Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 12 (2022)

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Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 12 (2022)

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Research Articles

Article
Unravelling the molecular basis of AM-6494 high potency at BACE1 in Alzheimer’s disease: an integrated dynamic interaction investigation
Samuel C. Ugbaja, Patrick Appiah-Kubi, Monsurat M. Lawal, Nelisiwe S. Gumede & Hezekiel M. Kumalo
Pages: 5253-5265
Published online: 07 Jan 2021
AbstractforUnravelling the molecular basis of AM-6494 high potency at BACE1 in Alzheimer’s disease: an integrated dynamic interaction investigation | Full Text | References | PDF (3.7 MB) | EPUB
  • 377 Views
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Article
Virtual screening and repurposing of FDA-approved drugs from ZINC database to identify potential autophagy inhibitors exploiting autophagy related 4A cysteine peptidase as a target: potential as novel anti-cancer molecule.
Umesh , Kumari Prerna & Vikash Kumar Dubey
Pages: 5266-5282
Published online: 07 Jan 2021
AbstractforVirtual screening and repurposing of FDA-approved drugs from ZINC database to identify potential autophagy inhibitors exploiting autophagy related 4A cysteine peptidase as a target: potential as novel anti-cancer molecule. | Full Text | References | PDF (5.5 MB) | EPUB | Supplemental
  • 567 Views
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Article
Exploring of paritaprevir and glecaprevir resistance due to A156T mutation of HCV NS3/4A protease: molecular dynamics simulation study
Thitiya Boonma, Bodee Nutho, Nitchakan Darai, Thanyada Rungrotmongkol & Nadtanet Nunthaboot
Pages: 5283-5294
Published online: 11 Jan 2021
AbstractforExploring of paritaprevir and glecaprevir resistance due to A156T mutation of HCV NS3/4A protease: molecular dynamics simulation study | Full Text | References | PDF (3.3 MB) | EPUB
  • 293 Views
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Article
Withanolides from Withania somnifera as an immunity booster and their therapeutic options against COVID-19
Pukar Khanal, Rupesh Chikhale, Yadu Nandan Dey, Ismail Pasha, Sharad Chand, Nilambari Gurav, Muniappan Ayyanar, B. M. Patil & Shailendra Gurav
Pages: 5295-5308
Published online: 18 Jan 2021
AbstractforWithanolides from Withania somnifera as an immunity booster and their therapeutic options against COVID-19 | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 3561 Views
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Article
Identification of novel potential ricin inhibitors by virtual screening, molecular docking, molecular dynamics and MM-PBSA calculations: a drug repurposing approach
Fernanda D. Botelho, Marcelo C. Santos, Arlan S. Gonçalves, Tanos C. C. França, Steven R. LaPlante & Joyce S. F. D. de Almeida
Pages: 5309-5319
Published online: 07 Jan 2021
AbstractforIdentification of novel potential ricin inhibitors by virtual screening, molecular docking, molecular dynamics and MM-PBSA calculations: a drug repurposing approach | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 298 Views
  • 3 CrossRef citations
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Article
Utilization of O/S-doped graphene nanoclusters for ultrasensitive detection of flurane derivatives-DFT investigations
Jamelah S. Al-Otaibi, Aljawhara H. Almuqrin, Y. Sheena Mary & Y. Shyma Mary
Pages: 5320-5327
Published online: 07 Jan 2021
AbstractforUtilization of O/S-doped graphene nanoclusters for ultrasensitive detection of flurane derivatives-DFT investigations | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 155 Views
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Article
Exploring the binding interactions of janus green blue with serum albumins from spectroscopic and calorimetric studies aided by in silico calculations
Saumen Saha, Snehasish Bhattacharjee & Joydeep Chowdhury
Pages: 5328-5344
Published online: 07 Jan 2021
AbstractforExploring the binding interactions of janus green blue with serum albumins from spectroscopic and calorimetric studies aided by in silico calculations | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 204 Views
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Article
Influence of the dimensionality of the periodic boundary conditions on the transport of a drug–peptide complex across model cell membranes
Nikoleta Ivanova & Anela Ivanova
Pages: 5345-5356
Published online: 08 Jan 2021
AbstractforInfluence of the dimensionality of the periodic boundary conditions on the transport of a drug–peptide complex across model cell membranes | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 111 Views
  • 1 CrossRef citations
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Article
Inhibition of biofilm formation, quorum sensing and other virulence factors in Pseudomonas aeruginosa by polyphenols of Gynura procumbens leaves
Zulkar Nain, Fariha Jasin Mansur, Shifath Bin Syed, Md Ariful Islam, Hiroyuki Azakami, Md Rezuanul Islam & Mohammad Minnatul Karim
Pages: 5357-5371
Published online: 06 Jan 2021
AbstractforInhibition of biofilm formation, quorum sensing and other virulence factors in Pseudomonas aeruginosa by polyphenols of Gynura procumbens leaves | Full Text | References | PDF (3.4 MB) | EPUB
  • 399 Views
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Article
In silico analysis of antiviral phytochemicals efficacy against Epstein–Barr virus glycoprotein H
Shweta Jakhmola, Zaved Hazarika, Anupam Nath Jha & Hem Chandra Jha
Pages: 5372-5385
Published online: 13 Jan 2021
AbstractforIn silico analysis of antiviral phytochemicals efficacy against Epstein–Barr virus glycoprotein H | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 646 Views
  • 16 CrossRef citations
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Article
Identification of novel potential cyclooxygenase-2 inhibitors using ligand- and structure-based virtual screening approaches
Josiane V. Cruz, Silvana Giuliatti, Levy B. Alves, Raí C. Silva, Elenilze F. B. Ferreira, Njogu M. Kimani, Carlos H. T. P. Silva, João S. N. de Souza, José M. Espejo-Román & Cleydson B. R. Santos
Pages: 5386-5408
Published online: 10 Jan 2021
AbstractforIdentification of novel potential cyclooxygenase-2 inhibitors using ligand- and structure-based virtual screening approaches | Full Text | References | PDF (6.4 MB) | EPUB | Supplemental
  • 497 Views
  • 3 CrossRef citations
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Article
Synthesis, antimicrobial activities, docking studies and computational calculations of new bis-1,4-phenylene -1H-1,2,3-triazole derivatives utilized ultrasonic energy
Sahar Soror, Asmaa M. Fahim, Samia Elabbady, Ekhlass Nassar & Asmaa Aboelnaga
Pages: 5409-5426
Published online: 01 Feb 2021
AbstractforSynthesis, antimicrobial activities, docking studies and computational calculations of new bis-1,4-phenylene -1H-1,2,3-triazole derivatives utilized ultrasonic energy | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 306 Views
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Article
Discovery of RTA ricin subunit inhibitors: a computational study using PM7 quantum chemical method and steered molecular dynamics
Elton José Ferreira Chaves, Luiz Eduardo Gomes da Cruz, Itácio Queiroz Mello Padilha, Carlos Henrique Silveira, Demetrius Antônio Machado Araujo & Gerd Bruno Rocha
Pages: 5427-5445
Published online: 02 Feb 2021
AbstractforDiscovery of RTA ricin subunit inhibitors: a computational study using PM7 quantum chemical method and steered molecular dynamics | Full Text | References | PDF (5.7 MB) | EPUB | Supplemental
  • 183 Views
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Article
Novel copper complexes of metronidazole and metronidazole benzoate: synthesis, characterization, biological and computational studies
Bushra Rafique, Kainat Shafique, Sabahat Hamid, Saima Kalsoom, Muhammad Hashim, Bushra Mirza, Laila Jafri & Mudassir Iqbal
Pages: 5446-5461
Published online: 11 Jan 2021
AbstractforNovel copper complexes of metronidazole and metronidazole benzoate: synthesis, characterization, biological and computational studies | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 299 Views
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Article
Identification of 1,2,3-triazole-phthalimide derivatives as potential drugs against COVID-19: a virtual screening, docking and molecular dynamic study
Vanderlan Nogueira Holanda, Elton Marlon de Araújo Lima, Welson Vicente da Silva, Rafael Trindade Maia, Rafael de Lima Medeiros, Arabinda Ghosh, Vera Lúcia de Menezes Lima & Regina Celia Bressan Queiroz de Figueiredo
Pages: 5462-5480
Published online: 18 Jan 2021
AbstractforIdentification of 1,2,3-triazole-phthalimide derivatives as potential drugs against COVID-19: a virtual screening, docking and molecular dynamic study | Full Text | References | PDF (5.3 MB) | EPUB | Supplemental
  • 2706 Views
  • 10 CrossRef citations
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Article
Can molecular dynamics explain decreased pathogenicity in mutant camphecene-resistant influenza virus?
Sophia S. Borisevich, Maxim A. Gureev, Оlga I. Yarovaya, Vladimir V. Zarubaev, Gennadiy A. Kostin, Yuriy B. Porozov & Nariman F. Salakhutdinov
Pages: 5481-5492
Published online: 22 Jan 2021
AbstractforCan molecular dynamics explain decreased pathogenicity in mutant camphecene-resistant influenza virus? | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 557 Views
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Article
ACE2-derived peptides interact with the RBD domain of SARS-CoV-2 spike glycoprotein, disrupting the interaction with the human ACE2 receptor
Pedro F. N. Souza, Jackson L. Amaral, Leandro P. Bezerra, Francisco E. S. Lopes, Valder N. Freire, Jose T. A. Oliveira & Cleverson D. T. Freitas
Pages: 5493-5506
Published online: 10 Jan 2021
AbstractforACE2-derived peptides interact with the RBD domain of SARS-CoV-2 spike glycoprotein, disrupting the interaction with the human ACE2 receptor | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 1721 Views
  • 7 CrossRef citations
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Article
Exploring potential inhibitor of SARS-CoV2 replicase from FDA approved drugs using insilico drug discovery methods
Anshuman Chandra, Vaishali Gurjar, Mohammad Z. Ahmed, Ali S. Alqahtani, Imteyaz Qamar & Nagendra Singh
Pages: 5507-5514
Published online: 25 Jan 2021
AbstractforExploring potential inhibitor of SARS-CoV2 replicase from FDA approved drugs using insilico drug discovery methods | Full Text | References | PDF (1.7 MB) | EPUB
  • 692 Views
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Article
Flavonol morin targets host ACE2, IMP-α, PARP-1 and viral proteins of SARS-CoV-2, SARS-CoV and MERS-CoV critical for infection and survival: a computational analysis
Anamika Gupta, Rumana Ahmad, Sahabjada Siddiqui, Kusum Yadav, Aditi Srivastava, Anchal Trivedi, Bilal Ahmad, Mohsin Ali Khan, Amit Kumar Shrivastava & Girish Kumar Singh
Pages: 5515-5546
Published online: 01 Feb 2021
AbstractforFlavonol morin targets host ACE2, IMP-α, PARP-1 and viral proteins of SARS-CoV-2, SARS-CoV and MERS-CoV critical for infection and survival: a computational analysis | Full Text | References | PDF (6.6 MB) | EPUB | Supplemental
  • 2171 Views
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Article
Enhancing bactericidal strategy with selected aromatic compounds: in vitro and in silico study
Aykut Oztekin, Kenan Karagoz, Sevki Adem & Veysel Comakli
Pages: 5547-5555
Published online: 18 Jan 2021
AbstractforEnhancing bactericidal strategy with selected aromatic compounds: in vitro and in silico study | Full Text | References | PDF (2.1 MB) | EPUB
  • 364 Views
  • 2 CrossRef citations
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Article
Structure analysis of the proteins associated with polyA repeat expansion disorders
Rolando Hernandez & Julio C. Facelli
Pages: 5556-5565
Published online: 18 Jan 2021
AbstractforStructure analysis of the proteins associated with polyA repeat expansion disorders | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 153 Views
  • 1 CrossRef citations
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Article
Enfuvirtide, an HIV-1 fusion inhibitor peptide, can act as a potent SARS-CoV-2 fusion inhibitor: an in silico drug repurposing study
Khadijeh Ahmadi, Alireza Farasat, Mosayeb Rostamian, Behrooz Johari & Hamid Madanchi
Pages: 5566-5576
Published online: 13 Jan 2021
AbstractforEnfuvirtide, an HIV-1 fusion inhibitor peptide, can act as a potent SARS-CoV-2 fusion inhibitor: an in silico drug repurposing study | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 2421 Views
  • 16 CrossRef citations
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Article
Insights in the structural understanding of amyloidogenicity and mutation-led conformational dynamics of amyloid beta (Aβ) through molecular dynamics simulations and principal component analysis
Sriram Srinivasa Raghavan, Saleem Iqbal, Niraikulam Ayyadurai & Krishnasamy Gunasekaran
Pages: 5577-5587
Published online: 13 Jan 2021
AbstractforInsights in the structural understanding of amyloidogenicity and mutation-led conformational dynamics of amyloid beta (Aβ) through molecular dynamics simulations and principal component analysis | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 444 Views
  • 5 CrossRef citations
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Article
In silico study indicates antimalarials as direct inhibitors of SARS-CoV-2-RNA dependent RNA polymerase
Pawan Kumar Doharey, Vishal Singh, Mallikarjuna Rao Gedda, Amaresh Kumar Sahoo, Pritish Kumar Varadwaj & Bechan Sharma
Pages: 5588-5605
Published online: 21 Jan 2021
AbstractforIn silico study indicates antimalarials as direct inhibitors of SARS-CoV-2-RNA dependent RNA polymerase | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 1663 Views
  • 20 CrossRef citations
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Article
Oncogenic potential of ATAD2 in stomach cancer and insights into the protein-protein interactions at its AAA + ATPase domain and bromodomain
Aditi Nayak, Sugandh Kumar, Shivaram Prasad Singh, Asima Bhattacharyya, Anshuman Dixit & Anasuya Roychowdhury
Pages: 5606-5622
Published online: 13 Jan 2021
AbstractforOncogenic potential of ATAD2 in stomach cancer and insights into the protein-protein interactions at its AAA + ATPase domain and bromodomain | Full Text | References | PDF (4.3 MB) | EPUB | Supplemental
  • 507 Views
  • 3 CrossRef citations
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Article
Delineation of an epitope recognized by a chikungunya virus anti-capsid monoclonal antibody on the protease domain using an immuno-informatics approach
Aabha Thite, Megha Agrawal, Daya Pavitrakar, Sarah Cherian & Rekha Damle
Pages: 5623-5633
Published online: 22 Jan 2021
AbstractforDelineation of an epitope recognized by a chikungunya virus anti-capsid monoclonal antibody on the protease domain using an immuno-informatics approach | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 172 Views
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Article
Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study
Mohammad Mahmoudi Gomari, Neda Rostami, Hossein Omidi-Ardali & Seyed Shahriar Arab
Pages: 5634-5642
Published online: 21 Jan 2021
AbstractforInsight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study | Full Text | References | PDF (2.1 MB) | EPUB
  • 2628 Views
  • 16 CrossRef citations
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Article
Prospecting for Cressa cretica to treat COVID-19 via in silico molecular docking models of the SARS-CoV-2
Sapan Shah, Dinesh Chaple, Sumit Arora, Subhash Yende, Chetan Mehta & Usha Nayak
Pages: 5643-5652
Published online: 15 Jan 2021
AbstractforProspecting for Cressa cretica to treat COVID-19 via in silico molecular docking models of the SARS-CoV-2 | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 2006 Views
  • 8 CrossRef citations
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Article
An in silico analysis of Ibuprofen enantiomers in high concentrations of sodium chloride with SARS-CoV-2 main protease
C. M. Clemente, M. I. Freiberger, S. Ravetti, D. M. Beltramo & A. G. Garro
Pages: 5653-5664
Published online: 18 Jan 2021
AbstractforAn in silico analysis of Ibuprofen enantiomers in high concentrations of sodium chloride with SARS-CoV-2 main protease | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 1453 Views
  • 4 CrossRef citations
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Article
Molecular docking and simulation studies of natural compounds of Vitex negundo L. against papain-like protease (PLpro) of SARS CoV-2 (coronavirus) to conquer the pandemic situation in the world
Debasis Mitra, Devvret Verma, Bhaswatimayee Mahakur, Anshul Kamboj, Rakesh Srivastava, Sugam Gupta, Ajita Pandey, Bhawna Arora, Kumud Pant, P. Panneerselvam, Arabinda Ghosh, Durga P. Barik & Pradeep K. Das Mohapatra
Pages: 5665-5686
Published online: 18 Jan 2021
AbstractforMolecular docking and simulation studies of natural compounds of Vitex negundo L. against papain-like protease (PLpro) of SARS CoV-2 (coronavirus) to conquer the pandemic situation in the world | Full Text | References | PDF (4.3 MB) | EPUB
  • 3701 Views
  • 11 CrossRef citations
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Article
Dimeric phosphorylation of glyoxalase I alters its symmetry and substrate binding mechanism: simulation studies
Lisa Michelle Barber, Zakir Hussain, Merlin Thomas & Andrew Hung
Pages: 5687-5701
Published online: 18 Jan 2021
AbstractforDimeric phosphorylation of glyoxalase I alters its symmetry and substrate binding mechanism: simulation studies | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 121 Views
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Review Articles

Review Article
Shell disorder and the HIV vaccine mystery: lessons from the legendary Oswald Avery
Gerard Kian-Meng Goh & Vladimir N. Uversky
Pages: 5702-5711
Published online: 07 Jan 2021
AbstractforShell disorder and the HIV vaccine mystery: lessons from the legendary Oswald Avery | Full Text | References | PDF (1.7 MB) | EPUB
  • 157 Views
  • 3 CrossRef citations
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Review Article
Exploration of structural requirements for the inhibition of VEGFR-2 tyrosine kinase: Binding site analysis of type II, ‘DFG-out’ inhibitors
Siddharth J. Modi & Vithal M. Kulkarni
Pages: 5712-5727
Published online: 18 Jan 2021
AbstractforExploration of structural requirements for the inhibition of VEGFR-2 tyrosine kinase: Binding site analysis of type II, ‘DFG-out’ inhibitors | Full Text | References | PDF (5.1 MB) | EPUB
  • 416 Views
  • 4 CrossRef citations
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