Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 17 (2021)

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Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 17 (2021)

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Research Articles

Article
Designing novel inhibitors against cyclopropane mycolic acid synthase 3 (PcaA): targeting dormant state of Mycobacterium tuberculosis
Jyoti Verma & Naidu Subbarao
Pages: 6339-6354
Published online: 27 Jul 2020
AbstractforDesigning novel inhibitors against cyclopropane mycolic acid synthase 3 (PcaA): targeting dormant state of Mycobacterium tuberculosis | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 357 Views
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Article
Molecular modeling studies of novel naphthyridine and isoquinoline derivatives as CDK8 inhibitors
Qunlin Li, Kairui Feng, Jianxin Liu & Yujie Ren
Pages: 6355-6369
Published online: 28 Jul 2020
AbstractforMolecular modeling studies of novel naphthyridine and isoquinoline derivatives as CDK8 inhibitors | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 283 Views
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Article
Molecular crowding and conserved interface interactions of human argonaute protein-miRNA-target mRNA complex
Dheeraj Chitara, Richa Anand & B. S. Sanjeev
Pages: 6370-6383
Published online: 05 Aug 2020
AbstractforMolecular crowding and conserved interface interactions of human argonaute protein-miRNA-target mRNA complex | Full Text | References | PDF (3.7 MB) | EPUB
  • 190 Views
  • 1 CrossRef citations
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Article
Experimental and theoretical investigations on the interaction of glucose molecules with myoglobin in the aqueous solution using theoretical and experimental methods
Rasoul Eslami-Farsani, Behzad Shareghi, Sadegh Farhadian & Lida Momeni
Pages: 6384-6395
Published online: 10 Aug 2020
AbstractforExperimental and theoretical investigations on the interaction of glucose molecules with myoglobin in the aqueous solution using theoretical and experimental methods | Full Text | References | PDF (2.3 MB) | EPUB
  • 221 Views
  • 11 CrossRef citations
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Article
Homology modeling and in silico design of novel and potential dual-acting inhibitors of human histone deacetylases HDAC5 and HDAC9 isozymes
Ammar D. Elmezayen & Kemal Yelekçi
Pages: 6396-6414
Published online: 27 Jul 2020
AbstractforHomology modeling and in silico design of novel and potential dual-acting inhibitors of human histone deacetylases HDAC5 and HDAC9 isozymes | Full Text | References | PDF (5.6 MB) | EPUB | Supplemental
  • 472 Views
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Article
Shear-induced aggregation of amyloid β (1–40) in a parallel plate geometry
Laipubam Gayatri Sharma & Lalit M. Pandey
Pages: 6415-6423
Published online: 27 Jul 2020
AbstractforShear-induced aggregation of amyloid β (1–40) in a parallel plate geometry | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 668 Views
  • 7 CrossRef citations
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Article
Inhibitory effects of curcumin on aldose reductase and cyclooxygenase-2 enzymes
Mahmoud Mirzaei, Kun Harismah, Mehdi Soleimani & Sarah Mousavi
Pages: 6424-6430
Published online: 31 Jul 2020
AbstractforInhibitory effects of curcumin on aldose reductase and cyclooxygenase-2 enzymes | Full Text | References | PDF (1.1 MB) | EPUB | Supplemental
  • 221 Views
  • 15 CrossRef citations
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Article
An investigation into the allosteric mechanism of GPCR A2A adenosine receptor with trajectory-based information theory and complex network model
Qiankun Wang, Shan Zhang, Zhongjie Han, Huifang Fan & Chunhua Li
Pages: 6431-6439
Published online: 03 Aug 2020
AbstractforAn investigation into the allosteric mechanism of GPCR A2A adenosine receptor with trajectory-based information theory and complex network model | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 300 Views
  • 1 CrossRef citations
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Article
Molecular basis for the inhibitory effects of 5-hydroxycyclopenicillone on the conformational transition of Aβ40 monomer
Huitu Zhang, Jingcheng Sang, Li Li, Luying Jiang, Fuping Lu, Shan He, Wei Cui, Xiaoqing Zhang & Fufeng Liu
Pages: 6440-6451
Published online: 29 Jul 2020
AbstractforMolecular basis for the inhibitory effects of 5-hydroxycyclopenicillone on the conformational transition of Aβ40 monomer | Full Text | References | PDF (3.2 MB) | EPUB
  • 118 Views
  • 2 CrossRef citations
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Article
Valorisation of stachysetin from cultivated Stachys iva Griseb. as anti-diabetic agent: a multi-spectroscopic and molecular docking approach
Aristeidis Pritsas, Ekaterina-Michaela Tomou, Eleni Tsitsigianni, Christina D. Papaemmanouil, Dimitrios A. Diamantis, Paschalina Chatzopoulou, Andreas G. Tzakos & Helen Skaltsa
Pages: 6452-6466
Published online: 31 Jul 2020
AbstractforValorisation of stachysetin from cultivated Stachys iva Griseb. as anti-diabetic agent: a multi-spectroscopic and molecular docking approach | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 283 Views
  • 8 CrossRef citations
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Article
In silico drug design and molecular docking studies targeting Akt1 (RAC-alpha serine/threonine-protein kinase) and Akt2 (RAC-beta serine/threonine-protein kinase) proteins and investigation of CYP (cytochrome P450) inhibitors against MAOB (monoamine oxidase B) for OSCC (oral squamous cell carcinoma) treatment
Mohammad Kawsar Sharif Siam, Anusree Sarker & Mohammad Manzur Sharif Sayeem
Pages: 6467-6479
Published online: 04 Aug 2020
AbstractforIn silico drug design and molecular docking studies targeting Akt1 (RAC-alpha serine/threonine-protein kinase) and Akt2 (RAC-beta serine/threonine-protein kinase) proteins and investigation of CYP (cytochrome P450) inhibitors against MAOB (monoamine oxidase B) for OSCC (oral squamous cell carcinoma) treatment | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 545 Views
  • 13 CrossRef citations
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Article
Synthesis, characterization, powder X-ray diffraction analysis, thermal stability, antioxidant properties and enzyme inhibitions of M(II)-Schiff base ligand complexes
Kenan Buldurun, Nevin Turan, Ercan Bursal, Abdulmelik Aras, Asim Mantarcı, Naki Çolak, Fikret Türkan & İlhami Gülçin
Pages: 6480-6487
Published online: 05 Aug 2020
AbstractforSynthesis, characterization, powder X-ray diffraction analysis, thermal stability, antioxidant properties and enzyme inhibitions of M(II)-Schiff base ligand complexes | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 895 Views
  • 16 CrossRef citations
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Article
Density functional theory, molecular docking and in vivo muscle relaxant, sedative, and analgesic studies of indanone derivatives isolated from Heterophragma adenophyllum
Abdullah S. M. Aljohani, Tareq Abu-Izneid, Zafar Ali Shah, Umer Rashid, Khurshid Ayub, Abdur Rauf, Naveed Muhammad, Fahad A. Alhumaydhi, Maria Asghar, Mohammad S. Mubarak, Mohammad Ali Shariati & Haiyuan Zhang
Pages: 6488-6499
Published online: 05 Aug 2020
AbstractforDensity functional theory, molecular docking and in vivo muscle relaxant, sedative, and analgesic studies of indanone derivatives isolated from Heterophragma adenophyllum | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 197 Views
  • 3 CrossRef citations
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Article
Spectroscopic, SOD, anticancer, antimicrobial, molecular docking and DNA binding properties of bioactive VO(IV), Cu(II), Zn(II), Co(II), Mn(II) and Ni(II) complexes obtained from 3-(2-hydroxy-3-methoxybenzylidene)pentane-2,4-dione
A. Sakthivel, B Thangagiri, N. Raman, J. Joseph, Ramu Guda, Mamatha Kasula & L. Mitu
Pages: 6500-6514
Published online: 14 Aug 2020
AbstractforSpectroscopic, SOD, anticancer, antimicrobial, molecular docking and DNA binding properties of bioactive VO(IV), Cu(II), Zn(II), Co(II), Mn(II) and Ni(II) complexes obtained from 3-(2-hydroxy-3-methoxybenzylidene)pentane-2,4-dione | Full Text | References | PDF (2.6 MB) | EPUB
  • 299 Views
  • 8 CrossRef citations
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Article
The impact of some phenolic compounds on serum acetylcholinesterase: kinetic analysis of an enzyme/inhibitor interaction and molecular docking study
Mesut Işık & Şükrü Beydemir
Pages: 6515-6523
Published online: 04 Aug 2020
AbstractforThe impact of some phenolic compounds on serum acetylcholinesterase: kinetic analysis of an enzyme/inhibitor interaction and molecular docking study | Full Text | References | PDF (1.7 MB) | EPUB
  • 493 Views
  • 9 CrossRef citations
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Article
Molecular dynamics simulation for screening phytochemicals as α-amylase inhibitors from medicinal plants
Priyanka Sharma, Tushar Joshi, Tanuja Joshi, Subhash Chandra & Sushma Tamta
Pages: 6524-6538
Published online: 04 Aug 2020
AbstractforMolecular dynamics simulation for screening phytochemicals as α-amylase inhibitors from medicinal plants | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 627 Views
  • 19 CrossRef citations
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Article
Understanding the structure, stability, and anti-sigma factor-binding thermodynamics of an anti-anti-sigma factor from Staphylococcus aureus
Debabrata Sinha, Tushar Chakraborty, Debasmita Sinha, Asim Poddar, Rajagopal Chattopadhyaya & Subrata Sau
Pages: 6539-6552
Published online: 05 Aug 2020
AbstractforUnderstanding the structure, stability, and anti-sigma factor-binding thermodynamics of an anti-anti-sigma factor from Staphylococcus aureus | Full Text | References | PDF (3 MB) | EPUB
  • 235 Views
  • 2 CrossRef citations
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Article
A comprehensive in silico exploration of pharmacological properties, bioactivities and COX-2 inhibitory potential of eleutheroside B from Eleutherococcus senticosus (Rupr. & Maxim.) Maxim.
Sium Ahmed, Dil Afroj Moni, Kailas Dashrath Sonawane, Kee Yoeup Paek & Abdullah Mohammad Shohael
Pages: 6553-6566
Published online: 06 Aug 2020
AbstractforA comprehensive in silico exploration of pharmacological properties, bioactivities and COX-2 inhibitory potential of eleutheroside B from Eleutherococcus senticosus (Rupr. & Maxim.) Maxim. | Full Text | References | PDF (2.1 MB) | EPUB
  • 349 Views
  • 16 CrossRef citations
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Article
A self-assembled polymer therapeutic for simultaneously enhancing solubility and antimicrobial activity and lowering serum albumin binding of fusidic acid
Mohammed Salih, Pavan Walvekar, Calvin A. Omolo, Ahmed A. Elrashedy, Nikita Devnarain, Victoria Fasiku, Ayman Y. Waddad, Chunderika Mocktar & Thirumala Govender
Pages: 6567-6584
Published online: 08 Aug 2020
AbstractforA self-assembled polymer therapeutic for simultaneously enhancing solubility and antimicrobial activity and lowering serum albumin binding of fusidic acid | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 409 Views
  • 1 CrossRef citations
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Article
Designing novel epitope-based polyvalent vaccines against herpes simplex virus-1 and 2 exploiting the immunoinformatics approach
Bishajit Sarkar, Md. Asad Ullah, Yusha Araf, Sowmen Das, Md. Hasanur Rahman & Abu Tayab Moin
Pages: 6585-6605
Published online: 07 Aug 2020
AbstractforDesigning novel epitope-based polyvalent vaccines against herpes simplex virus-1 and 2 exploiting the immunoinformatics approach | Full Text | References | PDF (4.7 MB) | EPUB | Supplemental
  • 312 Views
  • 12 CrossRef citations
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Article
Curcumin–silica nanocomplex preparation, hemoglobin and DNA interaction and photocytotoxicity against melanoma cancer cells
Mehrgan Ghazaeian, Khatereh Khorsandi, Reza Hosseinzadeh, Asieh Naderi & Heidi Abrahamse
Pages: 6606-6616
Published online: 07 Aug 2020
AbstractforCurcumin–silica nanocomplex preparation, hemoglobin and DNA interaction and photocytotoxicity against melanoma cancer cells | Full Text | References | PDF (2.9 MB) | EPUB
  • 356 Views
  • 6 CrossRef citations
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Article
Virtual screening, ADMET prediction and dynamics simulation of potential compounds targeting the main protease of SARS-CoV-2
Rohitash Yadav, Mohammed Imran, Puneet Dhamija, Dheeraj Kumar Chaurasia & Shailendra Handu
Pages: 6617-6632
Published online: 25 Jul 2020
AbstractforVirtual screening, ADMET prediction and dynamics simulation of potential compounds targeting the main protease of SARS-CoV-2 | Full Text | References | PDF (3.3 MB) | EPUB
  • 3122 Views
  • 20 CrossRef citations
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Article
Identification of a potential SARS-CoV2 inhibitor via molecular dynamics simulations and amino acid decomposition analysis
Nima Razzaghi-Asl, Ahmad Ebadi, Sara Shahabipour & Danial Gholamin
Pages: 6633-6648
Published online: 24 Jul 2020
AbstractforIdentification of a potential SARS-CoV2 inhibitor via molecular dynamics simulations and amino acid decomposition analysis | Full Text | References | PDF (3.5 MB) | EPUB
  • 2365 Views
  • 13 CrossRef citations
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Article
Identification of potential drug candidates to combat COVID-19: a structural study using the main protease (mpro) of SARS-CoV-2
Pradeep Sharma, Viswanathan Vijayan, Pradeep Pant, Mohita Sharma, Naval Vikram, Punit Kaur, T. P. Singh & Sujata Sharma
Pages: 6649-6659
Published online: 03 Aug 2020
AbstractforIdentification of potential drug candidates to combat COVID-19: a structural study using the main protease (mpro) of SARS-CoV-2 | Full Text | References | PDF (2.9 MB) | EPUB
  • 3033 Views
  • 13 CrossRef citations
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Article
Identification of potential anti-TMPRSS2 natural products through homology modelling, virtual screening and molecular dynamics simulation studies
Rupesh V. Chikhale, Vivek K. Gupta, Gaber E. Eldesoky, Saikh M. Wabaidur, Shripad A. Patil & Md Ataul Islam
Pages: 6660-6675
Published online: 03 Aug 2020
AbstractforIdentification of potential anti-TMPRSS2 natural products through homology modelling, virtual screening and molecular dynamics simulation studies | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 5328 Views
  • 30 CrossRef citations
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Article
Antiviral potential of some novel structural analogs of standard drugs repurposed for the treatment of COVID-19
Mohamed F. AlAjmi, Asim Azhar, Mohd Owais, Summya Rashid, Sadaf Hasan, Afzal Hussain & Md Tabish Rehman
Pages: 6676-6688
Published online: 30 Jul 2020
AbstractforAntiviral potential of some novel structural analogs of standard drugs repurposed for the treatment of COVID-19 | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 1969 Views
  • 15 CrossRef citations
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Article
Tackling COVID-19: identification of potential main protease inhibitors via structural analysis, virtual screening, molecular docking and MM-PBSA calculations
Nizar A. Al-Shar’i
Pages: 6689-6704
Published online: 31 Jul 2020
AbstractforTackling COVID-19: identification of potential main protease inhibitors via structural analysis, virtual screening, molecular docking and MM-PBSA calculations | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 2165 Views
  • 7 CrossRef citations
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Article
Deciphering the protein motion of S1 subunit in SARS-CoV-2 spike glycoprotein through integrated computational methods
Hao Tian & Peng Tao
Pages: 6705-6712
Published online: 04 Aug 2020
AbstractforDeciphering the protein motion of S1 subunit in SARS-CoV-2 spike glycoprotein through integrated computational methods | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 1479 Views
  • 8 CrossRef citations
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Article
Identification of promising drug candidates against NSP16 of SARS-CoV-2 through computational drug repurposing study
Viswanathan Vijayan, Pradeep Pant, Naval Vikram, Punit Kaur, T. P. Singh, Sujata Sharma & Pradeep Sharma
Pages: 6713-6727
Published online: 03 Aug 2020
AbstractforIdentification of promising drug candidates against NSP16 of SARS-CoV-2 through computational drug repurposing study | Full Text | References | PDF (4.2 MB) | EPUB
  • 2719 Views
  • 11 CrossRef citations
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Article
Predictive modeling by deep learning, virtual screening and molecular dynamics study of natural compounds against SARS-CoV-2 main protease
Tanuja Joshi, Tushar Joshi, Hemlata Pundir, Priyanka Sharma, Shalini Mathpal & Subhash Chandra
Pages: 6728-6746
Published online: 05 Aug 2020
AbstractforPredictive modeling by deep learning, virtual screening and molecular dynamics study of natural compounds against SARS-CoV-2 main protease | Full Text | References | PDF (4.8 MB) | EPUB
  • 2848 Views
  • 20 CrossRef citations
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Article
Identification of polyphenols from Broussonetia papyrifera as SARS CoV-2 main protease inhibitors using in silico docking and molecular dynamics simulation approaches
Rajesh Ghosh, Ayon Chakraborty, Ashis Biswas & Snehasis Chowdhuri
Pages: 6747-6760
Published online: 07 Aug 2020
AbstractforIdentification of polyphenols from Broussonetia papyrifera as SARS CoV-2 main protease inhibitors using in silico docking and molecular dynamics simulation approaches | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 2976 Views
  • 34 CrossRef citations
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Article
In silico virtual screening, characterization, docking and molecular dynamics studies of crucial SARS-CoV-2 proteins
Meshari Alazmi & Olaa Motwalli
Pages: 6761-6771
Published online: 07 Aug 2020
AbstractforIn silico virtual screening, characterization, docking and molecular dynamics studies of crucial SARS-CoV-2 proteins | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 4578 Views
  • 30 CrossRef citations
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Article
In silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials
Seref Gul, Onur Ozcan, Sinan Asar, Alper Okyar, Ibrahim Barıs & Ibrahim Halil Kavakli
Pages: 6772-6791
Published online: 05 Aug 2020
AbstractforIn silico identification of widely used and well-tolerated drugs as potential SARS-CoV-2 3C-like protease and viral RNA-dependent RNA polymerase inhibitors for direct use in clinical trials | Full Text | References | PDF (5.1 MB) | EPUB | Supplemental
  • 4570 Views
  • 27 CrossRef citations
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Article
In silico investigation of phytoconstituents from Indian medicinal herb ‘Tinospora cordifolia (giloy)’ against SARS-CoV-2 (COVID-19) by molecular dynamics approach
Papia Chowdhury
Pages: 6792-6809
Published online: 07 Aug 2020
AbstractforIn silico investigation of phytoconstituents from Indian medicinal herb ‘Tinospora cordifolia (giloy)’ against SARS-CoV-2 (COVID-19) by molecular dynamics approach | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 7492 Views
  • 59 CrossRef citations
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Article
Protein reliability analysis and virtual screening of natural inhibitors for SARS-CoV-2 main protease (Mpro) through docking, molecular mechanic & dynamic, and ADMET profiling
Karina Kapusta, Supratik Kar, Jasmine T. Collins, Latasha M. Franklin, Wojciech Kolodziejczyk, Jerzy Leszczynski & Glake A. Hill
Pages: 6810-6827
Published online: 14 Aug 2020
AbstractforProtein reliability analysis and virtual screening of natural inhibitors for SARS-CoV-2 main protease (Mpro) through docking, molecular mechanic & dynamic, and ADMET profiling | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
  • 2689 Views
  • 17 CrossRef citations
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Review Articles

Review Article
Current status and strategic possibilities on potential use of combinational drug therapy against COVID-19 caused by SARS-CoV-2
Arif Jamal Siddiqui, Sadaf Jahan, Syed Amir Ashraf, Mousa Alreshidi, Mohammad Saquib Ashraf, Mitesh Patel, Mejdi Snoussi, Ritu Singh & Mohd Adnan
Pages: 6828-6841
Published online: 05 Aug 2020
AbstractforCurrent status and strategic possibilities on potential use of combinational drug therapy against COVID-19 caused by SARS-CoV-2 | Full Text | References | PDF (2.2 MB) | EPUB
  • 4827 Views
  • 22 CrossRef citations
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Review Article
Acute respiratory distress syndrome: a life threatening associated complication of SARS-CoV-2 infection inducing COVID-19
Riadh Badraoui, Mousa M. Alrashedi, Michèle Véronique El-May & Fevzi Bardakci
Pages: 6842-6851
Published online: 05 Aug 2020
AbstractforAcute respiratory distress syndrome: a life threatening associated complication of SARS-CoV-2 infection inducing COVID-19 | Full Text | References | PDF (1.3 MB) | EPUB
  • 2780 Views
  • 25 CrossRef citations
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