Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 2 (2022)

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Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 2 (2022)

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Research Articles

Article
Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease
Shivanika C, Deepak Kumar S.Venkataraghavan Ragunathan, Pawan Tiwari, Sumitha A.Brindha Devi P
Pages: 585-611
Published online: 08 Sep 2020
AbstractforMolecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease | Full Text | References | PDF (5.4 MB) | EPUB | Supplemental
  • 14460 Views
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Article
Molecular modeling and dynamic simulation of chicken Mx protein with the S631N polymorphism
Vijayakumar Gosu, Donghyun Shin, Ki-Duk Song, Jaeyoung Heo & Jae-Don Oh
Pages: 612-621
Published online: 22 Sep 2020
AbstractforMolecular modeling and dynamic simulation of chicken Mx protein with the S631N polymorphism | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 241 Views
  • 3 CrossRef citations
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Article
Theoretical evaluation of EGFR kinase inhibition and toxicity of di-indol-3-yl disulphides with anti-cancer potency
Teresa Żołek, Aleksandra Trzeciak & Dorota Maciejewska
Pages: 622-634
Published online: 03 Sep 2020
AbstractforTheoretical evaluation of EGFR kinase inhibition and toxicity of di-indol-3-yl disulphides with anti-cancer potency | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 137 Views
  • 3 CrossRef citations
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Article
Point mutations in the different domains of the Saccharomyces cerevisiae plasma membrane PMA1 ATPase cause redistribution among fractions of inorganic polyphosphates
Alexandr A. Tomashevsky & Valery V. Petrov
Pages: 635-647
Published online: 02 Sep 2020
AbstractforPoint mutations in the different domains of the Saccharomyces cerevisiae plasma membrane PMA1 ATPase cause redistribution among fractions of inorganic polyphosphates | Full Text | References | PDF (1.6 MB) | EPUB
  • 150 Views
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Article
Design of a multi-epitope peptide vaccine candidate against chandipura virus: an immuno-informatics study
Daya V. Pavitrakar, Nitin M. Atre, Anuradha S. Tripathy & Pratip Shil
Pages: 648-659
Published online: 08 Sep 2020
AbstractforDesign of a multi-epitope peptide vaccine candidate against chandipura virus: an immuno-informatics study | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 193 Views
  • 6 CrossRef citations
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Article
Structural and spectral analysis of anticancer active cyclo(Ala–His) dipeptide
Sefa Celik, Gozde Yilmaz, Aysen E. Ozel & Sevim Akyuz
Pages: 660-672
Published online: 10 Sep 2020
AbstractforStructural and spectral analysis of anticancer active cyclo(Ala–His) dipeptide | Full Text | References | PDF (1.9 MB) | EPUB
  • 314 Views
  • 9 CrossRef citations
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Article
Screening natural inhibitors against upregulated G-protein coupled receptors as potential therapeutics of Alzheimer’s disease
Amit Chaudhary, Vishal Singh, Pritish Kumar Varadwaj & Ashutosh Mani
Pages: 673-684
Published online: 09 Sep 2020
AbstractforScreening natural inhibitors against upregulated G-protein coupled receptors as potential therapeutics of Alzheimer’s disease | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 328 Views
  • 2 CrossRef citations
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Article
Virtual screening of approved clinic drugs with main protease (3CLpro) reveals potential inhibitory effects on SARS-CoV-2
Qiang Wang, Ying Zhao, Xiaojia Chen & An Hong
Pages: 685-695
Published online: 10 Sep 2020
AbstractforVirtual screening of approved clinic drugs with main protease (3CLpro) reveals potential inhibitory effects on SARS-CoV-2 | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 2220 Views
  • 17 CrossRef citations
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Article
Screening of plant-based natural compounds as a potential COVID-19 main protease inhibitor: an in silico docking and molecular dynamics simulation approach
Ranabir Majumder & Mahitosh Mandal
Pages: 696-711
Published online: 08 Sep 2020
AbstractforScreening of plant-based natural compounds as a potential COVID-19 main protease inhibitor: an in silico docking and molecular dynamics simulation approach | Full Text | References | PDF (4.3 MB) | EPUB | Supplemental
  • 6122 Views
  • 42 CrossRef citations
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Article
Synthesis of exfoliated multilayer graphene and its putative interactions with SARS-CoV-2 virus investigated through computational studies
Bhargav Raval, Amit Kumar Srivastav, Sanjeev K. Gupta, Umesh Kumar, S. K. Mahapatra, P. N. Gajjar & I. Banerjee
Pages: 712-721
Published online: 11 Sep 2020
AbstractforSynthesis of exfoliated multilayer graphene and its putative interactions with SARS-CoV-2 virus investigated through computational studies | Full Text | References | PDF (3.6 MB) | EPUB
  • 1809 Views
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Article
Investigation of binding interaction between human serum albumin with zirconium complex of curcumin and curcumin
Hamid Dezhampanah & Zahra Shabanzade
Pages: 722-732
Published online: 15 Sep 2020
AbstractforInvestigation of binding interaction between human serum albumin with zirconium complex of curcumin and curcumin | Full Text | References | PDF (2.3 MB) | EPUB
  • 171 Views
  • 7 CrossRef citations
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Article
Phthalocyanine complexes with (4-isopropylbenzyl)oxy substituents: preparation and evaluation of anti-carbonic anhydrase, anticholinesterase enzymes and molecular docking studies
Emre Güzel, Ümit M. Koçyiğit, Parham Taslimi, İlhami Gülçin, Sultan Erkan, Mehmet Nebioğlu, Barış S. Arslan & İlkay Şişman
Pages: 733-741
Published online: 21 Sep 2020
AbstractforPhthalocyanine complexes with (4-isopropylbenzyl)oxy substituents: preparation and evaluation of anti-carbonic anhydrase, anticholinesterase enzymes and molecular docking studies | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 943 Views
  • 15 CrossRef citations
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Article
Mechanistic insight of DACH1 receptor in the development of carcinoma insurgence through MD simulation studies
Mubashir Hassan, Sara Zahid, Saba Shahzadi, Erum Malik, Sumera Zaib, Jamshed Iqbal, Saba Shamim & Arif Malik
Pages: 742-751
Published online: 14 Sep 2020
AbstractforMechanistic insight of DACH1 receptor in the development of carcinoma insurgence through MD simulation studies | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 196 Views
  • 3 CrossRef citations
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Article
Exploring structural dynamics of the MERS-CoV receptor DPP4 and mutant DPP4 receptors
Ahmed L. Alaofi
Pages: 752-763
Published online: 10 Sep 2020
AbstractforExploring structural dynamics of the MERS-CoV receptor DPP4 and mutant DPP4 receptors | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 669 Views
  • 5 CrossRef citations
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Article
Insights into zinc-sensing metalloregulator ‘Zur’ deciphering mechanism of zinc transportation in Bacillus spp. by modeling, simulation and molecular docking
Kalpana Bhatt & Dinesh Kumar Maheshwari
Pages: 764-779
Published online: 14 Sep 2020
AbstractforInsights into zinc-sensing metalloregulator ‘Zur’ deciphering mechanism of zinc transportation in Bacillus spp. by modeling, simulation and molecular docking | Full Text | References | PDF (4.9 MB) | EPUB | Supplemental
  • 259 Views
  • 5 CrossRef citations
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Article
SARS-CoV Mpro inhibitory activity of aromatic disulfide compounds: QSAR model
Andrey A. Toropov, Alla P. Toropova, Aleksandar M. Veselinović, Danuta Leszczynska & Jerzy Leszczynski
Pages: 780-786
Published online: 09 Sep 2020
AbstractforSARS-CoV Mpro inhibitory activity of aromatic disulfide compounds: QSAR model | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 2106 Views
  • 15 CrossRef citations
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Article
N-{2-[(2-chlorothieno[3,2-d]pyrimidin-4-yl)amino]ethyl}-3-methoxybenzamide: design, synthesis, crystal structure, antiproliferative activity, DFT, Hirshfeld surface analysis and molecular docking study
Pei Huang, Juan Zhao, Yan-Hong Gao, Ling-Xia Jin, Qin Wang, Xiao-Hu Yu, Xiao-Hui Ji & Jiu-Fu Lu
Pages: 787-795
Published online: 11 Sep 2020
AbstractforN-{2-[(2-chlorothieno[3,2-d]pyrimidin-4-yl)amino]ethyl}-3-methoxybenzamide: design, synthesis, crystal structure, antiproliferative activity, DFT, Hirshfeld surface analysis and molecular docking study | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 193 Views
  • 3 CrossRef citations
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Article
Using Chou’s 5-steps rule to identify N6-methyladenine sites by ensemble learning combined with multiple feature extraction methods
Zhongwang Zhang & Lidong Wang
Pages: 796-806
Published online: 18 Sep 2020
AbstractforUsing Chou’s 5-steps rule to identify N6-methyladenine sites by ensemble learning combined with multiple feature extraction methods | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 141 Views
  • 3 CrossRef citations
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Article
Smac peptide and doxorubicin-encapsulated nanoparticles: design, preparation, computational molecular approach and in vitro studies on cancer cells
Mojgan Nejabat, Fatemeh Soltani, Mona Alibolandi, Masoud Nejabat, Khalil Abnous, Farzin Hadizadeh & Mohammad Ramezani
Pages: 807-819
Published online: 10 Sep 2020
AbstractforSmac peptide and doxorubicin-encapsulated nanoparticles: design, preparation, computational molecular approach and in vitro studies on cancer cells | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 286 Views
  • 3 CrossRef citations
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Article
An able-cryoprotectant and a moderate denaturant: distinctive character of ethylene glycol on protein stability
K. Tejaswi Naidu & N. Prakash Prabhu
Pages: 820-832
Published online: 21 Sep 2020
AbstractforAn able-cryoprotectant and a moderate denaturant: distinctive character of ethylene glycol on protein stability | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 184 Views
  • 1 CrossRef citations
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Article
Proteome-wide mapping and reverse vaccinology-based B and T cell multi-epitope subunit vaccine designing for immune response reinforcement against Porphyromonas gingivalis
Shahzeb Khan, Syed Shujait Ali, Iqra Zaheer, Shoaib Saleem, Ziaullah, Nasib Zaman, Arshad Iqbal, Muhammad Suleman, Abdul Wadood, Ashfaq Ur Rehman, Asghar Khan, Abbas Khan & Dong-Qing Wei
Pages: 833-847
Published online: 14 Sep 2020
AbstractforProteome-wide mapping and reverse vaccinology-based B and T cell multi-epitope subunit vaccine designing for immune response reinforcement against Porphyromonas gingivalis | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 581 Views
  • 9 CrossRef citations
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Article
Deciphering the interaction of puerarin with cancer macromolecules: An in silico investigation
Oluwafemi Adeleke Ojo, Raphael Taiwo Aruleba, Tayo Alex Adekiya, Nicole Remaliah Samantha Sibuyi, Adebola Busola Ojo, Basiru Olaitan Ajiboye, Babatunji Emmanuel Oyinloye, Henry Ademola Adeola & Adewale Oluwaseun Fadaka
Pages: 848-859
Published online: 14 Sep 2020
AbstractforDeciphering the interaction of puerarin with cancer macromolecules: An in silico investigation | Full Text | References | PDF (3.8 MB) | EPUB
  • 374 Views
  • 13 CrossRef citations
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Article
In silico investigation of spice molecules as potent inhibitor of SARS-CoV-2
Janmejaya Rout, Bikash Chandra Swain & Umakanta Tripathy
Pages: 860-874
Published online: 17 Sep 2020
AbstractforIn silico investigation of spice molecules as potent inhibitor of SARS-CoV-2 | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 5090 Views
  • 25 CrossRef citations
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Article
Computational insight of dexamethasone against potential targets of SARS-CoV-2
Adewale Oluwaseun Fadaka, Nicole Remaliah Samantha Sibuyi, Abram Madimabe Madiehe & Mervin Meyer
Pages: 875-885
Published online: 14 Sep 2020
AbstractforComputational insight of dexamethasone against potential targets of SARS-CoV-2 | Full Text | References | PDF (2.4 MB) | EPUB
  • 2421 Views
  • 18 CrossRef citations
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Article
In silico drug discovery of IKK-β inhibitors from 2-amino-3-cyano-4-alkyl-6-(2-hydroxyphenyl) pyridine derivatives based on QSAR, docking, molecular dynamics and drug-likeness evaluation studies
Nour-El-Houda Hammoudi, Yacine Benguerba, Ayoub Attoui, Cecilia Hognon, Tarek Lemaoui, Widad Sobhi, Mohamed Benaicha, Michael Badawi & Antonio Monari
Pages: 886-902
Published online: 18 Sep 2020
AbstractforIn silico drug discovery of IKK-β inhibitors from 2-amino-3-cyano-4-alkyl-6-(2-hydroxyphenyl) pyridine derivatives based on QSAR, docking, molecular dynamics and drug-likeness evaluation studies | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 475 Views
  • 7 CrossRef citations
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Article
Potential protease inhibitors and their combinations to block SARS-CoV-2
Chandran S. Abhinand, Achuthsankar S. Nair, Anand Krishnamurthy, Oommen V. Oommen & Perumana R. Sudhakaran
Pages: 903-917
Published online: 14 Sep 2020
AbstractforPotential protease inhibitors and their combinations to block SARS-CoV-2 | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 2659 Views
  • 10 CrossRef citations
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Article
Targeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach
Ozal Mutlu, Osman Mutluhan Ugurel, Emrah Sariyer, Oguz Ata, Tugba Gul Inci, Erennur Ugurel, Sinem Kocer & Dilek Turgut-Balik
Pages: 918-930
Published online: 16 Sep 2020
AbstractforTargeting SARS-CoV-2 Nsp12/Nsp8 interaction interface with approved and investigational drugs: an in silico structure-based approach | Full Text | References | PDF (4.4 MB) | EPUB
  • 4868 Views
  • 15 CrossRef citations
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Article
Synthesis of novel pancreatic lipase inhibitors: Biological investigation and in silico studies
Arif Mermer, Serpil Demirci & Gizem Tatar
Pages: 931-940
Published online: 11 Jul 2021
AbstractforSynthesis of novel pancreatic lipase inhibitors: Biological investigation and in silico studies | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 431 Views
  • 2 CrossRef citations
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Article
Identification of potential inhibitors of SARS-CoV-2 main protease and spike receptor from 10 important spices through structure-based virtual screening and molecular dynamic study
Debanjan Sen, Pradip Debnath, Bimal Debnath, Samhita Bhaumik & Sudhan Debnath
Pages: 941-962
Published online: 18 Sep 2020
AbstractforIdentification of potential inhibitors of SARS-CoV-2 main protease and spike receptor from 10 important spices through structure-based virtual screening and molecular dynamic study | Full Text | References | PDF (5.8 MB) | EPUB | Supplemental
  • 4363 Views
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