Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 15 (2021)

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Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 15 (2021)

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Research Articles

Article
On interactions of P-glycoprotein with various anti-tumor drugs by binding free energy calculations
Bo Zhang, Junqiao Zhang, Zhengzhong Kang, Lijun Liang, Yingchun Liu & Qi Wang
Pages: 5335-5347
Published online: 01 Jul 2020
AbstractforOn interactions of P-glycoprotein with various anti-tumor drugs by binding free energy calculations | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 249 Views
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Article
Insight into the sequence-structure relationship of TLR cytoplasm’s Toll/Interleukin-1 receptor domain towards understanding the conserved functionality of TLR 2 heterodimer in mammals
Soumya Kanti Ghosh, Bhaskar Saha & Raja Banerjee
Pages: 5348-5357
Published online: 08 Jul 2020
AbstractforInsight into the sequence-structure relationship of TLR cytoplasm’s Toll/Interleukin-1 receptor domain towards understanding the conserved functionality of TLR 2 heterodimer in mammals | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 287 Views
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Article
Design and screening of FAK, CDK 4/6 dual inhibitors by pharmacophore model, molecular docking, and molecular dynamics simulation
Chuance Sun, Lijun Feng, Xiaohua Sun, Rilei Yu & Congmin Kang
Pages: 5358-5367
Published online: 06 Jul 2020
AbstractforDesign and screening of FAK, CDK 4/6 dual inhibitors by pharmacophore model, molecular docking, and molecular dynamics simulation | Full Text | References | PDF (2.6 MB) | EPUB
  • 274 Views
  • 6 CrossRef citations
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Article
Possibility of HIV-1 protease inhibitors-clinical trial drugs as repurposed drugs for SARS-CoV-2 main protease: a molecular docking, molecular dynamics and binding free energy simulation study
Iruthayaraj Ancy, Mugudeeswaran Sivanandam & Poomani Kumaradhas
Pages: 5368-5375
Published online: 06 Jul 2020
AbstractforPossibility of HIV-1 protease inhibitors-clinical trial drugs as repurposed drugs for SARS-CoV-2 main protease: a molecular docking, molecular dynamics and binding free energy simulation study | Full Text | References | PDF (1.8 MB) | EPUB
  • 2202 Views
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Article
Development of triple mutant T790M/C797S allosteric EGFR inhibitors: a computational approach
Kshipra S. Karnik, Aniket P. Sarkate, Deepak K. Lokwani, Ishudeep S. Narula, Prasad V. L. S. Burra & Pravin S. Wakte
Pages: 5376-5398
Published online: 01 Jul 2020
AbstractforDevelopment of triple mutant T790M/C797S allosteric EGFR inhibitors: a computational approach | Full Text | References | PDF (7.7 MB) | EPUB
  • 386 Views
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Article
Computational insight into the selective allosteric inhibition for PTP1B versus TCPTP: a molecular modelling study
Garcia-Marin Javier
Pages: 5399-5410
Published online: 08 Jul 2020
AbstractforComputational insight into the selective allosteric inhibition for PTP1B versus TCPTP: a molecular modelling study | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 387 Views
  • 5 CrossRef citations
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Article
A quantum chemical view of the interaction of RNA nucleobases and base pairs with the side chains of polar amino acids
Ashita Ohri, Preethi P. Seelam & Purshotam Sharma
Pages: 5411-5426
Published online: 14 Jul 2020
AbstractforA quantum chemical view of the interaction of RNA nucleobases and base pairs with the side chains of polar amino acids | Full Text | References | PDF (5.3 MB) | EPUB | Supplemental
  • 148 Views
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Article
The computational quantum mechanical study of sulfamide drug adsorption onto X12Y12 fullerene-like nanocages: detailed DFT and QTAIM investigations
Rahman Padash, Milad Rabbani Esfahani & Ali Shokuhi Rad
Pages: 5427-5437
Published online: 14 Jul 2020
AbstractforThe computational quantum mechanical study of sulfamide drug adsorption onto X12Y12 fullerene-like nanocages: detailed DFT and QTAIM investigations | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 408 Views
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Article
Probing the dynamics between the substrate and the product towards glucose tolerance of Halothermothrix orenii β-glucosidase
Sukanya Konar, Sushant K. Sinha, Supratim Datta & Pradip Kr. Ghorai
Pages: 5438-5448
Published online: 28 Jul 2020
AbstractforProbing the dynamics between the substrate and the product towards glucose tolerance of Halothermothrix orenii β-glucosidase | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 150 Views
  • 2 CrossRef citations
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Article
Benzenesulfonamide derivatives as potent acetylcholinesterase, α-glycosidase, and glutathione S-transferase inhibitors: biological evaluation and molecular docking studies
Parham Taslimi, Mesut Işık, Fikret Türkan, Mustafa Durgun, Cüneyt Türkeş, İlhami Gülçin & Şükrü Beydemir
Pages: 5449-5460
Published online: 21 Jul 2020
AbstractforBenzenesulfonamide derivatives as potent acetylcholinesterase, α-glycosidase, and glutathione S-transferase inhibitors: biological evaluation and molecular docking studies | Full Text | References | PDF (2.6 MB) | EPUB
  • 1315 Views
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Article
In-silico analysis of Calcium Dependent Protein Kinase 6 of Cryptosporidium parvum through molecular modeling, docking, and dynamics simulation study
Ajit Kumar Dhal, Alok Pani, Soon-IL Yun & Rajani Kanta Mahapatra
Pages: 5461-5470
Published online: 07 Jul 2020
AbstractforIn-silico analysis of Calcium Dependent Protein Kinase 6 of Cryptosporidium parvum through molecular modeling, docking, and dynamics simulation study | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 293 Views
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Article
Exploration and evaluation of bioactive phytocompounds against BRCA proteins by in silico approach
H. Prabhavathi, K. R. Dasegowda, K. H. Renukananda, K. Lingaraju & H. Raja Naika
Pages: 5471-5485
Published online: 08 Jul 2020
AbstractforExploration and evaluation of bioactive phytocompounds against BRCA proteins by in silico approach | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 366 Views
  • 9 CrossRef citations
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Article
Oxidative polymerization of hydroxytyrosol catalyzed by laccase, tyrosinase or horseradish peroxidase: influencing factors and molecular simulations
Pujun Xie, Linlin Fan, Lixin Huang & Caihong Zhang
Pages: 5486-5497
Published online: 11 Aug 2020
AbstractforOxidative polymerization of hydroxytyrosol catalyzed by laccase, tyrosinase or horseradish peroxidase: influencing factors and molecular simulations | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 373 Views
  • 2 CrossRef citations
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Article
Complete chemical shift assignment and molecular modeling studies of two chromene derivatives as potential leads for new anticancer drugs
Priscila Ivo Rubim de Santana, Denise Cristian Ferreira Neto, Arlan da Silva Goncalves, Joyce Sobreiro Francisco Diz de Almeida, Tanos Celmar Costa França & José Daniel Figueroa-Villar
Pages: 5498-5508
Published online: 13 Jul 2020
AbstractforComplete chemical shift assignment and molecular modeling studies of two chromene derivatives as potential leads for new anticancer drugs | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 106 Views
  • 1 CrossRef citations
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Article
Structural study of letrozole and metronidazole and formation of self-assembly with graphene and fullerene with the enhancement of physical, chemical and biological activities
Aljawhara H. Almuqrin, Jamelah S. Al-Otaibi, Y. Sheena Mary, Y. Shyma Mary & Renjith Thomas
Pages: 5509-5515
Published online: 13 Jul 2020
AbstractforStructural study of letrozole and metronidazole and formation of self-assembly with graphene and fullerene with the enhancement of physical, chemical and biological activities | Full Text | References | PDF (792.4 KB) | EPUB | Supplemental
  • 338 Views
  • 29 CrossRef citations
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Article
Unravelling the unfolding pathway of human Fas-activated serine/threonine kinase induced by urea
Khalid A. Alamry, Saurabha Srivastava, Mohd Shahbaaz, Parvez Khan, Preeti Gupta, Sunayana Begum Syed, Naved Azum, Abdullah M. Asiri, Asimul Islam, Faizan Ahmad & Md. Imtaiyaz Hassan
Pages: 5516-5525
Published online: 14 Jul 2020
AbstractforUnravelling the unfolding pathway of human Fas-activated serine/threonine kinase induced by urea | Full Text | References | PDF (2.1 MB) | EPUB
  • 242 Views
  • 1 CrossRef citations
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Article
Dynamics and allostery of Zika virus non-structural protein 5 methyltransferase
Marcelo Chagas, Willian Rocha & Adolfo Moraes
Pages: 5526-5538
Published online: 16 Jul 2020
AbstractforDynamics and allostery of Zika virus non-structural protein 5 methyltransferase | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 326 Views
  • 1 CrossRef citations
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Article
Cytotoxic effects, carbonic anhydrase isoenzymes, α-glycosidase and acetylcholinesterase inhibitory properties, and molecular docking studies of heteroatom-containing sulfonyl hydrazone derivatives
Hasan Ufuk Celebioglu, Yavuz Erden, Fatma Hamurcu, Parham Taslimi, Ozan Sanlı Şentürk, Ümmühan Özdemir Özmen, Burak Tuzun & İlhami Gulçin
Pages: 5539-5550
Published online: 21 Jul 2020
AbstractforCytotoxic effects, carbonic anhydrase isoenzymes, α-glycosidase and acetylcholinesterase inhibitory properties, and molecular docking studies of heteroatom-containing sulfonyl hydrazone derivatives | Full Text | References | PDF (3.2 MB) | EPUB
  • 1023 Views
  • 21 CrossRef citations
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Article
Identification of some novel oxazine substituted 9-anilinoacridines as SARS-CoV-2 inhibitors for COVID-19 by molecular docking, free energy calculation and molecular dynamics studies
Kalirajan Rajagopal, Potlapati Varakumar, Baliwada Aparna, Gowramma Byran & Srikanth Jupudi
Pages: 5551-5562
Published online: 28 Jul 2020
AbstractforIdentification of some novel oxazine substituted 9-anilinoacridines as SARS-CoV-2 inhibitors for COVID-19 by molecular docking, free energy calculation and molecular dynamics studies | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 2561 Views
  • 14 CrossRef citations
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Article
Chemical evolution: from formamide to nucleobases and amino acids without the presence of catalyst
Venelin Enchev, Ivan Angelov, Ivayla Dincheva, Nina Stoyanova, Sofia Slavova, Miroslav Rangelov & Nadezhda Markova
Pages: 5563-5578
Published online: 17 Jul 2020
AbstractforChemical evolution: from formamide to nucleobases and amino acids without the presence of catalyst | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 463 Views
  • 9 CrossRef citations
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Article
Computational improvement of small-molecule inhibitors of Bacillus anthracis protective antigen activation through isostere-based substitutions
Sandra V. R. L. Silva & Pedro J. Silva
Pages: 5579-5587
Published online: 14 Jul 2020
AbstractforComputational improvement of small-molecule inhibitors of Bacillus anthracis protective antigen activation through isostere-based substitutions | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 147 Views
  • 1 CrossRef citations
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Article
Extrapolation of hydroxytyrosol and its analogues as potential anti-inflammatory agents
Naresh Kumar, Biswajit Gorai, Saurabh Gupta, Shiva & Nidhi Goel
Pages: 5588-5599
Published online: 16 Jul 2020
AbstractforExtrapolation of hydroxytyrosol and its analogues as potential anti-inflammatory agents | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 230 Views
  • 8 CrossRef citations
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Article
Molecular docking, photocatalytic activity and biomedical investigations of some metal complexes
Liji John, R. Selwin Joseyphus & I. Hubert Joe
Pages: 5600-5612
Published online: 20 Jul 2020
AbstractforMolecular docking, photocatalytic activity and biomedical investigations of some metal complexes | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 159 Views
  • 2 CrossRef citations
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Article
Understanding dual delivery of doxorubicin and paclitaxel with boron nitride and phosphorene nanosheets as highly efficient drug delivery systems
Hassan Hashemzadeh & Heidar Raissi
Pages: 5613-5618
Published online: 16 Jul 2020
AbstractforUnderstanding dual delivery of doxorubicin and paclitaxel with boron nitride and phosphorene nanosheets as highly efficient drug delivery systems | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 362 Views
  • 5 CrossRef citations
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Review Article

Review Article
Characteristics, dynamics and mechanisms of actions of some major stress-induced biomacromolecules; addressing Artemia as an excellent biological model
Hamidreza Khodajou-Masouleh, S. Shirin Shahangian, Farnoosh Attar, Reza H. Sajedi & Behnam Rasti
Pages: 5619-5637
Published online: 31 Jul 2020
AbstractforCharacteristics, dynamics and mechanisms of actions of some major stress-induced biomacromolecules; addressing Artemia as an excellent biological model | Full Text | References | PDF (1.9 MB) | EPUB
  • 209 Views
  • 1 CrossRef citations
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Research Articles

Article
Computer-aided screening for potential TMPRSS2 inhibitors: a combination of pharmacophore modeling, molecular docking and molecular dynamics simulation approaches
Mukhtar Oluwaseun Idris, Abeeb Abiodun Yekeen, Oluwaseun Suleiman Alakanse & Olanrewaju Ayodeji Durojaye
Pages: 5638-5656
Published online: 16 Jul 2020
AbstractforComputer-aided screening for potential TMPRSS2 inhibitors: a combination of pharmacophore modeling, molecular docking and molecular dynamics simulation approaches | Full Text | References | PDF (5.1 MB) | EPUB
  • 3984 Views
  • 32 CrossRef citations
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Article
Identification of potential drugs against SARS-CoV-2 non-structural protein 1 (nsp1)
Gabriela de Lima Menezes & Roosevelt Alves da Silva
Pages: 5657-5667
Published online: 13 Jul 2020
AbstractforIdentification of potential drugs against SARS-CoV-2 non-structural protein 1 (nsp1) | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 4225 Views
  • 17 CrossRef citations
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Article
Identification of bioactive molecule from Withania somnifera (Ashwagandha) as SARS-CoV-2 main protease inhibitor
Manish Kumar Tripathi, Pushpendra Singh, Sujata Sharma, Tej P. Singh, A. S. Ethayathulla & Punit Kaur
Pages: 5668-5681
Published online: 08 Jul 2020
AbstractforIdentification of bioactive molecule from Withania somnifera (Ashwagandha) as SARS-CoV-2 main protease inhibitor | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 7445 Views
  • 74 CrossRef citations
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Article
Classification of the COVID-19 infected patients using DenseNet201 based deep transfer learning
Aayush Jaiswal, Neha Gianchandani, Dilbag Singh, Vijay Kumar & Manjit Kaur
Pages: 5682-5689
Published online: 03 Jul 2020
AbstractforClassification of the COVID-19 infected patients using DenseNet201 based deep transfer learning | Full Text | References | PDF (1.6 MB) | EPUB
  • 13276 Views
  • 293 CrossRef citations
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Article
Epitope based peptide vaccine against SARS-COV2: an immune-informatics approach
Richa Bhatnager, Maheshwar Bhasin, Jyoti Arora & Amita S. Dang
Pages: 5690-5705
Published online: 03 Jul 2020
AbstractforEpitope based peptide vaccine against SARS-COV2: an immune-informatics approach | Full Text | References | PDF (2.7 MB) | EPUB
  • 4333 Views
  • 29 CrossRef citations
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Article
Bacterial protein azurin and derived peptides as potential anti-SARS-CoV-2 agents: insights from molecular docking and molecular dynamics simulations
Santanu Sasidharan, Chandrabose Selvaraj, Sanjeev Kumar Singh, Vikash Kumar Dubey, Sachin Kumar, Arsenio M. Fialho & Prakash Saudagar
Pages: 5706-5721
Published online: 03 Jul 2020
AbstractforBacterial protein azurin and derived peptides as potential anti-SARS-CoV-2 agents: insights from molecular docking and molecular dynamics simulations | Full Text | References | PDF (5 MB) | EPUB
  • 2781 Views
  • 12 CrossRef citations
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Article
Natural-like products as potential SARS-CoV-2 Mpro inhibitors: in-silico drug discovery
Mahmoud A. A. Ibrahim, Khlood A. A. Abdeljawaad, Alaa H. M. Abdelrahman & Mohamed-Elamir F. Hegazy
Pages: 5722-5734
Published online: 08 Jul 2020
AbstractforNatural-like products as potential SARS-CoV-2 Mpro inhibitors: in-silico drug discovery | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 6846 Views
  • 50 CrossRef citations
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Article
Drug repurposing studies targeting SARS-CoV-2: an ensemble docking approach on drug target 3C-like protease (3CLpro)
Shruti Koulgi, Vinod Jani, Mallikarjunachari Uppuladinne, Uddhavesh Sonavane, Asheet Kumar Nath, Hemant Darbari & Rajendra Joshi
Pages: 5735-5755
Published online: 17 Jul 2020
AbstractforDrug repurposing studies targeting SARS-CoV-2: an ensemble docking approach on drug target 3C-like protease (3CLpro) | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 2940 Views
  • 27 CrossRef citations
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Article
In-silico drug repurposing and molecular dynamics puzzled out potential SARS-CoV-2 main protease inhibitors
Mahmoud A. A. Ibrahim, Alaa H. M. Abdelrahman & Mohamed-Elamir F. Hegazy
Pages: 5756-5767
Published online: 20 Jul 2020
AbstractforIn-silico drug repurposing and molecular dynamics puzzled out potential SARS-CoV-2 main protease inhibitors | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 5458 Views
  • 31 CrossRef citations
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Article
Targeting virus–host interaction by novel pyrimidine derivative: an in silico approach towards discovery of potential drug against COVID-19
Jitendra Subhash Rane, Preeti Pandey, Aroni Chatterjee, Rajni Khan, Abhijeet Kumar, Amresh Prakash & Shashikant Ray
Pages: 5768-5778
Published online: 20 Jul 2020
AbstractforTargeting virus–host interaction by novel pyrimidine derivative: an in silico approach towards discovery of potential drug against COVID-19 | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 2371 Views
  • 19 CrossRef citations
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Article
Computational discovery of small drug-like compounds as potential inhibitors of SARS-CoV-2 main protease
Alexander M. Andrianov, Yuri V. Kornoushenko, Anna D. Karpenko, Ivan P. Bosko & Alexander V. Tuzikov
Pages: 5779-5791
Published online: 14 Jul 2020
AbstractforComputational discovery of small drug-like compounds as potential inhibitors of SARS-CoV-2 main protease | Full Text | References | PDF (3.1 MB) | EPUB
  • 6743 Views
  • 16 CrossRef citations
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Article
Approach to the mechanism of action of hydroxychloroquine on SARS-CoV-2: a molecular docking study
Ismail Celı̇k, Arzu Onay-Besı̇kcı̇ & Gulgun Ayhan-Kilcigı̇l
Pages: 5792-5798
Published online: 17 Jul 2020
AbstractforApproach to the mechanism of action of hydroxychloroquine on SARS-CoV-2: a molecular docking study | Full Text | References | PDF (1.4 MB) | EPUB
  • 2837 Views
  • 16 CrossRef citations
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Express Communications

Article
Screening of phytochemical compounds of Tinospora cordifolia for their inhibitory activity on SARS-CoV-2: an in silico study
S. Krupanidhi, K. Abraham Peele, T. C. Venkateswarulu, Vijaya Sai Ayyagari, Md. Nazneen Bobby, D. John Babu, A. Venkata Narayana & G. Aishwarya
Pages: 5799-5803
Published online: 06 Jul 2020
AbstractforScreening of phytochemical compounds of Tinospora cordifolia for their inhibitory activity on SARS-CoV-2: an in silico study | Full Text | References | PDF (1.2 MB) | EPUB
  • 4976 Views
  • 52 CrossRef citations
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Article
Potential of NO donor furoxan as SARS-CoV-2 main protease (Mpro) inhibitors: in silico analysis
Abdullah G. Al-Sehemi, Mehboobali Pannipara, Rishikesh S. Parulekar, Omkar Patil, Prafulla B. Choudhari, M. S. Bhatia, P. K. Zubaidha & Yasinalli Tamboli
Pages: 5804-5818
Published online: 08 Jul 2020
AbstractforPotential of NO donor furoxan as SARS-CoV-2 main protease (Mpro) inhibitors: in silico analysis | Full Text | References | PDF (4.1 MB) | EPUB
  • 3811 Views
  • 19 CrossRef citations
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Article
Natural derivatives with dual binding potential against SARS-CoV-2 main protease and human ACE2 possess low oral bioavailability: a brief computational analysis
Priyanka Sharma & Asifkhan Shanavas
Pages: 5819-5830
Published online: 21 Jul 2020
AbstractforNatural derivatives with dual binding potential against SARS-CoV-2 main protease and human ACE2 possess low oral bioavailability: a brief computational analysis | Full Text | References | PDF (3.3 MB) | EPUB
  • 2691 Views
  • 14 CrossRef citations
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Hypothesis Paper

Article
On the potential role of exosomes in the COVID-19 reinfection/reactivation opportunity
Fatma Elrashdy, Abdullah A. Aljaddawi, Elrashdy M. Redwan & Vladimir N. Uversky
Pages: 5831-5842
Published online: 09 Jul 2020
AbstractforOn the potential role of exosomes in the COVID-19 reinfection/reactivation opportunity | Full Text | References | PDF (1.8 MB) | EPUB
  • 12479 Views
  • 46 CrossRef citations
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