Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 9 (2021)

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Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 9 (2021)

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Research Articles

Article
Interaction of selected biomolecules and metabolites with amyloidogenic proteins
Debanjan Kundu, Umesh & Vikash Kumar Dubey
Pages: 3061-3070
Published online: 12 May 2020
AbstractforInteraction of selected biomolecules and metabolites with amyloidogenic proteins | Full Text | References | PDF (1.4 MB) | EPUB
  • 286 Views
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Article
Computer-Aided aptamer design for sulfadimethoxine antibiotic: step by step mutation based on MD simulation approach
Zahra Khoshbin & Mohammad Reza Housaindokht
Pages: 3071-3079
Published online: 06 May 2020
AbstractforComputer-Aided aptamer design for sulfadimethoxine antibiotic: step by step mutation based on MD simulation approach | Full Text | References | PDF (3.2 MB) | EPUB
  • 608 Views
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Article
Design, synthesis, molecular docking, density functional theory and antimicrobial studies of some novel benzoxazole derivatives as structural bioisosteres of nucleotides
Meryem Erol, Ismail Celik, Ozlem Temiz-Arpaci, Fatma Kaynak-Onurdag & Suzan Okten
Pages: 3080-3091
Published online: 13 May 2020
AbstractforDesign, synthesis, molecular docking, density functional theory and antimicrobial studies of some novel benzoxazole derivatives as structural bioisosteres of nucleotides | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 840 Views
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Article
Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: an in silico approach
Sukanth Kumar Enmozhi, Kavitha Raja, Irudhayasamy Sebastine & Jerrine Joseph
Pages: 3092-3098
Published online: 05 May 2020
AbstractforAndrographolide as a potential inhibitor of SARS-CoV-2 main protease: an in silico approach | Full Text | References | PDF (1 MB) | EPUB | Supplemental
  • 25105 Views
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Article
Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease
Rakesh S. Joshi, Shounak S. Jagdale, Sneha B. Bansode, S. Shiva Shankar, Meenakshi B. Tellis, Vaibhav Kumar Pandya, Anita Chugh, Ashok P. Giri & Mahesh J. Kulkarni
Pages: 3099-3114
Published online: 05 May 2020
AbstractforDiscovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 12812 Views
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Article
Molecular modeling approaches of selective adenosine receptor type 2A agonists as potential anti-inflammatory drugs
Cleydson B. R. Santos, Kelton L. B. Santos, Jorddy N. Cruz, Franco H. A. Leite, Rosivaldo S. Borges, Carlton A. Taft, Joaquín M. Campos & Carlos H. T. P. Silva
Pages: 3115-3127
Published online: 06 May 2020
AbstractforMolecular modeling approaches of selective adenosine receptor type 2A agonists as potential anti-inflammatory drugs | Full Text | References | PDF (3.2 MB) | EPUB
  • 377 Views
  • 27 CrossRef citations
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Article
Dynamic information of the time-dependent tobullian biomolecular structure using a high-accuracy size-dependent theory
Xianwen Zhang, Milad Shamsodin, Hanying Wang, Omid NoormohammadiArani, Aqib Mashood Khan, Mostafa Habibi & M. S. H. Al-Furjan
Pages: 3128-3143
Published online: 13 May 2020
AbstractforDynamic information of the time-dependent tobullian biomolecular structure using a high-accuracy size-dependent theory | Full Text | References | PDF (2.6 MB) | EPUB
  • 221 Views
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Article
Structural insights on binding mechanism of CAD complexes (CPSase, ATCase and DHOase)
Surekha Kanagarajan, Prabhu Dhamodharan, Nachiappan Mutharasappan, Sanjay Kumar Choubey, Prajisha Jayaprakash, Jayashree Biswal & Jeyakanthan Jeyaraman
Pages: 3144-3157
Published online: 05 May 2020
AbstractforStructural insights on binding mechanism of CAD complexes (CPSase, ATCase and DHOase) | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 175 Views
  • 1 CrossRef citations
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Article
The molecular mechanism behind protein kinase B natural mutant E17K affecting the allosteric inhibitor sensitivity: a molecular dynamics simulation study
Yan Wang, Ran Jia & Wen Tan
Pages: 3158-3171
Published online: 02 Jun 2020
AbstractforThe molecular mechanism behind protein kinase B natural mutant E17K affecting the allosteric inhibitor sensitivity: a molecular dynamics simulation study | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 280 Views
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Article
Structural insights of catalytic mechanism in mutant pyrazinamidase of Mycobacterium tuberculosis
Muhammad Junaid, Cheng-Dong Li, Jiayi Li, Abbas Khan, Syed Shujait Ali, Syed Baber Jamal, Shah Saud, Arif Ali & Dong-Qing Wei
Pages: 3172-3185
Published online: 12 May 2020
AbstractforStructural insights of catalytic mechanism in mutant pyrazinamidase of Mycobacterium tuberculosis | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 289 Views
  • 6 CrossRef citations
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Article
Synthesis of Ni0.5Co0.5-xCdxFe1.78Nd0.02O4 (x ≤ 0.25) nanofibers by using electrospinning technique induce anti-cancer and anti-bacterial activities
F. Alahmari, S. Rehman, M. Almessiere, F. A Khan, Y. Slimani & A. Baykal
Pages: 3186-3193
Published online: 13 May 2020
AbstractforSynthesis of Ni0.5Co0.5-xCdxFe1.78Nd0.02O4 (x ≤ 0.25) nanofibers by using electrospinning technique induce anti-cancer and anti-bacterial activities | Full Text | References | PDF (1.8 MB) | EPUB
  • 254 Views
  • 22 CrossRef citations
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Article
Natural products may interfere with SARS-CoV-2 attachment to the host cell
Abdo A. Elfiky
Pages: 3194-3203
Published online: 05 May 2020
AbstractforNatural products may interfere with SARS-CoV-2 attachment to the host cell | Full Text | References | PDF (2.2 MB) | EPUB
  • 8311 Views
  • 84 CrossRef citations
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Article
SARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective
Abdo A. Elfiky
Pages: 3204-3212
Published online: 06 May 2020
AbstractforSARS-CoV-2 RNA dependent RNA polymerase (RdRp) targeting: an in silico perspective | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 16036 Views
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Article
A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2
Rajib Islam, Md. Rimon Parves, Archi Sundar Paul, Nizam Uddin, Md. Sajjadur Rahman, Abdulla Al Mamun, Md. Nayeem Hossain, Md. Ackas Ali & Mohammad A. Halim
Pages: 3213-3224
Published online: 12 May 2020
AbstractforA molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2 | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 18007 Views
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Article
Stilbene-based natural compounds as promising drug candidates against COVID-19
Hussain Mustatab Wahedi, Sajjad Ahmad & Sumra Wajid Abbasi
Pages: 3225-3234
Published online: 12 May 2020
AbstractforStilbene-based natural compounds as promising drug candidates against COVID-19 | Full Text | References | PDF (2.3 MB) | EPUB
  • 13020 Views
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Article
To be ionized or not to be ionized: the vital role of physicochemical properties of galbanic acid derivatives in AChE assay
Ahmad Ebadi, Seyed Sajad Olyaie & Dara Dastan
Pages: 3235-3243
Published online: 15 May 2020
AbstractforTo be ionized or not to be ionized: the vital role of physicochemical properties of galbanic acid derivatives in AChE assay | Full Text | References | PDF (2 MB) | EPUB
  • 81 Views
  • 5 CrossRef citations
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Article
An in-silico evaluation of different Saikosaponins for their potency against SARS-CoV-2 using NSP15 and fusion spike glycoprotein as targets
Saurabh K. Sinha, Anshul Shakya, Satyendra K. Prasad, Shashikant Singh, Nilambari S. Gurav, Rupali S. Prasad & Shailendra S. Gurav
Pages: 3244-3255
Published online: 13 May 2020
AbstractforAn in-silico evaluation of different Saikosaponins for their potency against SARS-CoV-2 using NSP15 and fusion spike glycoprotein as targets | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 5560 Views
  • 130 CrossRef citations
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Article
Irreversible thermal inactivation and conformational lock of alpha glucosidase
Loghman Alaei, Zhila Izadi, Samira Jafari, Fatemeh Jahanshahi, Mehdi Jaymand, Pantea Mohammadi, Bilal Ahamad Paray, Anwarul Hasan, Mojtaba Falahati, Behrang Shiri Varnamkhasti, Ali Akbar Saboury, Zahra Moosavi-Nejad, Mehrnaz Sheikh-Hosseini & Hossein Derakhshankhah
Pages: 3256-3262
Published online: 14 May 2020
AbstractforIrreversible thermal inactivation and conformational lock of alpha glucosidase | Full Text | References | PDF (1.4 MB) | EPUB
  • 173 Views
  • 4 CrossRef citations
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Article
In silico study the inhibition of angiotensin converting enzyme 2 receptor of COVID-19 by Ammoides verticillata components harvested from Western Algeria
Imane Abdelli, Faiçal Hassani, Sohayb Bekkel Brikci & Said Ghalem
Pages: 3263-3276
Published online: 14 May 2020
AbstractforIn silico study the inhibition of angiotensin converting enzyme 2 receptor of COVID-19 by Ammoides verticillata components harvested from Western Algeria | Full Text | References | PDF (3.3 MB) | EPUB
  • 19869 Views
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Article
Inhibition effects of isoproterenol, chlorpromazine, carbamazepine, tamoxifen drugs on glutathione S-transferase, cholinesterases enzymes and molecular docking studies
Fikret Türkan, Mehmet Harbi Calimli, Gülşah Saydan Kanberoğlu & Muhammet Karaman
Pages: 3277-3284
Published online: 13 May 2020
AbstractforInhibition effects of isoproterenol, chlorpromazine, carbamazepine, tamoxifen drugs on glutathione S-transferase, cholinesterases enzymes and molecular docking studies | Full Text | References | PDF (1.5 MB) | EPUB
  • 687 Views
  • 7 CrossRef citations
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Article
Discovery of new potential CDK2/VEGFR2 type II inhibitors by fragmentation and virtual screening of natural products
Andrés Felipe Vásquez, Alejandro Reyes Muñoz, Jorge Duitama & Andrés González Barrios
Pages: 3285-3299
Published online: 13 May 2020
AbstractforDiscovery of new potential CDK2/VEGFR2 type II inhibitors by fragmentation and virtual screening of natural products | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 372 Views
  • 4 CrossRef citations
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Article
Molecular dynamics simulation study of Plasmodium falciparum and Escherichia coli SufA: Exploration of conformational changes possibly involved in iron-sulfur cluster transfer
Priyadarsini Kadirvel, Ahalyaa Subramanian, Niranjana Sridharan, Sreelakshmi Subramanian, Senthamizhan Vimaladhasan & Sharmila Anishetty
Pages: 3300-3311
Published online: 15 May 2020
AbstractforMolecular dynamics simulation study of Plasmodium falciparum and Escherichia coli SufA: Exploration of conformational changes possibly involved in iron-sulfur cluster transfer | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 223 Views
  • 2 CrossRef citations
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Article
Cirsimaritin, a lung squamous carcinoma cells (NCIH-520) proliferation inhibitor
Gauri Pathak, Shilpi Singh, Priyanka Kumari, Waseem Raza, Yusuf Hussain & Abha Meena
Pages: 3312-3323
Published online: 13 May 2020
AbstractforCirsimaritin, a lung squamous carcinoma cells (NCIH-520) proliferation inhibitor | Full Text | References | PDF (1.9 MB) | EPUB
  • 317 Views
  • 15 CrossRef citations
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Article
Formation of a DNA triple helical structure at BOLF1 gene of human herpesvirus 4 (HH4) genome
Shikha Kaushik & Shrikant Kukreti
Pages: 3324-3335
Published online: 19 May 2020
AbstractforFormation of a DNA triple helical structure at BOLF1 gene of human herpesvirus 4 (HH4) genome | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 123 Views
  • 3 CrossRef citations
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Article
The biological activities, molecular docking studies, and anticancer effects of 1-arylsuphonylpyrazole derivatives
Parham Taslimi, Yavuz Erden, Sabir Mamedov, Lala Zeynalova, Nina Ladokhina, Recep Tas, Burak Tuzun, Afsun Sujayev, Nastaran Sadeghian, Saleh H. Alwasel & Ilhami Gulcin
Pages: 3336-3346
Published online: 15 May 2020
AbstractforThe biological activities, molecular docking studies, and anticancer effects of 1-arylsuphonylpyrazole derivatives | Full Text | References | PDF (2.7 MB) | EPUB
  • 1279 Views
  • 36 CrossRef citations
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Article
An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study
Sourav Das, Sharat Sarmah, Sona Lyndem & Atanu Singha Roy
Pages: 3347-3357
Published online: 13 May 2020
AbstractforAn investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 12411 Views
  • 224 CrossRef citations
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Article
Analysis of the interaction behavior between Nano-Curcumin and two human serum proteins: combining spectroscopy and molecular stimulation to understand protein-protein interaction
Parisa Mokaberi, Fatemeh Babayan-Mashhadi, Zeinab Amiri Tehrani Zadeh, Mohammad Reza Saberi & Jamshidkhan Chamani
Pages: 3358-3377
Published online: 20 May 2020
AbstractforAnalysis of the interaction behavior between Nano-Curcumin and two human serum proteins: combining spectroscopy and molecular stimulation to understand protein-protein interaction | Full Text | References | PDF (5.4 MB) | EPUB | Supplemental
  • 804 Views
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Article
Identification of novel antiplasmodial compound by hierarquical virtual screening and in vitro assays
David Bacelar Costa Júnior, Janay Stefany Carneiro Araújo, Larissa de Mattos Oliveira, Flávio Simas Moreira Neri, Paulo Otávio Lourenço Moreira, Alex Gutterres Taranto, Amanda Luisa Fonseca, Fernando de Pilla Varotti & Franco Henrique Andrade Leite
Pages: 3378-3386
Published online: 13 May 2020
AbstractforIdentification of novel antiplasmodial compound by hierarquical virtual screening and in vitro assays | Full Text | References | PDF (1.5 MB) | EPUB
  • 172 Views
  • 4 CrossRef citations
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Article
Using integrated computational approaches to identify safe and rapid treatment for SARS-CoV-2
Khattab Al-Khafaji, Dunya AL-Duhaidahawi & Tugba Taskin Tok
Pages: 3387-3395
Published online: 15 May 2020
AbstractforUsing integrated computational approaches to identify safe and rapid treatment for SARS-CoV-2 | Full Text | References | PDF (2 MB) | EPUB
  • 5541 Views
  • 92 CrossRef citations
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Article
Potential inhibitors of coronavirus 3-chymotrypsin-like protease (3CLpro): an in silico screening of alkaloids and terpenoids from African medicinal plants
Gideon A. Gyebi, Olalekan B. Ogunro, Adegbenro P. Adegunloye, Oludare M. Ogunyemi & Saheed O. Afolabi
Pages: 3396-3408
Published online: 18 May 2020
AbstractforPotential inhibitors of coronavirus 3-chymotrypsin-like protease (3CLpro): an in silico screening of alkaloids and terpenoids from African medicinal plants | Full Text | References | PDF (2.9 MB) | EPUB
  • 8069 Views
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Review Article

Review Article
Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment
Subramanian Boopathi, Adolfo B. Poma & Ponmalai Kolandaivel
Pages: 3409-3418
Published online: 30 Apr 2020
AbstractforNovel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 54254 Views
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Hypothesis Paper

Article
FDA-approved thiol-reacting drugs that potentially bind into the SARS-CoV-2 main protease, essential for viral replication
Naún Lobo-Galo, Manuel Terrazas-López, Alejandro Martínez-Martínez & Ángel Gabriel Díaz-Sánchez
Pages: 3419-3427
Published online: 14 May 2020
AbstractforFDA-approved thiol-reacting drugs that potentially bind into the SARS-CoV-2 main protease, essential for viral replication | Full Text | References | PDF (2.2 MB) | EPUB
  • 7624 Views
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Express Communication

Article
Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target
Umesh  , Debanjan Kundu, Chandrabose Selvaraj, Sanjeev Kumar Singh & Vikash Kumar Dubey
Pages: 3428-3434
Published online: 13 May 2020
AbstractforIdentification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 6993 Views
  • 105 CrossRef citations
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