Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 16 (2021)

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Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 16 (2021)

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Research Articles

Article
AMBER force field parameters for the Zn (II) ions of the tunneling-fold enzymes GTP cyclohydrolase I and 6‐pyruvoyl tetrahydropterin synthase
Afrah Khairallah, Özlem Tastan Bishop & Vuyani Moses
Pages: 5843-5860
Published online: 28 Jul 2020
AbstractforAMBER force field parameters for the Zn (II) ions of the tunneling-fold enzymes GTP cyclohydrolase I and 6‐pyruvoyl tetrahydropterin synthase | Full Text | References | PDF (5.5 MB) | EPUB | Supplemental
  • 385 Views
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Article
Toxicity assessment of carmine and its interaction with calf thymus DNA
Amin Arif, Ajaz Ahmad & Masood Ahmad
Pages: 5861-5871
Published online: 21 Jul 2020
AbstractforToxicity assessment of carmine and its interaction with calf thymus DNA | Full Text | References | PDF (2.5 MB) | EPUB
  • 233 Views
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Article
Prospecting for new catechol-O-methyltransferase (COMT) inhibitors as a potential treatment for Parkinson’s disease: a study by molecular dynamics and structure-based virtual screening
Iasmin Ramos da Silva, Michelle Rocha Parise, Maristela Pereira & Roosevelt Alves da Silva
Pages: 5872-5891
Published online: 21 Jul 2020
AbstractforProspecting for new catechol-O-methyltransferase (COMT) inhibitors as a potential treatment for Parkinson’s disease: a study by molecular dynamics and structure-based virtual screening | Full Text | References | PDF (7.1 MB) | EPUB | Supplemental
  • 353 Views
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Article
Exploring the energetic basis of binding of currently used drugs against HIV-1 subtype CRF01_AE protease via molecular dynamics simulations
Md Fulbabu Sk, Nisha Amarnath Jonniya & Parimal Kar
Pages: 5892-5909
Published online: 22 Jul 2020
AbstractforExploring the energetic basis of binding of currently used drugs against HIV-1 subtype CRF01_AE protease via molecular dynamics simulations | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 357 Views
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Article
Computational evaluation of a fusion protein consisted of pertussis toxin and filamentous hemagglutinin from Bordetella pertussis to target Claudin-4 using C-terminal fragment of Clostridium perfringens enterotoxin
Negar Souod, Elham Rismani, Fariborz Bahrami, Saeed Reza Pakzad & Soheila Ajdary
Pages: 5910-5919
Published online: 21 Jul 2020
AbstractforComputational evaluation of a fusion protein consisted of pertussis toxin and filamentous hemagglutinin from Bordetella pertussis to target Claudin-4 using C-terminal fragment of Clostridium perfringens enterotoxin | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 124 Views
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Article
Structural insight into TNF-α inhibitors through combining pharmacophore-based virtual screening and molecular dynamic simulation
Hina Qaiser, Maria Saeed, Dmitry Nerukh & Zaheer Ul-Haq
Pages: 5920-5939
Published online: 24 Jul 2020
AbstractforStructural insight into TNF-α inhibitors through combining pharmacophore-based virtual screening and molecular dynamic simulation | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 433 Views
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Article
Profiling selectivity of chagasin mutants towards cysteine proteases cruzain or cathepsin L through molecular dynamics simulations
Núbia Prates Toman, Anna Sophia Kamenik, Lucianna Helene Santos, Florian Hofer, Klaus R. Liedl & Rafaela Salgado Ferreira
Pages: 5940-5952
Published online: 25 Jul 2020
AbstractforProfiling selectivity of chagasin mutants towards cysteine proteases cruzain or cathepsin L through molecular dynamics simulations | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
  • 215 Views
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Article
Anticancer activity, topoisomerase I inhibition, DNA ‘light switch’ behavior and molecular docking of two ruthenium complexes containing phenazine ring
Xue-Wen Liu, Ning-Yi Liu, Yuan-Qing Deng, Shan Wang, Ting Liu, Yu-Cai Tang, Yuan-Dao Chen & Ji-Lin Lu
Pages: 5953-5962
Published online: 28 Jul 2020
AbstractforAnticancer activity, topoisomerase I inhibition, DNA ‘light switch’ behavior and molecular docking of two ruthenium complexes containing phenazine ring | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 244 Views
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Article
Insights into amyotrophic lateral sclerosis linked Pro525Arg mutation in the fused in sarcoma protein through in silico analysis and molecular dynamics simulation
Sompriya Chatterjee, Abbas Salimi & Jin Yong Lee
Pages: 5963-5976
Published online: 20 Jul 2020
AbstractforInsights into amyotrophic lateral sclerosis linked Pro525Arg mutation in the fused in sarcoma protein through in silico analysis and molecular dynamics simulation | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 407 Views
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Article
Identification of the naphthoquinone derivative inhibitors binding site in heat shock protein 90: an induced-fit docking, molecular dynamics and 3D-QSAR study
Claudio Godoy-Castillo, Nicolas Bravo-Acuña, Gloria Arriagada, Fernando Faunes, Roberto León & Jorge Soto-Delgado
Pages: 5977-5987
Published online: 17 Aug 2020
AbstractforIdentification of the naphthoquinone derivative inhibitors binding site in heat shock protein 90: an induced-fit docking, molecular dynamics and 3D-QSAR study | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 221 Views
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Article
Screening and identification of secondary metabolites in the bark of Bauhinia variegata to treat Alzheimer’s disease by using molecular docking and molecular dynamics simulations
Noopur Khare, Sanjiv Kumar Maheshwari & Abhimanyu Kumar Jha
Pages: 5988-5998
Published online: 28 Jul 2020
AbstractforScreening and identification of secondary metabolites in the bark of Bauhinia variegata to treat Alzheimer’s disease by using molecular docking and molecular dynamics simulations | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 362 Views
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Article
Study on effects of co-solvents on the structure of DhaA by molecular dynamics simulation
He Zheng, Yong-Chao Zheng, Yan Cui, Jian-Jun Zhu & Jin-Yi Zhong
Pages: 5999-6007
Published online: 22 Jul 2020
AbstractforStudy on effects of co-solvents on the structure of DhaA by molecular dynamics simulation | Full Text | References | PDF (2 MB) | EPUB
  • 153 Views
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Article
Polysaccharides like pentagalloylglucose, parishin a and stevioside inhibits the viral entry by binding the Zika virus envelope protein
Nitin Sharma, Prateek Kumar & Rajanish Giri
Pages: 6008-6020
Published online: 24 Jul 2020
AbstractforPolysaccharides like pentagalloylglucose, parishin a and stevioside inhibits the viral entry by binding the Zika virus envelope protein | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 331 Views
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Article
Pharmacophore-based virtual screening and molecular docking to identify promising dual inhibitors of human acetylcholinesterase and butyrylcholinesterase
Ana Mércia Silva Mascarenhas, Raquel Bianca Marchesine de Almeida, Moysés Fagundes de Araujo Neto, Géssica Oliveira Mendes, Jorddy Neves da Cruz, Cleydson Breno Rodrigues dos Santos, Mariana Borges Botura & Franco Henrique Andrade Leite
Pages: 6021-6030
Published online: 24 Jul 2020
AbstractforPharmacophore-based virtual screening and molecular docking to identify promising dual inhibitors of human acetylcholinesterase and butyrylcholinesterase | Full Text | References | PDF (2.4 MB) | EPUB
  • 718 Views
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Article
Identification of potential modulator of Anopheles gambiae odorant binding protein 1 by hierarchical virtual screening and molecular dynamics
Mayra Ramos do Bomfim, Janay Stefany Carneiro Araújo, Williams Jorge da Cruz Macêdo, Cleydson Breno Rodrigues dos Santos & Franco Henrique Andrade Leite
Pages: 6031-6043
Published online: 22 Jul 2020
AbstractforIdentification of potential modulator of Anopheles gambiae odorant binding protein 1 by hierarchical virtual screening and molecular dynamics | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 199 Views
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Article
Evaluation of biomolecular interactions and cytotoxic activity of organometallic binuclear Ru(II) complexes of ferrocenyl thiosemicarbazones
Priyanka Khanvilkar, Soumya R. Dash, Alisagar Vohra, Ranjitsinh Devkar & Debjani Chakraborty
Pages: 6044-6055
Published online: 30 Jul 2020
AbstractforEvaluation of biomolecular interactions and cytotoxic activity of organometallic binuclear Ru(II) complexes of ferrocenyl thiosemicarbazones | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 180 Views
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Article
In vitro and in silico analysis of L. donovani enoyl acyl carrier protein reductase - A possible drug target
Shalini Yadav, Haraprasad Mandal, Vijayakumar Saravanan, Pradeep Das & Shubhankar Kumar Singh
Pages: 6056-6069
Published online: 07 Aug 2020
AbstractforIn vitro and in silico analysis of L. donovani enoyl acyl carrier protein reductase - A possible drug target | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 133 Views
  • 1 CrossRef citations
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Article
RNA-targeted Cu(II)-based potential antitumor drug entity: comprehensive structural, biological {DNA/RNA binding, cleavage, cytotoxicity} and computational studies
Sabiha Parveen, Kaneez Fatima, Siffeen Zehra & Farukh Arjmand
Pages: 6070-6083
Published online: 25 Jul 2020
AbstractforRNA-targeted Cu(II)-based potential antitumor drug entity: comprehensive structural, biological {DNA/RNA binding, cleavage, cytotoxicity} and computational studies | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 259 Views
  • 8 CrossRef citations
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Article
Vaccine candidate designed against carcinoembryonic antigen-related cell adhesion molecules using immunoinformatics tools
Aditya Gupta, Andrew J. Rosato & Feng Cui
Pages: 6084-6098
Published online: 28 Jul 2020
AbstractforVaccine candidate designed against carcinoembryonic antigen-related cell adhesion molecules using immunoinformatics tools | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 2007 Views
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Open Access
Article
Exploiting the rationale behind substrate recognition by promiscuous thermophilic NDP-sugar pyrophosphorylase for expanding glycorandomization: an in silico study
Prerana Gogoi, Prerana Mordina & Shankar Prasad Kanaujia
Pages: 6099-6111
Published online: 21 Jul 2020
AbstractforExploiting the rationale behind substrate recognition by promiscuous thermophilic NDP-sugar pyrophosphorylase for expanding glycorandomization: an in silico study | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 237 Views
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Article
Design, synthesis, molecular modeling and neuroprotective effects of a new framework of cholinesterase inhibitors for Alzheimer’s disease
Vanessa S. Zanon, Josélia A. Lima, Rackele F. Amaral, Flavia R. S. Lima, Daniel A. S. Kitagawa, Tanos C. C. França & Maria D. Vargas
Pages: 6112-6125
Published online: 25 Jul 2020
AbstractforDesign, synthesis, molecular modeling and neuroprotective effects of a new framework of cholinesterase inhibitors for Alzheimer’s disease | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 221 Views
  • 7 CrossRef citations
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Article
Revealing the role of fluorine pharmacophore in chalcone scaffold for shifting the MAO-B selectivity: investigation of a detailed molecular dynamics and quantum chemical study
Fisayo A. Olotu, Monu Joy, Mohamed A. Abdelgawad, Siju E. Narayanan, Mahmoud E. Soliman & Bijo Mathew
Pages: 6126-6139
Published online: 24 Jul 2020
AbstractforRevealing the role of fluorine pharmacophore in chalcone scaffold for shifting the MAO-B selectivity: investigation of a detailed molecular dynamics and quantum chemical study | Full Text | References | PDF (4.4 MB) | EPUB
  • 224 Views
  • 2 CrossRef citations
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Article
Synthesis, characterization, alkaline phosphatase inhibition assay and molecular modeling studies of 1-benzylidene-2-(4-tert- butylthiazol-2-yl) hydrazines
Hamid Aziz, Abid Mahmood, Sumera Zaib, Aamer Saeed, Hesham R. El-Seedi, Julie Pelletier, Jean Sévigny & Jamshed Iqbal
Pages: 6140-6153
Published online: 11 Aug 2020
AbstractforSynthesis, characterization, alkaline phosphatase inhibition assay and molecular modeling studies of 1-benzylidene-2-(4-tert- butylthiazol-2-yl) hydrazines | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 473 Views
  • 5 CrossRef citations
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Article
Exploring 3-Benzyloxyflavones as new lead cholinesterase inhibitors: synthesis, structure–activity relationship and molecular modelling simulations
Ehsan Ullah Mughal, Amina Sadiq, Momna Ayub, Nafeesa Naeem, Asif Javid, Sajjad Hussain Sumrra, Muhammad Naveed Zafar, Bilal Ahmad Khan, Fouzia Perveen Malik & Ishtiaq Ahmed
Pages: 6154-6167
Published online: 05 Aug 2020
AbstractforExploring 3-Benzyloxyflavones as new lead cholinesterase inhibitors: synthesis, structure–activity relationship and molecular modelling simulations | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 454 Views
  • 12 CrossRef citations
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Hypothesis Paper

Article
The latitude hypothesis, vitamin D, and SARS-Co-V2
Robert Hedlund, Trude K. Diamond & Vladimir N. Uversky
Pages: 6168-6170
Published online: 17 Jul 2020
AbstractforThe latitude hypothesis, vitamin D, and SARS-Co-V2 | Full Text | References | PDF (403.2 KB) | EPUB
  • 2077 Views
  • 6 CrossRef citations
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Research Articles

Article
Anthocyanin derivatives as potent inhibitors of SARS-CoV-2 main protease: An in-silico perspective of therapeutic targets against COVID-19 pandemic
Zeynab Fakhar, Bahar Faramarzi, Severina Pacifico & Shadab Faramarzi
Pages: 6171-6183
Published online: 03 Aug 2020
AbstractforAnthocyanin derivatives as potent inhibitors of SARS-CoV-2 main protease: An in-silico perspective of therapeutic targets against COVID-19 pandemic | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 4152 Views
  • 22 CrossRef citations
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Article
Antimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19
Moussa Sehailia & Smain Chemat
Pages: 6184-6194
Published online: 22 Jul 2020
AbstractforAntimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19 | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 4347 Views
  • 28 CrossRef citations
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Article
Network analysis, sequence and structure dynamics of key proteins of coronavirus and human host, and molecular docking of selected phytochemicals of nine medicinal plants
Toluwase Hezekiah Fatoki, Omodele Ibraheem, Ibukun Oladejo Ogunyemi, Afolabi Clement Akinmoladun, Harriet U. Ugboko, Catherine Joke Adeseko, Oladoja A. Awofisayo, Sunday Joseph Olusegun & Jesupemi Mercy Enibukun
Pages: 6195-6217
Published online: 20 Jul 2020
AbstractforNetwork analysis, sequence and structure dynamics of key proteins of coronavirus and human host, and molecular docking of selected phytochemicals of nine medicinal plants | Full Text | References | PDF (4.8 MB) | EPUB
  • 4373 Views
  • 15 CrossRef citations
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Article
Cyanobacterial metabolites as promising drug leads against the Mpro and PLpro of SARS-CoV-2: an in silico analysis
Devashan Naidoo, Ayan Roy, Pallab Kar, Taurai Mutanda & Akash Anandraj
Pages: 6218-6230
Published online: 21 Jul 2020
AbstractforCyanobacterial metabolites as promising drug leads against the Mpro and PLpro of SARS-CoV-2: an in silico analysis | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 2964 Views
  • 26 CrossRef citations
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Article
Virtual screening, molecular dynamics and structure–activity relationship studies to identify potent approved drugs for Covid-19 treatment
Md. Mahbubur Rahman, Titon Saha, Kazi Jahidul Islam, Rasel Hosen Suman, Sourav Biswas, Emon Uddin Rahat, Md. Rubel Hossen, Rajib Islam, Md Nayeem Hossain, Abdulla Al Mamun, Maksud Khan, Md Ackas Ali & Mohammad A. Halim
Pages: 6231-6241
Published online: 21 Jul 2020
AbstractforVirtual screening, molecular dynamics and structure–activity relationship studies to identify potent approved drugs for Covid-19 treatment | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 6317 Views
  • 40 CrossRef citations
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Article
Computational drug repurposing for the identification of SARS-CoV-2 main protease inhibitors
Diego Fiorucci, Eva Milletti, Francesco Orofino, Antonella Brizzi, Claudia Mugnaini & Federico Corelli
Pages: 6242-6248
Published online: 24 Jul 2020
AbstractforComputational drug repurposing for the identification of SARS-CoV-2 main protease inhibitors | Full Text | References | PDF (1.5 MB) | EPUB
  • 2509 Views
  • 7 CrossRef citations
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Article
Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA‐dependent RNA polymerase (RdRp) inhibition: an in-silico analysis
Satyam Singh, Md Fulbabu Sk, Avinash Sonawane, Parimal Kar & Sushabhan Sadhukhan
Pages: 6249-6264
Published online: 28 Jul 2020
AbstractforPlant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA‐dependent RNA polymerase (RdRp) inhibition: an in-silico analysis | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 6585 Views
  • 65 CrossRef citations
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Article
In-Silico approach for identification of effective and stable inhibitors for COVID-19 main protease (Mpro) from flavonoid based phytochemical constituents of Calendula officinalis
Pratik Das, Ranabir Majumder, Mahitosh Mandal & Piyali Basak
Pages: 6265-6280
Published online: 24 Jul 2020
AbstractforIn-Silico approach for identification of effective and stable inhibitors for COVID-19 main protease (Mpro) from flavonoid based phytochemical constituents of Calendula officinalis | Full Text | References | PDF (5.6 MB) | EPUB | Supplemental
  • 4837 Views
  • 43 CrossRef citations
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Article
Molecular docking and dynamics study of natural compound for potential inhibition of main protease of SARS-CoV-2
Shafi Mahmud, Mohammad Abu Raihan Uddin, Meemtaheena Zaman, Khaled Mahmud Sujon, Md. Ekhtiar Rahman, Mobasshir Noor Shehab, Ariful Islam, Md. Wasim Alom, Al Amin, Al Shahriar Akash & Md. Abu Saleh
Pages: 6281-6289
Published online: 24 Jul 2020
AbstractforMolecular docking and dynamics study of natural compound for potential inhibition of main protease of SARS-CoV-2 | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 3599 Views
  • 27 CrossRef citations
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Article
Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2
Sinthyia Ahmed, Rumana Mahtarin, Sayeda Samina Ahmed, Shaila Akter, Md. Shamiul Islam, Abdulla Al Mamun, Rajib Islam, Md Nayeem Hossain, Md Ackas Ali, Mossammad U. C. Sultana, MD. Rimon Parves, M. Obayed Ullah & Mohammad A. Halim
Pages: 6290-6305
Published online: 28 Jul 2020
AbstractforInvestigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2 | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
  • 4678 Views
  • 17 CrossRef citations
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Article
Targeting SARS-CoV-2 spike protein of COVID-19 with naturally occurring phytochemicals: an in silico study for drug development
Preeti Pandey, Jitendra Subhash Rane, Aroni Chatterjee, Abhijeet Kumar, Rajni Khan, Amresh Prakash & Shashikant Ray
Pages: 6306-6316
Published online: 22 Jul 2020
AbstractforTargeting SARS-CoV-2 spike protein of COVID-19 with naturally occurring phytochemicals: an in silico study for drug development | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 11022 Views
  • 87 CrossRef citations
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Article
Comparative molecular investigation of the potential inhibitors against SARS-CoV-2 main protease: a molecular docking study
Md. Arif Khan, Shafi Mahmud, A. S. M. Rubayet Ul Alam, Md. Ekhtiar Rahman, Firoz Ahmed & Mohammed Rahmatullah
Pages: 6317-6323
Published online: 22 Jul 2020
AbstractforComparative molecular investigation of the potential inhibitors against SARS-CoV-2 main protease: a molecular docking study | Full Text | References | PDF (1.6 MB) | EPUB
  • 3103 Views
  • 20 CrossRef citations
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Express Communication

Article
Dual inhibitors of SARS-CoV-2 proteases: pharmacophore and molecular dynamics based drug repositioning and phytochemical leads
Kartik Mitra, Prasanth Ghanta, Sushank Acharya, Gayathri Chakrapani, Basavaraju Ramaiah & Mukesh Doble
Pages: 6324-6337
Published online: 22 Jul 2020
AbstractforDual inhibitors of SARS-CoV-2 proteases: pharmacophore and molecular dynamics based drug repositioning and phytochemical leads | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 2991 Views
  • 14 CrossRef citations
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