500163","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47617497","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 : 2022-12-09DOI: 10.1142/s2737416523500151
S. Aadheeswari, P. Anbarasan, A. Arunkumar, M. Shkir
{"title":"Computational Study on D-π-A-based Metal-Free Donor-Tuned Molecules for Efficient Organic Dye-Sensitized Solar Cells","authors":"S. Aadheeswari, P. Anbarasan, A. Arunkumar, M. Shkir","doi":"10.1142/s2737416523500151","DOIUrl":"https://doi.org/10.1142/s2737416523500151","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47114167","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 : 2022-12-07DOI: 10.1142/s273741652350014x
Elliot Perry, Simon Chapman, Yaozhong Xu
SARS-CoV-2 Main protease (Mpro) is pivotal in viral replication and transcription. Mpro mediates proteolysis of translated products of replicase genes ORF1a and ORF1ab. Surveying pre-clinical trial Mpro inhibitors suggests potential enhanced efficacy for some moieties. Concordant with promising in vitro and in silico data, the protease inhibitor GC376 was chosen as a lead. Modification of GC376 analogues yielded a series of promising Mpro inhibitors. Design optimization identified compound G59i as lead candidate, displaying a binding energy of −10.54kcal/mol for the complex. Robust interactivity was noted between G59i and Mpro. With commendable ADMET characteristics and enhanced potency, further G59i analysis may be advantageous;moreover, identified key Mpro residues could contribute to the design of neotenic inhibitors. [ FROM AUTHOR]
{"title":"SARS-CoV-2 main protease inhibitors: Structure-based enhancement to anti-viral pre-clinical GC376 encourages further development","authors":"Elliot Perry, Simon Chapman, Yaozhong Xu","doi":"10.1142/s273741652350014x","DOIUrl":"https://doi.org/10.1142/s273741652350014x","url":null,"abstract":"SARS-CoV-2 Main protease (Mpro) is pivotal in viral replication and transcription. Mpro mediates proteolysis of translated products of replicase genes ORF1a and ORF1ab. Surveying pre-clinical trial Mpro inhibitors suggests potential enhanced efficacy for some moieties. Concordant with promising in vitro and in silico data, the protease inhibitor GC376 was chosen as a lead. Modification of GC376 analogues yielded a series of promising Mpro inhibitors. Design optimization identified compound G59i as lead candidate, displaying a binding energy of −10.54kcal/mol for the complex. Robust interactivity was noted between G59i and Mpro. With commendable ADMET characteristics and enhanced potency, further G59i analysis may be advantageous;moreover, identified key Mpro residues could contribute to the design of neotenic inhibitors. [ FROM AUTHOR]","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46563855","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 : 2022-12-01DOI: 10.1142/s2737416523500138
A. Arunkumar, P. Anbarasan, M. Shkir, V. Balasubramani
{"title":"Computational Screening of D-π-A Structured with Acceptor Tuned Metal-Free Organic Dye Molecules for DSSCs","authors":"A. Arunkumar, P. Anbarasan, M. Shkir, V. Balasubramani","doi":"10.1142/s2737416523500138","DOIUrl":"https://doi.org/10.1142/s2737416523500138","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48418712","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 : 2022-11-30DOI: 10.1142/s2737416523500060
Shirin Fathi, A. Sakhteman, Aida Solhjoo
Prostate carcinoma is one of the most commonly diagnosed visceral malignancies and the fifth leading cause of cancer-related mortality in males. Reportedly, a series of dietary lipids are identified as 1-cis-4-cis-pentadiene polyunsaturated fatty acids (PUFAs), which play a dominant role in prostate carcinogenesis. Four species of human lipoxygenases (LOXs), a family of nonheme iron-containing enzymes, mediate the deoxygenation of the aforementioned PUFAs. 15-LOX-1 in particular metabolizes the [Formula: see text]-6 lipids and generates certain metabolites (e.g., 13-(S)-hydroxyoctadecaenoic acid) which results in vascular homeostasis, cell proliferation and tissue differentiation in the prostate. Furthermore, in prostate cancer (PCa), the expression of 15-LOX-1 is elevated and positively correlated with the Gleason score of the tumor (an indicator of the disease severity). As membrane receptors, kinases and transcriptional factors are all affected by carcinogenic signals of 15-LOX-1, therapeutic agents that directly inhibit this enzyme can be advantageous in the treatment of PCa. To our knowledge, there are limited effective treatments for PCa, and there is no therapy for its metastatic condition. In this respect, 15-LOX-1, as an appropriate candidate for drug development, was subjected to homology modeling, phylogenic assessment, cross-docking analysis and molecular dynamics (MD) simulation to identify an eligible inhibiting agent amongst a library of 30 potential targeting compounds for PCa management.
{"title":"Unveiling Attributes of Human 15-Lipoxygenase-1 as a Potential Candidate for Prostate Cancer Drug Development Using in Silico Approaches","authors":"Shirin Fathi, A. Sakhteman, Aida Solhjoo","doi":"10.1142/s2737416523500060","DOIUrl":"https://doi.org/10.1142/s2737416523500060","url":null,"abstract":"Prostate carcinoma is one of the most commonly diagnosed visceral malignancies and the fifth leading cause of cancer-related mortality in males. Reportedly, a series of dietary lipids are identified as 1-cis-4-cis-pentadiene polyunsaturated fatty acids (PUFAs), which play a dominant role in prostate carcinogenesis. Four species of human lipoxygenases (LOXs), a family of nonheme iron-containing enzymes, mediate the deoxygenation of the aforementioned PUFAs. 15-LOX-1 in particular metabolizes the [Formula: see text]-6 lipids and generates certain metabolites (e.g., 13-(S)-hydroxyoctadecaenoic acid) which results in vascular homeostasis, cell proliferation and tissue differentiation in the prostate. Furthermore, in prostate cancer (PCa), the expression of 15-LOX-1 is elevated and positively correlated with the Gleason score of the tumor (an indicator of the disease severity). As membrane receptors, kinases and transcriptional factors are all affected by carcinogenic signals of 15-LOX-1, therapeutic agents that directly inhibit this enzyme can be advantageous in the treatment of PCa. To our knowledge, there are limited effective treatments for PCa, and there is no therapy for its metastatic condition. In this respect, 15-LOX-1, as an appropriate candidate for drug development, was subjected to homology modeling, phylogenic assessment, cross-docking analysis and molecular dynamics (MD) simulation to identify an eligible inhibiting agent amongst a library of 30 potential targeting compounds for PCa management.","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46288457","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 : 2022-11-25DOI: 10.1142/s2737416523400069
V. Puneeth, S. Manjunatha, M. S. Anwar, M. Oreijah, Kamel Geudri, O. Bafakeeh, A. Galal
Due to the higher coefficients of heat and mass transfer, the jet flow has become an effective source for the transfer of heat and mass in various industries. Due to these high coefficients, the heat and mass transfer rates will be high in the appliances equipped with the jet flow. Further, the existence of the magnetic field helps in controlling the velocity and the presence of the gyrotactic microorganisms ensure proper mixing of nanoparticles. A dilute nanoparticle suspension is assumed so that it will not affect the movement of motile cells that leads to bioconvection. Hence, this paper aims to analyze the characteristics of heat transfer as well as mass transfer of the jet flow of Williamson nanofluid past a porous stretching sheet in the existence of microorganisms. The mathematical model obtained as a result of these assumptions is transformed into nonlinear ordinary differential equations for which acceptable solutions are obtained using the numerical method. The results thus obtained are presented graphically and based on the outcomes, it is perceived that the magnetic field has control over the velocity profile thus influencing the thermal profile. The increase in the Williamson parameter also reduces the velocity of the fluid flow. Further, an increase was noticed in the thermal and concentration profiles of the nanofluid for higher values of thermophoresis parameter and the increase in the porosity reduced the speed of the flow of nanofluid.
{"title":"Stratified Bioconvective Jet Flow of Williamson Nanofluid in Porous Medium in the Presence of Arrhenius Activation Energy","authors":"V. Puneeth, S. Manjunatha, M. S. Anwar, M. Oreijah, Kamel Geudri, O. Bafakeeh, A. Galal","doi":"10.1142/s2737416523400069","DOIUrl":"https://doi.org/10.1142/s2737416523400069","url":null,"abstract":"Due to the higher coefficients of heat and mass transfer, the jet flow has become an effective source for the transfer of heat and mass in various industries. Due to these high coefficients, the heat and mass transfer rates will be high in the appliances equipped with the jet flow. Further, the existence of the magnetic field helps in controlling the velocity and the presence of the gyrotactic microorganisms ensure proper mixing of nanoparticles. A dilute nanoparticle suspension is assumed so that it will not affect the movement of motile cells that leads to bioconvection. Hence, this paper aims to analyze the characteristics of heat transfer as well as mass transfer of the jet flow of Williamson nanofluid past a porous stretching sheet in the existence of microorganisms. The mathematical model obtained as a result of these assumptions is transformed into nonlinear ordinary differential equations for which acceptable solutions are obtained using the numerical method. The results thus obtained are presented graphically and based on the outcomes, it is perceived that the magnetic field has control over the velocity profile thus influencing the thermal profile. The increase in the Williamson parameter also reduces the velocity of the fluid flow. Further, an increase was noticed in the thermal and concentration profiles of the nanofluid for higher values of thermophoresis parameter and the increase in the porosity reduced the speed of the flow of nanofluid.","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49394508","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 : 2022-11-25DOI: 10.1142/s2737416523500059
Kamal Rullah, M. Roney, Z. Ibrahim, Nur Farisya Shamsudin, Deri Islami, Q. Ahmed, L. Wai, M. Aluwi
This study explored a series of reported 5-lipoxygenase-activating protein (FLAP) inhibitors to understand their structural requirements and identify potential new inhibitor scaffolds through automated unbiased procedures. Docking studies have revealed that inhibitor binding affinity can be influenced by several key binding interactions with Phe114 and Lys116 from chain B and Val21, Phe25, His28 and Lys29 from chain C in the FLAP-binding site. A ligand-based alignment three-dimensional (3D)-quantitative structure–activity relationship (QSAR) was adopted, resulting in a robust model with a statistically significant noncross-validated coefficient ([Formula: see text]), a cross-validated correlation coefficient ([Formula: see text]) and a predictive squared correlation coefficient ([Formula: see text]). Overall, the analysis revealed the important electrostatic and steric attributes responsible for the FLAP inhibitory activity, which appeared to correlate well with the docking results. In addition, two statistically significant two-dimensional (2D)-QSAR models ([Formula: see text], [Formula: see text] and [Formula: see text], [Formula: see text]) were developed by a genetic function approximation (GFA). HypoGen 1, a proposed pharmacophore model, was used for database mining to identify potential new FLAP inhibitors. The bioactivity of the retrieved hits was then evaluated in silico based on the validated QSAR models, followed by pharmacokinetics and toxicity predictions.
{"title":"Identification of Novel 5-Lipoxygenase-Activating Protein (FLAP) Inhibitors by an Integrated Method of Pharmacophore Virtual Screening, Docking, QSAR and ADMET Analyses","authors":"Kamal Rullah, M. Roney, Z. Ibrahim, Nur Farisya Shamsudin, Deri Islami, Q. Ahmed, L. Wai, M. Aluwi","doi":"10.1142/s2737416523500059","DOIUrl":"https://doi.org/10.1142/s2737416523500059","url":null,"abstract":"This study explored a series of reported 5-lipoxygenase-activating protein (FLAP) inhibitors to understand their structural requirements and identify potential new inhibitor scaffolds through automated unbiased procedures. Docking studies have revealed that inhibitor binding affinity can be influenced by several key binding interactions with Phe114 and Lys116 from chain B and Val21, Phe25, His28 and Lys29 from chain C in the FLAP-binding site. A ligand-based alignment three-dimensional (3D)-quantitative structure–activity relationship (QSAR) was adopted, resulting in a robust model with a statistically significant noncross-validated coefficient ([Formula: see text]), a cross-validated correlation coefficient ([Formula: see text]) and a predictive squared correlation coefficient ([Formula: see text]). Overall, the analysis revealed the important electrostatic and steric attributes responsible for the FLAP inhibitory activity, which appeared to correlate well with the docking results. In addition, two statistically significant two-dimensional (2D)-QSAR models ([Formula: see text], [Formula: see text] and [Formula: see text], [Formula: see text]) were developed by a genetic function approximation (GFA). HypoGen 1, a proposed pharmacophore model, was used for database mining to identify potential new FLAP inhibitors. The bioactivity of the retrieved hits was then evaluated in silico based on the validated QSAR models, followed by pharmacokinetics and toxicity predictions.","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47990079","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 : 2022-11-25DOI: 10.1142/s2737416523500126
George A. Kaminski, Greggory W. Raymond
{"title":"Determining Zn(II) binding affinities of the YiiP zinc transporter and UFsc (Uno Ferro Single Chain) Protein with a novel modification of the PKA17 software","authors":"George A. Kaminski, Greggory W. Raymond","doi":"10.1142/s2737416523500126","DOIUrl":"https://doi.org/10.1142/s2737416523500126","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41412640","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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