Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 14 (2022)

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Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 14 (2022)

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Research Articles

Article
Synthesis, molecular docking and ADME studies of thiazole-thiazolidinedione hybrids as antimicrobial agents
Shankar G. Alegaon, Venkatasubramanian U, K. R. Alagawadi, Dushyant Kumar, Rohini S. Kavalapure, Shriram D. Ranade, Soundarya Priya A & Sunil S. Jalalpure
Pages: 6211-6227
Published online: 04 Feb 2021
AbstractforSynthesis, molecular docking and ADME studies of thiazole-thiazolidinedione hybrids as antimicrobial agents | Full Text | References | PDF (5.6 MB) | EPUB | Supplemental
  • 282 Views
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Article
Identification of novel anti-cancer agents, applying in silico method for SENP1 protease inhibition
Somayye Taghvaei, Farzaneh Sabouni, Zarrin Minuchehr & Alireza Taghvaei
Pages: 6228-6242
Published online: 03 Feb 2021
AbstractforIdentification of novel anti-cancer agents, applying in silico method for SENP1 protease inhibition | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 431 Views
  • 7 CrossRef citations
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Article
Impact of dimerization and N3 binding on molecular dynamics of SARS-CoV and SARS-CoV-2 main proteases
Mustafa Tekpinar & Ahmet Yildirim
Pages: 6243-6254
Published online: 02 Feb 2021
AbstractforImpact of dimerization and N3 binding on molecular dynamics of SARS-CoV and SARS-CoV-2 main proteases | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 1933 Views
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Article
Repurposing of FDA approved drugs and their validation against potential drug targets for Salmonella enterica through molecular dynamics simulation
Akanksha Kesharwani, Dheeraj Kumar Chaurasia & Pramod Katara
Pages: 6255-6271
Published online: 02 Feb 2021
AbstractforRepurposing of FDA approved drugs and their validation against potential drug targets for Salmonella enterica through molecular dynamics simulation | Full Text | References | PDF (4.7 MB) | EPUB | Supplemental
  • 314 Views
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Article
Structural analysis of alternate sigma factor ComX with RpoC, RpoB and its cognate CIN promoter reveals a distinctive promoter melting mechanism
P. C. Kunthavai, Muthu Kannan & Preethi Ragunathan
Pages: 6272-6285
Published online: 08 Feb 2021
AbstractforStructural analysis of alternate sigma factor ComX with RpoC, RpoB and its cognate CIN promoter reveals a distinctive promoter melting mechanism | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 201 Views
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Article
Targeting the N-terminal domain of the RNA-binding protein of the SARS-CoV-2 with high affinity natural compounds to abrogate the protein-RNA interaction: a molecular dynamics study
Sohail Khan, Zahid Hussain, Muhammad Safdar, Abbas Khan & Dong-Qing Wei
Pages: 6286-6294
Published online: 08 Feb 2021
AbstractforTargeting the N-terminal domain of the RNA-binding protein of the SARS-CoV-2 with high affinity natural compounds to abrogate the protein-RNA interaction: a molecular dynamics study | Full Text | References | PDF (2 MB) | EPUB
  • 565 Views
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Article
A novel antiplasmodial compound: integration of in silico and in vitro assays
David Bacelar Costa Júnior, Janay Stefany Carneiro Araújo, Larissa de Mattos Oliveira, Flávio Simas Moreira Neri, Paulo Otávio Lourenço Moreira, Alex Gutterres Taranto, Amanda Luisa Fonseca, Fernando de Pilla Varotti & Franco Henrique Andrade Leite
Pages: 6295-6307
Published online: 08 Feb 2021
AbstractforA novel antiplasmodial compound: integration of in silico and in vitro assays | Full Text | References | PDF (2.4 MB) | EPUB
  • 202 Views
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Article
In silico design of enzyme α-amylase and α-glucosidase inhibitors using molecular docking, molecular dynamic, conceptual DFT investigation and pharmacophore modelling
Hadjer Chenafa, Fouzia Mesli, Ismail Daoud, Radja Achiri, Said Ghalem & Abdelhak Neghra
Pages: 6308-6329
Published online: 08 Feb 2021
AbstractforIn silico design of enzyme α-amylase and α-glucosidase inhibitors using molecular docking, molecular dynamic, conceptual DFT investigation and pharmacophore modelling | Full Text | References | PDF (6.3 MB) | EPUB | Supplemental
  • 647 Views
  • 16 CrossRef citations
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Article
Functional annotation and comparative modeling of ligninolytic enzymes from Trametes villosa (SW.) Kreisel for biotechnological applications
Dalila de Souza Santos Ferreira, Cleidineia Souza de Santana, Isis Bugia Santana, Janay Stefany Carneiro Araújo, Bruno Cruz de Souza, Franco Henrique Andrade Leite, Rodrigo Bentes Kato, Raquel Guimarães Benevides & Aristóteles Góes-Neto
Pages: 6330-6339
Published online: 08 Feb 2021
AbstractforFunctional annotation and comparative modeling of ligninolytic enzymes from Trametes villosa (SW.) Kreisel for biotechnological applications | Full Text | References | PDF (2.9 MB) | EPUB
  • 150 Views
  • 1 CrossRef citations
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Article
Novel α-amylase and α-glucosidase inhibitors from selected Nigerian antidiabetic plants: an in silico approach
Ruth M. Ogboye, Rajesh B. Patil, Samson O. Famuyiwa & Kolade O. Faloye
Pages: 6340-6349
Published online: 13 Feb 2021
AbstractforNovel α-amylase and α-glucosidase inhibitors from selected Nigerian antidiabetic plants: an in silico approach | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 371 Views
  • 4 CrossRef citations
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Article
Investigation of sphingosine kinase 1 inhibitory potential of cinchonine and colcemid targeting anticancer therapy
Sonam Roy, Shama Khan, Deeba Shamim Jairajpuri, Afzal Hussain, Mohamed F. Alajmi, Asimul Islam, Suaib Luqman, Suhel Parvez & Md. Imtaiyaz Hassan
Pages: 6350-6362
Published online: 10 Feb 2021
AbstractforInvestigation of sphingosine kinase 1 inhibitory potential of cinchonine and colcemid targeting anticancer therapy | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 335 Views
  • 7 CrossRef citations
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Article
Exploring the cancer-testis antigen BORIS to design a novel multi-epitope vaccine against breast cancer based on immunoinformatics approaches
Elham Mahdevar, Ashkan Safavi, Ardavan Abiri, Amirhosein Kefayat, Seyed Hossein Hejazi, Seyed Mohsen Miresmaeili & Vahid Iranpur Mobarakeh
Pages: 6363-6380
Published online: 18 Feb 2021
AbstractforExploring the cancer-testis antigen BORIS to design a novel multi-epitope vaccine against breast cancer based on immunoinformatics approaches | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 550 Views
  • 32 CrossRef citations
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Article
Artificially expanded genetic information systems (AEGISs) as potent inhibitors of the RNA-dependent RNA polymerase of the SARS-CoV-2
N. R. Jena, Suyash Pant & Hemant Kumar Srivastava
Pages: 6381-6397
Published online: 10 Feb 2021
AbstractforArtificially expanded genetic information systems (AEGISs) as potent inhibitors of the RNA-dependent RNA polymerase of the SARS-CoV-2 | Full Text | References | PDF (4.7 MB) | EPUB | Supplemental
  • 1325 Views
  • 8 CrossRef citations
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Article
Insilico assisted identification of peppery aroma compound ‘rotundone’ backbone genes from black pepper
Johnson George Kokkat, Sreekumar Shelvy, Abdulkabeer Muhammed Fayad, Ahammed Shabeer T. P.Palaniyandi Umadevi, Rajaram Kale, Ulavappa Basavanneppa Angadi, Mir Asif Iquebal, Sarika Jaiswal, Anil Rai & Dinesh Kumar
Pages: 6398-6404
Published online: 10 Feb 2021
AbstractforInsilico assisted identification of peppery aroma compound ‘rotundone’ backbone genes from black pepper | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 259 Views
  • 1 CrossRef citations
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Article
Effect of variations in the conserved residues E371 and S359 on the structural dynamics of protein Z dependent protease inhibitor (ZPI): a molecular dynamic simulation study
Subash Chellam Gayathri, Suchetana Gupta, Aravind Suresh, Sanjib Senapati & Tanusree Sengupta
Pages: 6405-6414
Published online: 08 Feb 2021
AbstractforEffect of variations in the conserved residues E371 and S359 on the structural dynamics of protein Z dependent protease inhibitor (ZPI): a molecular dynamic simulation study | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 166 Views
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Article
Computational identification of potential lead molecules targeting rho receptor of Neisseria gonorrhoeae
Sundararaj Rajamanikandan, Soundarapandian Soundarya, Anandhi Paramasivam, Dhamodharan Prabhu, Jeyaraman Jeyakanthan & Vidhyavathi Ramasamy
Pages: 6415-6425
Published online: 16 Feb 2021
AbstractforComputational identification of potential lead molecules targeting rho receptor of Neisseria gonorrhoeae | Full Text | References | PDF (2.2 MB) | EPUB
  • 180 Views
  • 2 CrossRef citations
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Article
Metabolomic profiling of three Araucaria species, and their possible potential role against COVID-19
Seham S. El-Hawary, Mohamed A. Rabeh, Mohamed A. El Raey, Essam M. Abd El-Kadder, Mansor Sobeh, Usama Ramadan Abdelmohsen, Amgad Albohy, Alexander M. Andrianov, Ivan P. Bosko, Mohammad M. Al-Sanea & Dalia G. El-Kolobby
Pages: 6426-6438
Published online: 18 Feb 2021
AbstractforMetabolomic profiling of three Araucaria species, and their possible potential role against COVID-19 | Full Text | References | PDF (3.2 MB) | EPUB
  • 1406 Views
  • 9 CrossRef citations
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Article
Evaluation of binding of potential ADMET/tox screened saquinavir analogues for inhibition of HIV-protease via molecular dynamics and binding free energy calculations
Amit Jayaswal, Ekta Pathak, Hirdyesh Mishra & Kavita Shah
Pages: 6439-6449
Published online: 04 Mar 2021
AbstractforEvaluation of binding of potential ADMET/tox screened saquinavir analogues for inhibition of HIV-protease via molecular dynamics and binding free energy calculations | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 167 Views
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Article
Computationally-obtained structural insights into the molecular interactions between Pidilizumab and binding partners DLL1 and PD-1
Aline de Oliveira Albuquerque, Haroldo Cid da Silva Junior, Geraldo Rodrigues Sartori & João Hermínio Martins da Silva
Pages: 6450-6462
Published online: 09 Feb 2021
AbstractforComputationally-obtained structural insights into the molecular interactions between Pidilizumab and binding partners DLL1 and PD-1 | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 280 Views
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Article
Anti-HIV-drug and phyto-flavonoid combination against SARS-CoV-2: a molecular docking-simulation base assessment
Shasank S. Swain, Satya R. Singh, Alaka Sahoo, Tahziba Hussain & Sanghamitra Pati
Pages: 6463-6476
Published online: 15 Feb 2021
AbstractforAnti-HIV-drug and phyto-flavonoid combination against SARS-CoV-2: a molecular docking-simulation base assessment | Full Text | References | PDF (4.3 MB) | EPUB
  • 1904 Views
  • 11 CrossRef citations
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Article
Whole proteome screening and identification of potential epitopes of SARS-CoV-2 for vaccine design-an immunoinformatic, molecular docking and molecular dynamics simulation accelerated robust strategy
Md. Muzahid Ahmed Ezaj, Md. Junaid, Yeasmin Akter, Afsana Nahrin, Aysha Siddika, Syeda Samira Afrose, S. M. Abdul Nayeem, Md. Sajedul Haque, Mohammad Ali Moni & S. M. Zahid Hosen
Pages: 6477-6502
Published online: 15 Feb 2021
AbstractforWhole proteome screening and identification of potential epitopes of SARS-CoV-2 for vaccine design-an immunoinformatic, molecular docking and molecular dynamics simulation accelerated robust strategy | Full Text | References | PDF (7.4 MB) | EPUB | Supplemental
  • 1219 Views
  • 5 CrossRef citations
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Article
Structure and ligand-based drug discovery of IL-4 inhibitors via interaction-energy-based learning approaches
Sehrish Naz, Sajda Ashraf, Mohammad K. Parvez, Mohammed S. Al-Dosari & Zaheer Ul-Haq
Pages: 6503-6521
Published online: 23 Feb 2021
AbstractforStructure and ligand-based drug discovery of IL-4 inhibitors via interaction-energy-based learning approaches | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 224 Views
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Article
Multispectral and molecular modeling investigations on the binding behaviors of two anticoccidials with serum albumins
Xu Li, Rui Zhao, Di Shao, Yue Yuan & Shuyun Bi
Pages: 6522-6533
Published online: 15 Feb 2021
AbstractforMultispectral and molecular modeling investigations on the binding behaviors of two anticoccidials with serum albumins | Full Text | References | PDF (3.5 MB) | EPUB
  • 122 Views
  • 1 CrossRef citations
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Article
In silico identification and validation of natural antiviral compounds as potential inhibitors of SARS-CoV-2 methyltransferase
Anshuman Chandra, Meenakshi Chaudhary, Imteyaz Qamar, Nagendra Singh & Vikrant Nain
Pages: 6534-6544
Published online: 15 Feb 2021
AbstractforIn silico identification and validation of natural antiviral compounds as potential inhibitors of SARS-CoV-2 methyltransferase | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 1949 Views
  • 13 CrossRef citations
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Article
Structural genetics of circulating variants affecting the SARS-CoV-2 spike/human ACE2 complex
Francesco Ortuso, Daniele Mercatelli, Pietro Hiram Guzzi & Federico Manuel Giorgi
Pages: 6545-6555
Published online: 13 Feb 2021
AbstractforStructural genetics of circulating variants affecting the SARS-CoV-2 spike/human ACE2 complex | Full Text | References | PDF (2.2 MB) | EPUB
  • 1957 Views
  • 22 CrossRef citations
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Article
Finding potent inhibitors against SARS-CoV-2 main protease through virtual screening, ADMET, and molecular dynamics simulation studies
Rajarshi Roy, Md Fulbabu Sk, Nisha Amarnath Jonniya, Sayan Poddar & Parimal Kar
Pages: 6556-6568
Published online: 08 Mar 2021
AbstractforFinding potent inhibitors against SARS-CoV-2 main protease through virtual screening, ADMET, and molecular dynamics simulation studies | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 813 Views
  • 11 CrossRef citations
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Article
In silico prediction of SARS-CoV-2 main protease and polymerase inhibitors: 3D-Pharmacophore modelling
Mona Mosayebnia, Atefeh Hajiagha Bozorgi, Maliheh Rezaeianpour & Farzad Kobarfard
Pages: 6569-6586
Published online: 18 Feb 2021
AbstractforIn silico prediction of SARS-CoV-2 main protease and polymerase inhibitors: 3D-Pharmacophore modelling | Full Text | References | PDF (4.2 MB) | EPUB
  • 1022 Views
  • 2 CrossRef citations
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Article
Repurposing drugs and identification of inhibitors of integral proteins (spike protein and main protease) of SARS-CoV-2
F. O. Shode, A. S. K. Idowu, O. J. Uhomoibhi & S. Sabiu
Pages: 6587-6602
Published online: 16 Feb 2021
AbstractforRepurposing drugs and identification of inhibitors of integral proteins (spike protein and main protease) of SARS-CoV-2 | Full Text | References | PDF (5.3 MB) | EPUB | Supplemental
  • 1286 Views
  • 15 CrossRef citations
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Article
Targeting allosteric pockets of SARS-CoV-2 main protease Mpro
Zahoor Ahmad Bhat, Dheeraj Chitara, Jawed Iqbal, B. S. Sanjeev & Arumugam Madhumalar
Pages: 6603-6618
Published online: 27 Feb 2021
AbstractforTargeting allosteric pockets of SARS-CoV-2 main protease Mpro | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 579 Views
  • 6 CrossRef citations
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Article
Investigation into the site-specific binding interactions between chlorogenic acid and ovalbumin using multi-spectroscopic and in silico simulation studies
Manivel Perumal, Parthiban Marimuthu & Xiumin Chen
Pages: 6619-6633
Published online: 25 Feb 2021
AbstractforInvestigation into the site-specific binding interactions between chlorogenic acid and ovalbumin using multi-spectroscopic and in silico simulation studies | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 195 Views
  • 4 CrossRef citations
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Article
Identification of the binding interactions of some novel antiviral compounds against Nsp1 protein from SARS-CoV-2 (COVID-19) through high throughput screening
Nilkanta Chowdhury & Angshuman Bagchi
Pages: 6634-6641
Published online: 22 Feb 2021
AbstractforIdentification of the binding interactions of some novel antiviral compounds against Nsp1 protein from SARS-CoV-2 (COVID-19) through high throughput screening | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 914 Views
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Article
Synthesis, structural, spectral, antioxidant, bioactivity and molecular docking investigations of a novel triazole derivative
Can Alaşalvar, Nuri Öztürk, Halil Gökce, Aytaç Güder, Emre Menteşe & Hakan Bektaş
Pages: 6642-6655
Published online: 17 Feb 2021
AbstractforSynthesis, structural, spectral, antioxidant, bioactivity and molecular docking investigations of a novel triazole derivative | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 829 Views
  • 2 CrossRef citations
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Article
4-acetamido-3-nitrobenzoic acid - structural, quantum chemical studies, ADMET and molecular docking studies of SARS-CoV2
Gurumallappa, R. R. Arun Renganathan, M. K. Hema, C. S. Karthik, Sandhya Rani, M. Nethaji, H.S Jayanth, P. Mallu, N. K. Lokanath & V. Ravishankar Rai
Pages: 6656-6670
Published online: 24 Feb 2021
Abstractfor4-acetamido-3-nitrobenzoic acid - structural, quantum chemical studies, ADMET and molecular docking studies of SARS-CoV2 | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 477 Views
  • 3 CrossRef citations
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Article
A potential peptide inhibitor of SARS-CoV-2 S and human ACE2 complex
Grijesh Jaiswal, Shivani Yaduvanshi & Veerendra Kumar
Pages: 6671-6681
Published online: 01 Mar 2021
AbstractforA potential peptide inhibitor of SARS-CoV-2 S and human ACE2 complex | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 1016 Views
  • 3 CrossRef citations
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