Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 11 (2022)

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Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 11 (2022)

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Article
Electronic properties investigation of human dihydrofolate reductase complexes with ligands
Vladislav Naumovich, Maria Grishina, Jurica Novak, Prateek Pathak, Vladimir Potemkin, Mohd Shahbaaz & Magda H. Abdellattif
Pages: 4775-4790
Published online: 21 Dec 2020
AbstractforElectronic properties investigation of human dihydrofolate reductase complexes with ligands | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
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Article
Structural analyses and classification of novel isoniazid resistance coupled mutational landscapes in Mycobacterium tuberculosis: a combined molecular docking and MD simulation study
Mohd Shahbaaz, Sameer H. Qari, Magda H. Abdellattif & Mostafa A. Hussien
Pages: 4791-4800
Published online: 21 Dec 2020
AbstractforStructural analyses and classification of novel isoniazid resistance coupled mutational landscapes in Mycobacterium tuberculosis: a combined molecular docking and MD simulation study | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 209 Views
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Article
Synthesis of carbazole based α-aminophosphonate derivatives: design, molecular docking and in vitro cholinesterase activity
Sarfaraz Shaikh, Pratik Dhavan, Pinky Singh, Jasmin Uparkar, S. P. Vaidya, B. L. Jadhav & M. V. Ramana
Pages: 4801-4814
Published online: 21 Dec 2020
AbstractforSynthesis of carbazole based α-aminophosphonate derivatives: design, molecular docking and in vitro cholinesterase activity | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 360 Views
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Article
Mining of Ebola virus genome for the construction of multi-epitope vaccine to combat its infection
Uma Shankar, Neha Jain, Subodh Kumar Mishra, Md Fulbabu Sk, Parimal Kar & Amit Kumar
Pages: 4815-4831
Published online: 19 Jan 2021
AbstractforMining of Ebola virus genome for the construction of multi-epitope vaccine to combat its infection | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 484 Views
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Article
Identification of potential non-nucleoside MraY inhibitors for tuberculosis chemotherapy using structure-based virtual screening
Pankaj Pandey, Shamba Chatterjee, Tomayo Berida, Robert J. Doerksen & Sudeshna Roy
Pages: 4832-4849
Published online: 22 Dec 2020
AbstractforIdentification of potential non-nucleoside MraY inhibitors for tuberculosis chemotherapy using structure-based virtual screening | Full Text | References | PDF (4.6 MB) | EPUB | Supplemental
  • 280 Views
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Article
Computer-aided identification of human carbonic anhydrase isoenzyme VII inhibitors as potential antiepileptic agents
Avinash Kumar, Paridhi Agarwal, Ekta Rathi & Suvarna G. Kini
Pages: 4850-4865
Published online: 21 Dec 2020
AbstractforComputer-aided identification of human carbonic anhydrase isoenzyme VII inhibitors as potential antiepileptic agents | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 291 Views
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Article
Targeting a conserved pocket (n-octyl-β-D–glucoside) on the dengue virus envelope protein by small bioactive molecule inhibitors
P. Naresh, A. Selvaraj, P. Shyam Sundar, S. Murugesan, S. Sathianarayanan, Krishnan Namboori P. K.S. Jubie
Pages: 4866-4878
Published online: 21 Dec 2020
AbstractforTargeting a conserved pocket (n-octyl-β-D–glucoside) on the dengue virus envelope protein by small bioactive molecule inhibitors | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 249 Views
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Article
Prediction of potential inhibitors against SARS-CoV-2 endoribonuclease: RNA immunity sensing
Nihad A. M. Al-Rashedi, Murad G. Munahi & Laith AH ALObaidi
Pages: 4879-4892
Published online: 27 Dec 2020
AbstractforPrediction of potential inhibitors against SARS-CoV-2 endoribonuclease: RNA immunity sensing | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 1239 Views
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Article
Shedding light on the bimolecular interactions of Cafaminol and human serum albumin: spectroscopic characterization and in-silico investigation
Negar Parvizi, Delara Mohammad-Aghaie, Mohammad Navid Soltani Rad, Somayeh Behrouz & Mohamad Mehdi Alavianmehr
Pages: 4893-4904
Published online: 04 Jan 2021
AbstractforShedding light on the bimolecular interactions of Cafaminol and human serum albumin: spectroscopic characterization and in-silico investigation | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 112 Views
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Article
Design and in silico study of the novel coumarin derivatives against SARS-CoV-2 main enzymes
Mücahit Özdemir, Baybars Köksoy, Deniz Ceyhan, Koray Sayın, Erol Erçağ, Mustafa Bulut & Bahattin Yalçın
Pages: 4905-4920
Published online: 27 Dec 2020
AbstractforDesign and in silico study of the novel coumarin derivatives against SARS-CoV-2 main enzymes | Full Text | References | PDF (5.6 MB) | EPUB | Supplemental
  • 2083 Views
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Article
Comparative in vitro and DFT antioxidant studies of phenolic group substituted pyridine-based azo derivatives
Barış Sezgin, Tahir Tilki, Çiğdem Karabacak Atay & Bülent Dede
Pages: 4921-4932
Published online: 24 Dec 2020
AbstractforComparative in vitro and DFT antioxidant studies of phenolic group substituted pyridine-based azo derivatives | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 430 Views
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Article
Quantitative structure activity relationship studies of novel hydrazone derivatives as α-amylase inhibitors with index of ideality of correlation
Meenakshi Duhan, Jayant Sindhu, Parvin Kumar, Meena Devi, Rahul Singh, Ramesh Kumar, Sohan Lal, Ashwani Kumar, Sudhir Kumar & Khalid Hussain
Pages: 4933-4953
Published online: 24 Dec 2020
AbstractforQuantitative structure activity relationship studies of novel hydrazone derivatives as α-amylase inhibitors with index of ideality of correlation | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 279 Views
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Article
Computational approach to explore the inhibitory potential of biologically derived compounds against Spodoptera litura vitellogenin receptor (VgR) using structure based virtual screening and molecular dynamics
Veeranarayanan Surya Aathmanathan, Velusamy Arumugam & Muthukalingan Krishnan
Pages: 4954-4960
Published online: 24 Dec 2020
AbstractforComputational approach to explore the inhibitory potential of biologically derived compounds against Spodoptera litura vitellogenin receptor (VgR) using structure based virtual screening and molecular dynamics | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 161 Views
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Article
In vivo/in silico insight into the effect of titanium dioxide nanoparticle on serum paraoxonase 1 activity in rat
Hessameddin Mortazavi, Hossein Omidi-Ardali, Seyed Asadollah Amini, Javad Saffari-Chaleshtori & Keihan Ghatreh Samani
Pages: 4961-4971
Published online: 18 Jan 2021
AbstractforIn vivo/in silico insight into the effect of titanium dioxide nanoparticle on serum paraoxonase 1 activity in rat | Full Text | References | PDF (3.4 MB) | EPUB
  • 290 Views
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Article
A conserved arginine residue in a staphylococcal anti-sigma factor is required to preserve its kinase activity, structure, and stability
Debasmita Sinha, Debabrata Sinha, Nilanjan Banerjee, Priya Rai, Soham Seal, Tushar Chakraborty, Subhrangsu Chatterjee & Subrata Sau
Pages: 4972-4986
Published online: 24 Dec 2020
AbstractforA conserved arginine residue in a staphylococcal anti-sigma factor is required to preserve its kinase activity, structure, and stability | Full Text | References | PDF (3.3 MB) | EPUB
  • 231 Views
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Article
Dual inhibition of SARS-CoV-2 spike and main protease through a repurposed drug, rutin
Anchala Kumari, Vikrant Singh Rajput, Priya Nagpal, Himanshi Kukrety, Sonam Grover & Abhinav Grover
Pages: 4987-4999
Published online: 27 Dec 2020
AbstractforDual inhibition of SARS-CoV-2 spike and main protease through a repurposed drug, rutin | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 1649 Views
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Article
Novel P,C-orthopalladated complexes containing histidine and phenylalanine amino acids: synthesis, DNA and BSA interactions, in vitro antitumoral activity and molecular docking approach
Sara Hashemi, Kazem Karami, Zeinab Saberi Dehkordi, Amir Abbas Momtazi-Borojeni & Seyed Alireza Esmaeili
Pages: 5000-5015
Published online: 24 Dec 2020
AbstractforNovel P,C-orthopalladated complexes containing histidine and phenylalanine amino acids: synthesis, DNA and BSA interactions, in vitro antitumoral activity and molecular docking approach | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 133 Views
  • 3 CrossRef citations
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Article
Role of Thr199 residue in human β-carbonic anhydrase-II pH-dependent activity elucidated by microsecond simulation analysis
Pulala Raghuveer Yadav, Syed Hussain Basha & Pavan Kumar Pindi
Pages: 5016-5025
Published online: 24 Dec 2020
AbstractforRole of Thr199 residue in human β-carbonic anhydrase-II pH-dependent activity elucidated by microsecond simulation analysis | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 190 Views
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Article
Computational-aided design: minimal peptide sequence to block dengue virus transmission into cells
Aathe Cangaree Arumugam, Fatima Ezzahra Agharbaoui, Ahmad Suhail Khazali, Rohana Yusof, Noorsaadah Abd Rahman & Abdullah Al Hadi Ahmad Fuaad
Pages: 5026-5035
Published online: 31 Dec 2020
AbstractforComputational-aided design: minimal peptide sequence to block dengue virus transmission into cells | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 169 Views
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Article
Understanding the impact of anticancer halogenated inhibitors and various functional groups (X = Cl, F, CF3, CH3, NH2, OH, H) of casein kinase 2 (CK2)
Palanisamy Deepa & Duraisamy Thirumeignanam
Pages: 5036-5052
Published online: 29 Dec 2020
AbstractforUnderstanding the impact of anticancer halogenated inhibitors and various functional groups (X = Cl, F, CF3, CH3, NH2, OH, H) of casein kinase 2 (CK2) | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 74 Views
  • 1 CrossRef citations
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Article
In silico analysis of phytochemicals as potential inhibitors of proteases involved in SARS-CoV-2 infection
Palaniyandi Umadevi, Subramanian Manivannan, Abdulkabeer Muhammed Fayad & Sreekumar Shelvy
Pages: 5053-5059
Published online: 29 Dec 2020
AbstractforIn silico analysis of phytochemicals as potential inhibitors of proteases involved in SARS-CoV-2 infection | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 1859 Views
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Article
Computational studies of membrane pore formation induced by Pin2
José-Luis Velasco-Bolom & Ramón Garduño-Juárez
Pages: 5060-5068
Published online: 05 Jan 2021
AbstractforComputational studies of membrane pore formation induced by Pin2 | Full Text | References | PDF (1.9 MB) | EPUB
  • 289 Views
  • 2 CrossRef citations
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Article
Ensemble-based high-throughput virtual screening of natural ligands using the Super Natural-II database against cell-wall protein dTDP-4-dehydrorhamnose reductase (RmlD) in Mycobacterium tuberculosis
Rahul Ravichandran, Nor Farrah Wahidah Ridzwan & Saharuddin Bin Mohamad
Pages: 5069-5078
Published online: 31 Dec 2020
AbstractforEnsemble-based high-throughput virtual screening of natural ligands using the Super Natural-II database against cell-wall protein dTDP-4-dehydrorhamnose reductase (RmlD) in Mycobacterium tuberculosis | Full Text | References | PDF (1.8 MB) | EPUB
  • 240 Views
  • 2 CrossRef citations
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Article
Identification of potential SARS-CoV-2 Mpro inhibitors integrating molecular docking and water thermodynamics
M. Elizabeth Sobhia, Ketan Ghosh, Srikanth Sivangula, Siva Kumar & Harmanpreet Singh
Pages: 5079-5089
Published online: 08 Jan 2021
AbstractforIdentification of potential SARS-CoV-2 Mpro inhibitors integrating molecular docking and water thermodynamics | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 1370 Views
  • 5 CrossRef citations
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Article
Monte-Carlo method-based QSAR model to discover phytochemical urease inhibitors using SMILES and GRAPH descriptors
Kumar Sambhav Chopdar, Ganesh Chandra Dash, Pranab Kishor Mohapatra, Binata Nayak & Mukesh Kumar Raval
Pages: 5090-5099
Published online: 06 Jan 2021
AbstractforMonte-Carlo method-based QSAR model to discover phytochemical urease inhibitors using SMILES and GRAPH descriptors | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 233 Views
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Article
Revealing the cholinergic inhibition mechanism of Alzheimer’s by galantamine: a metadynamics simulation study
Shibaji Ghosh, Kalyanashis Jana, Padmaja D. Wakchaure & Bishwajit Ganguly
Pages: 5100-5111
Published online: 31 Dec 2020
AbstractforRevealing the cholinergic inhibition mechanism of Alzheimer’s by galantamine: a metadynamics simulation study | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 459 Views
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Article
Molecular mechanism of inhibition of COVID-19 main protease by β-adrenoceptor agonists and adenosine deaminase inhibitors using in silico methods
Pushyaraga P. Venugopal & Debashree Chakraborty
Pages: 5112-5127
Published online: 05 Jan 2021
AbstractforMolecular mechanism of inhibition of COVID-19 main protease by β-adrenoceptor agonists and adenosine deaminase inhibitors using in silico methods | Full Text | References | PDF (4.9 MB) | EPUB | Supplemental
  • 1366 Views
  • 3 CrossRef citations
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Article
Fisetin 8-C-glucoside as entry inhibitor in SARS CoV-2 infection: molecular modelling study
Abha Mishra, Upinder Kaur & Amit Singh
Pages: 5128-5137
Published online: 31 Dec 2020
AbstractforFisetin 8-C-glucoside as entry inhibitor in SARS CoV-2 infection: molecular modelling study | Full Text | References | PDF (2.1 MB) | EPUB
  • 1181 Views
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Article
Virtual screening of curcumin and its analogs against the spike surface glycoprotein of SARS-CoV-2 and SARS-CoV
Ashish Patel, Malathi Rajendran, Ashish Shah, Harnisha Patel, Suresh B. Pakala & Prashanthi Karyala
Pages: 5138-5146
Published online: 05 Jan 2021
AbstractforVirtual screening of curcumin and its analogs against the spike surface glycoprotein of SARS-CoV-2 and SARS-CoV | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 2600 Views
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Article
Virtual repurposing of ursodeoxycholate and chenodeoxycholate as lead candidates against SARS-Cov2-Envelope protein: A molecular dynamics investigation
Reena Yadav, Chinmayee Choudhury, Yashwant Kumar & Alka Bhatia
Pages: 5147-5158
Published online: 31 Dec 2020
AbstractforVirtual repurposing of ursodeoxycholate and chenodeoxycholate as lead candidates against SARS-Cov2-Envelope protein: A molecular dynamics investigation | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 1020 Views
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Article
Highly potent anti-malarial activity of benzopyrano(4,3-b)benzopyran derivatives and in silico interaction analysis with putative target Plasmodium falciparum lactate dehydrogenase
Nishant Joshi, Rahul Hada, Sonal Gupta, Juveria Khan, Jeremy Dobrowolski, Pawan K. Dhar, Naresh Kumar & Shailja Singh
Pages: 5159-5174
Published online: 08 Jan 2021
AbstractforHighly potent anti-malarial activity of benzopyrano(4,3-b)benzopyran derivatives and in silico interaction analysis with putative target Plasmodium falciparum lactate dehydrogenase | Full Text | References | PDF (3.2 MB) | EPUB
  • 307 Views
  • 4 CrossRef citations
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Article
Predictive medicinal metabolites from Momordica dioica against comorbidity related proteins of SARS-CoV-2 infections
Chavan Sakshi, A. Harikrishnan, Selvakumar Jayaraman, Ahana Roy Choudhury & V. Veena
Pages: 5175-5188
Published online: 11 Jan 2021
AbstractforPredictive medicinal metabolites from Momordica dioica against comorbidity related proteins of SARS-CoV-2 infections | Full Text | References | PDF (4 MB) | EPUB
  • 2184 Views
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Article
In silico design of multi-epitope-based peptide vaccine against SARS-CoV-2 using its spike protein
Debarghya Mitra, Janmejay Pandey, Alok Jain & Shiv Swaroop
Pages: 5189-5202
Published online: 06 Jan 2021
AbstractforIn silico design of multi-epitope-based peptide vaccine against SARS-CoV-2 using its spike protein | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 1637 Views
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Article
In-silico identification of potential inhibitors targeting the DNA binding domain of estrogen receptor α for the treatment of hormone therapy-resistant breast cancer
El Mehdi Bouricha, Mohammed Hakmi, Jihane Akachar, Fouad Zouaidia & Azeddine Ibrahimi
Pages: 5203-5210
Published online: 06 Jan 2021
AbstractforIn-silico identification of potential inhibitors targeting the DNA binding domain of estrogen receptor α for the treatment of hormone therapy-resistant breast cancer | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 306 Views
  • 1 CrossRef citations
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Article
Structural aspects of β-glucosidase of Myceliophthora thermophila (MtBgl3c) by homology modelling and molecular docking
Anica Dadwal, Vishal Singh, Shilpa Sharma & Tulasi Satyanarayana
Pages: 5211-5228
Published online: 08 Jan 2021
AbstractforStructural aspects of β-glucosidase of Myceliophthora thermophila (MtBgl3c) by homology modelling and molecular docking | Full Text | References | PDF (4.9 MB) | EPUB
  • 370 Views
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Article
Searching for potential drugs against SARS-CoV-2 through virtual screening on several molecular targets
Joyce S. F. D. Almeida, Fernanda D. Botelho, Felipe R. de Souza, Marcelo C. dos Santos, Arlan da Silva Goncalves, Rodrigo L. B. Rodrigues, Monique Cardozo, Daniel A. S. Kitagawa, Leandro A. Vieira, Raphael S. F. Silva, Samir F. A. Cavalcante, Leonardo da C. Bastos, Mariana de O. T. Nogueira, Priscila I. R. de Santana, Juliana de O. C. Brum, Eugenie Nepovimova, Kamil Kuca, Steven R. LaPlante, Erick B. F. Galante & Tanos C. C. Franca
Pages: 5229-5242
Published online: 08 Jan 2021
AbstractforSearching for potential drugs against SARS-CoV-2 through virtual screening on several molecular targets | Full Text | References | PDF (6.2 MB) | EPUB | Supplemental
  • 1519 Views
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Article
Interactions of large T-Antigen (LT) protein of polyomaviruses with p53 unfold their cancerogenic potential
Caroline Kellogg, Valentina L. Kouznetsova & Igor F. Tsigelny
Pages: 5243-5252
Published online: 08 Jan 2021
AbstractforInteractions of large T-Antigen (LT) protein of polyomaviruses with p53 unfold their cancerogenic potential | Full Text | References | PDF (3 MB) | EPUB
  • 196 Views
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