Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 18 (2021)

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Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 18 (2021)

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Research Articles

Article
Surface modified PAMAM dendrimers with gallic acid inhibit, cell proliferation, cell migration and inflammatory response to augment apoptotic cell death in human colon carcinoma cells
Khushbu Priyadarshi, Kavita Shirsath, N. Bhargav Waghela, Anupama Sharma, Ajay Kumar & Chandramani Pathak
Pages: 6853-6869
Published online: 05 Aug 2020
AbstractforSurface modified PAMAM dendrimers with gallic acid inhibit, cell proliferation, cell migration and inflammatory response to augment apoptotic cell death in human colon carcinoma cells | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
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Article
Binding of dipeptidyl peptidase III to the oxidative stress cell sensor Kelch-like ECH-associated protein 1 is a two-step process
Sara Matić, Ivana Kekez, Marko Tomin, Ferenc Bogár, Filip Šupljika, Saša Kazazić, Maja Hanić, Shalinee Jha, Hrvoje Brkić, Benjamin Bourgeois, Tobias Madl, Karl Gruber, Peter Macheroux, Dubravka Matković-Čalogović, Mihaela Matovina & Sanja Tomić
Pages: 6870-6881
Published online: 18 Aug 2020
AbstractforBinding of dipeptidyl peptidase III to the oxidative stress cell sensor Kelch-like ECH-associated protein 1 is a two-step process | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 359 Views
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Article
Blueprint of epitope-based multivalent and multipathogenic vaccines: targeted against the dengue and zika viruses
Bishajit Sarkar, Md. Asad Ullah, Yusha Araf, Sowmen Das & Mohammad Jakir Hosen
Pages: 6882-6902
Published online: 08 Aug 2020
AbstractforBlueprint of epitope-based multivalent and multipathogenic vaccines: targeted against the dengue and zika viruses | Full Text | References | PDF (5.1 MB) | EPUB | Supplemental
  • 291 Views
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Article
In silico designing of multi-epitope vaccine construct against human coronavirus infections
Arpita Devi & Nyshadham S. N. Chaitanya
Pages: 6903-6917
Published online: 10 Aug 2020
AbstractforIn silico designing of multi-epitope vaccine construct against human coronavirus infections | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 2775 Views
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Article
Studies on the antiglycating potential of zinc oxide nanoparticle and its interaction with BSA
Dinesh Kumar, Shruti G. Bhatkalkar, Shilpee Sachar & Ahmad Ali
Pages: 6918-6925
Published online: 07 Aug 2020
AbstractforStudies on the antiglycating potential of zinc oxide nanoparticle and its interaction with BSA | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 238 Views
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Article
An efficient synthesis of novel di-heterocyclic benzazole derivatives and evaluation of their antiproliferative activities
Oztekin Algul, Ronak Haj Ersan, Mehmet Abdullah Alagoz, Nizami Duran & Serdar Burmaoglu
Pages: 6926-6938
Published online: 08 Aug 2020
AbstractforAn efficient synthesis of novel di-heterocyclic benzazole derivatives and evaluation of their antiproliferative activities | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 956 Views
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Article
Investigation of biological activity of nickel (II) complex with naproxen and 1,10-phenanthroline ligands
Zeinab Mirzaei-Kalar, Ali Akbar Khandar, Jonathan M. White, Hoda Abolhasani, Tahereh Komeili Movahhed, Stephen P. Best & Abolghasem Jouyban
Pages: 6939-6954
Published online: 08 Aug 2020
AbstractforInvestigation of biological activity of nickel (II) complex with naproxen and 1,10-phenanthroline ligands | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 219 Views
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Article
Development of lipoprotein-drug conjugates for targeted drug delivery
Manish S. Bhatia, Sujata P. Choudhari, Rakesh P. Dhavale & Vinod L. Gaikwad
Pages: 6955-6973
Published online: 13 Aug 2020
AbstractforDevelopment of lipoprotein-drug conjugates for targeted drug delivery | Full Text | References | PDF (3.8 MB) | EPUB
  • 153 Views
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Article
A comparative pan-genomic analysis of 53 C. pseudotuberculosis strains based on functional domains
Juliana S. Bernardes, Raphael J. Eberle, Fabio R. J. Vieira & Mônika A. Coronado
Pages: 6974-6986
Published online: 11 Aug 2020
AbstractforA comparative pan-genomic analysis of 53 C. pseudotuberculosis strains based on functional domains | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 724 Views
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Open Access
Article
Insights of structure-based pharmacophore studies and inhibitor design against Gal3 receptor through molecular dynamics simulations
Gunalan Seshan, Somarathinam Kanagasabai, Sailapathi Ananthasri, Balaji Kannappan, A. Suvitha, S. M. Jaimohan, Sekar Kanagaraj & Gugan Kothandan
Pages: 6987-6999
Published online: 08 Aug 2020
AbstractforInsights of structure-based pharmacophore studies and inhibitor design against Gal3 receptor through molecular dynamics simulations | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 268 Views
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Article
Identification of potential Leishmania chagasi superoxide dismutase allosteric modulators by structure-based computational approaches: homology modelling, molecular dynamics and pharmacophore-based virtual screening
Bruno Cruz de Souza, Pedro Sousa Lacerda, Samuel Silva da Rocha Pita, Rodrigo Bentes Kato & Franco Henrique Andrade Leite
Pages: 7000-7016
Published online: 14 Aug 2020
AbstractforIdentification of potential Leishmania chagasi superoxide dismutase allosteric modulators by structure-based computational approaches: homology modelling, molecular dynamics and pharmacophore-based virtual screening | Full Text | References | PDF (4.4 MB) | EPUB
  • 281 Views
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Research Article

Article
In silico screening of hundred phytocompounds of ten medicinal plants as potential inhibitors of nucleocapsid phosphoprotein of COVID-19: an approach to prevent virus assembly
Rajan Rolta, Rohitash Yadav, Deeksha Salaria, Shubham Trivedi, Mohammad Imran, Anuradha Sourirajan, David J. Baumler & Kamal Dev
Pages: 7017-7034
Published online: 27 Aug 2020
AbstractforIn silico screening of hundred phytocompounds of ten medicinal plants as potential inhibitors of nucleocapsid phosphoprotein of COVID-19: an approach to prevent virus assembly | Full Text | References | PDF (4.3 MB) | EPUB | Supplemental
  • 4562 Views
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Research Articles

Article
Synthesis, computational studies and enzyme inhibitory kinetics of benzothiazole-linked thioureas as mushroom tyrosinase inhibitors
Rabail Ujan, Aamer Saeed, Saba Ashraf, Pervaiz Ali Channar, Qamar Abbas, Mahboob Ali Rind, Mubashir Hassan, Hussain Raza, Sung-Yum Seo & Hesham R. El-Seedi
Pages: 7035-7043
Published online: 07 Aug 2020
AbstractforSynthesis, computational studies and enzyme inhibitory kinetics of benzothiazole-linked thioureas as mushroom tyrosinase inhibitors | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 431 Views
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Article
Prediction and evaluation of deleterious and disease causing non-synonymous SNPs (nsSNPs) in human NF2 gene responsible for neurofibromatosis type 2 (NF2)
Brandon Havranek & Shahidul M. Islam
Pages: 7044-7055
Published online: 13 Aug 2020
AbstractforPrediction and evaluation of deleterious and disease causing non-synonymous SNPs (nsSNPs) in human NF2 gene responsible for neurofibromatosis type 2 (NF2) | Full Text | References | PDF (2.3 MB) | EPUB
  • 243 Views
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Article
Computational studies on bacterial secondary metabolites against breast cancer
Zina Ravnik, Indiraleka Muthiah & Premnath Dhanaraj
Pages: 7056-7064
Published online: 11 Aug 2020
AbstractforComputational studies on bacterial secondary metabolites against breast cancer | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 410 Views
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Article
Screening of potential drug for Alzheimer’s disease: a computational study with GSK-3 β inhibition through virtual screening, docking, and molecular dynamics simulation
Nandha Devi Elangovan, Anantha Krishnan Dhanabalan, Krishnasamy Gunasekaran, Ramesh Kandimalla & Devaraj Sankarganesh
Pages: 7065-7079
Published online: 11 Aug 2020
AbstractforScreening of potential drug for Alzheimer’s disease: a computational study with GSK-3 β inhibition through virtual screening, docking, and molecular dynamics simulation | Full Text | References | PDF (4.9 MB) | EPUB
  • 1020 Views
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Article
Investigation into archaeal extremophilic lifestyles through comparative proteogenomic analysis
Liang Wang, Mengmeng Wang, Xinyi Shi, Jianye Yang, Chenlu Qian, Qinghua Liu, Lixin Zong, Xin Liu, Zuobin Zhu, Daoquan Tang & Xiao Zhang
Pages: 7080-7092
Published online: 21 Aug 2020
AbstractforInvestigation into archaeal extremophilic lifestyles through comparative proteogenomic analysis | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 206 Views
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Article
Synthesis and spectroscopic characterization of new sulfanilamide-functionalized magnetic nanoparticles, and the usability for carbonic anhydrase purification: is there perspective for ‘cancer treatment’ application?
Nooshin Bijari, Monireh Falsafi, Khadijeh Pouraghajan & Reza Khodarahmi
Pages: 7093-7106
Published online: 21 Aug 2020
AbstractforSynthesis and spectroscopic characterization of new sulfanilamide-functionalized magnetic nanoparticles, and the usability for carbonic anhydrase purification: is there perspective for ‘cancer treatment’ application? | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 194 Views
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Article
Exploring 3-hydroxyflavone scaffolds as mushroom tyrosinase inhibitors: synthesis, X-ray crystallography, antimicrobial, fluorescence behaviour, structure-activity relationship and molecular modelling studies
Jamshaid Ashraf, Ehsan Ullah Mughal, Amina Sadiq, Maryam Bibi, Nafeesa Naeem, Anser Ali, Anam Massadaq, Nighat Fatima, Asif Javid, Muhammad Naveed Zafar, Bilal Ahmad Khan, Muhammad Faizan Nazar, Amara Mumtaz, Muhammad Nawaz Tahir & Masoud Mirzaei
Pages: 7107-7122
Published online: 17 Aug 2020
AbstractforExploring 3-hydroxyflavone scaffolds as mushroom tyrosinase inhibitors: synthesis, X-ray crystallography, antimicrobial, fluorescence behaviour, structure-activity relationship and molecular modelling studies | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 678 Views
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Article
In-silico virtual screening for identification of potent inhibitor for L2-β-lactamase from Stenotrophomonas maltophilia through molecular docking, molecular dynamics analysis study
Ridhi Sharma, Dhananjay Jade, Surender Mohan, Rahul Chandel & Shobana Sugumar
Pages: 7123-7137
Published online: 21 Aug 2020
AbstractforIn-silico virtual screening for identification of potent inhibitor for L2-β-lactamase from Stenotrophomonas maltophilia through molecular docking, molecular dynamics analysis study | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 360 Views
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Article
Three new acrylic acid derivatives from Achillea mellifolium as potential thymidine phosphorylase inhibitor: molecular docking and MD simulation studies
Sadia Naz, Umar Farooq, Hongwu Ma, Rizwana Sarwar & Nadia Riaz
Pages: 7138-7149
Published online: 20 Aug 2020
AbstractforThree new acrylic acid derivatives from Achillea mellifolium as potential thymidine phosphorylase inhibitor: molecular docking and MD simulation studies | Full Text | References | PDF (1.9 MB) | EPUB
  • 177 Views
  • 3 CrossRef citations
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Article
Arylidene analogues as selective COX-2 inhibitors: synthesis, characterization, in silico and in vitro studies
Dipti L. Namera, Sampark S. Thakkar, Parth Thakor, Umed Bhoya & Anamik Shah
Pages: 7150-7159
Published online: 14 Aug 2020
AbstractforArylidene analogues as selective COX-2 inhibitors: synthesis, characterization, in silico and in vitro studies | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 205 Views
  • 4 CrossRef citations
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Article
Exploring the binding mechanisms of inorganic magnetic nanocarrier containing L-Dopa with HSA protein utilizing multi spectroscopic techniques
Nahid Shahabadi & Mahtab Razlansari
Pages: 7160-7167
Published online: 14 Aug 2020
AbstractforExploring the binding mechanisms of inorganic magnetic nanocarrier containing L-Dopa with HSA protein utilizing multi spectroscopic techniques | Full Text | References | PDF (1.1 MB) | EPUB
  • 130 Views
  • 1 CrossRef citations
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Article
Novel potent natural peroxidases inhibitors with in vitro assays, inhibition mechanism and molecular docking of phenolic compounds and alkaloids
Khedidja Benarous, Fatima Zohra Benali, Ikram Cherifa Bekhaoua & Mohamed Yousfi
Pages: 7168-7180
Published online: 17 Aug 2020
AbstractforNovel potent natural peroxidases inhibitors with in vitro assays, inhibition mechanism and molecular docking of phenolic compounds and alkaloids | Full Text | References | PDF (2.4 MB) | EPUB
  • 214 Views
  • 3 CrossRef citations
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Article
In silico exploration of the fingerprints triggering modulation of glutaminyl cyclase inhibition for the treatment of Alzheimer’s disease using SMILES based attributes in Monte Carlo optimization
Ashwani Kumar, Kiran Bagri, Manisha Nimbhal & Parvin Kumar
Pages: 7181-7193
Published online: 14 Aug 2020
AbstractforIn silico exploration of the fingerprints triggering modulation of glutaminyl cyclase inhibition for the treatment of Alzheimer’s disease using SMILES based attributes in Monte Carlo optimization | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 194 Views
  • 9 CrossRef citations
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Article
A potent drug candidature of Cu(II) pyrazino[2,3‐f][1,10]phenanthroline complexes with bioactive ligands: synthesis, crystal structures, biomolecular interactions, radical scavenging and cytotoxicities
Duygu İnci, Rahmiye Aydın, Özgür Vatan & Yunus Zorlu
Pages: 7194-7212
Published online: 18 Aug 2020
AbstractforA potent drug candidature of Cu(II) pyrazino[2,3‐f][1,10]phenanthroline complexes with bioactive ligands: synthesis, crystal structures, biomolecular interactions, radical scavenging and cytotoxicities | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 368 Views
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Article
Calcium ion binding to calmodulin: binding free energy calculation using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method by incorporating implicit polarization
Abdul Basit, Rakesh Kumar Mishra & Pradipta Bandyopadhyay
Pages: 7213-7222
Published online: 24 Aug 2020
AbstractforCalcium ion binding to calmodulin: binding free energy calculation using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method by incorporating implicit polarization | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 648 Views
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Letter to the Editor

Letter
Precipitant ions influence on lysozyme oligomers stability investigated by molecular dynamics simulation at different temperatures
Yuliya V. Kordonskaya, Margarita A. Marchenkova, Vladimir I. Timofeev, Yulia A. Dyakova, Yurii V. Pisarevsky & Michael V. Kovalchuk
Pages: 7223-7230
Published online: 08 Aug 2020
First Page PreviewforPrecipitant ions influence on lysozyme oligomers stability investigated by molecular dynamics simulation at different temperatures | Full Text | References | PDF (2.4 MB) | EPUB
  • 116 Views
  • 7 CrossRef citations
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Research Articles

Article
Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study
Budheswar Dehury, Vishakha Raina, Namrata Misra & Mrutyunjay Suar
Pages: 7231-7245
Published online: 07 Aug 2020
AbstractforEffect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study | Full Text | References | PDF (4.9 MB) | EPUB | Supplemental
  • 3978 Views
  • 41 CrossRef citations
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Article
Molecular docking, molecular dynamics simulations and reactivity, studies on approved drugs library targeting ACE2 and SARS-CoV-2 binding with ACE2
Hadjer Khelfaoui, Dalal Harkati & Basil A. Saleh
Pages: 7246-7262
Published online: 05 Aug 2020
AbstractforMolecular docking, molecular dynamics simulations and reactivity, studies on approved drugs library targeting ACE2 and SARS-CoV-2 binding with ACE2 | Full Text | References | PDF (4.3 MB) | EPUB
  • 4795 Views
  • 31 CrossRef citations
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Article
New anti-viral drugs for the treatment of COVID-19 instead of favipiravir
Ahmet Aktaş, Burak Tüzün, Rukiye Aslan, Koray Sayin & Hilmi Ataseven
Pages: 7263-7273
Published online: 12 Aug 2020
AbstractforNew anti-viral drugs for the treatment of COVID-19 instead of favipiravir | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 5000 Views
  • 28 CrossRef citations
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Article
In-silico strategies for identification of potent inhibitor for MMP-1 to prevent metastasis of breast cancer
Velu Shunmuga Priya, Dhinakararajan Pradiba, Murali Aarthy, Sanjeev Kumar Singh, Anant Achary & Mani Vasanthi
Pages: 7274-7293
Published online: 02 Sep 2020
AbstractforIn-silico strategies for identification of potent inhibitor for MMP-1 to prevent metastasis of breast cancer | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 323 Views
  • 8 CrossRef citations
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Article
Molecular docking and simulation studies on SARS-CoV-2 Mpro reveals Mitoxantrone, Leucovorin, Birinapant, and Dynasore as potent drugs against COVID-19
Kiran Bharat Lokhande, Sayali Doiphode, Renu Vyas & K. Venkateswara Swamy
Pages: 7294-7305
Published online: 20 Aug 2020
AbstractforMolecular docking and simulation studies on SARS-CoV-2 Mpro reveals Mitoxantrone, Leucovorin, Birinapant, and Dynasore as potent drugs against COVID-19 | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 5202 Views
  • 53 CrossRef citations
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Article
In silico validation of coumarin derivatives as potential inhibitors against Main Protease, NSP10/NSP16-Methyltransferase, Phosphatase and Endoribonuclease of SARS CoV-2
Akhilesh Kumar Maurya & Nidhi Mishra
Pages: 7306-7321
Published online: 24 Aug 2020
AbstractforIn silico validation of coumarin derivatives as potential inhibitors against Main Protease, NSP10/NSP16-Methyltransferase, Phosphatase and Endoribonuclease of SARS CoV-2 | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 2243 Views
  • 25 CrossRef citations
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Express Communication

Article
Structural insight to hydroxychloroquine-3C-like proteinase complexation from SARS-CoV-2: inhibitor modelling study through molecular docking and MD-simulation study
Soumita Mukherjee, Subrata Dasgupta, Tapasendra Adhikary, Utpal Adhikari & Sujit Sankar Panja
Pages: 7322-7334
Published online: 10 Aug 2020
AbstractforStructural insight to hydroxychloroquine-3C-like proteinase complexation from SARS-CoV-2: inhibitor modelling study through molecular docking and MD-simulation study | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 2335 Views
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