Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 7 (2022)

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Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 7 (2022)

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Research Articles

Article
Synthesis, anticancer evaluation and molecular docking studies of methotrexate’s novel Schiff base derivatives against malignant glioma cell lines
Aifa Nemat, Ishaq N. Khan, Saima Kalsoom, Shoaib Ahmad Malik, Shahid Ayub, Fazal Adnan, Mohammad Amjad Kamal & Mudassir Iqbal
Pages: 2865-2877
Published online: 13 Nov 2020
AbstractforSynthesis, anticancer evaluation and molecular docking studies of methotrexate’s novel Schiff base derivatives against malignant glioma cell lines | Full Text | References | PDF (4 MB) | EPUB
  • 506 Views
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Article
Drug repurposing for Alzheimer’s disease: in silico and in vitro investigation of FDA-approved drugs as acetylcholinesterase inhibitors
Navneet Kumar, Anuj Gahlawat, Rajaram Naresh Kumar, Yash Pal Singh, Gyan Modi & Prabha Garg
Pages: 2878-2892
Published online: 10 Nov 2020
AbstractforDrug repurposing for Alzheimer’s disease: in silico and in vitro investigation of FDA-approved drugs as acetylcholinesterase inhibitors | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 1209 Views
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Article
Integrated computational approach toward discovery of multi-targeted natural products from Thumbai (Leucas aspera) for attuning NKT cells
Vishwa Jyoti Baruah, Rasana Paul, Dhrubajyoti Gogoi, Nirmal Mazumder, Subrata Chakraborty, Aparoopa Das, Tapan Kumar Mondal & Bhaswati Sarmah
Pages: 2893-2907
Published online: 12 Nov 2020
AbstractforIntegrated computational approach toward discovery of multi-targeted natural products from Thumbai (Leucas aspera) for attuning NKT cells | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
  • 366 Views
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Article
Investigation of binding characteristics of ritonavir with calf thymus DNA with the help of spectroscopic techniques and molecular simulation
Song-Bo Kou, Kai-Li Zhou, Zhen-Yi Lin, Yan-Yue Lou, Bao-Li Wang, Jie-Hua Shi & Ying-Xin Liu
Pages: 2908-2916
Published online: 08 Nov 2020
AbstractforInvestigation of binding characteristics of ritonavir with calf thymus DNA with the help of spectroscopic techniques and molecular simulation | Full Text | References | PDF (1.9 MB) | EPUB
  • 166 Views
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Article
Multi-epitope vaccine against SARS-CoV-2 applying immunoinformatics and molecular dynamics simulation approaches
Jyotisha , Samayaditya Singh & Insaf Ahmed Qureshi
Pages: 2917-2933
Published online: 09 Nov 2020
AbstractforMulti-epitope vaccine against SARS-CoV-2 applying immunoinformatics and molecular dynamics simulation approaches | Full Text | References | PDF (3.7 MB) | EPUB
  • 3113 Views
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Article
Weak spots inhibition in the Mycobacterium tuberculosis antigen 85C target for antitubercular drug design through selective irreversible covalent inhibitor-SER124
Adeniyi T. Adewumi, Ahmed Elrashedy, Opeyemi S. Soremekun, Mary B. Ajadi & Mahmoud E. S. Soliman
Pages: 2934-2954
Published online: 06 Nov 2020
AbstractforWeak spots inhibition in the Mycobacterium tuberculosis antigen 85C target for antitubercular drug design through selective irreversible covalent inhibitor-SER124 | Full Text | References | PDF (8.8 MB) | EPUB
  • 295 Views
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Article
Methionine 58 is a key residue in the modulation of BmK scorpion toxin AGP-SYPU2 activity through in silico and in vivo studies
Yong Cui, Ting Wang, Zhihui Hao, Jinghai Zhang & Yongshan Zhao
Pages: 2955-2962
Published online: 23 Nov 2020
AbstractforMethionine 58 is a key residue in the modulation of BmK scorpion toxin AGP-SYPU2 activity through in silico and in vivo studies | Full Text | References | PDF (1.5 MB) | EPUB
  • 98 Views
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Article
Design of a multi-epitope-based vaccine targeting M-protein of SARS-CoV2: an immunoinformatics approach
Vijaya Sai Ayyagari, Venkateswarulu T. C.Abraham Peele K.Krupanidhi Srirama
Pages: 2963-2977
Published online: 30 Nov 2020
AbstractforDesign of a multi-epitope-based vaccine targeting M-protein of SARS-CoV2: an immunoinformatics approach | Full Text | References | PDF (3.5 MB) | EPUB
  • 3185 Views
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Article
Probing the dual inhibitory mechanisms of novel thiophenecarboxamide derivatives against Mycobacterium tuberculosis PyrG and PanK: an insight from biomolecular modeling study
Murtala A. Ejalonibu, Ahmed A. Elrashedy, Monsurat M. Lawal, Hezekiel M. Kumalo & Ndumiso N. Mhlongo
Pages: 2978-2990
Published online: 06 Nov 2020
AbstractforProbing the dual inhibitory mechanisms of novel thiophenecarboxamide derivatives against Mycobacterium tuberculosis PyrG and PanK: an insight from biomolecular modeling study | Full Text | References | PDF (4.7 MB) | EPUB
  • 287 Views
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Article
Metal contained Phthalocyanines with 3,4-Dimethoxyphenethoxy substituents: their anticancer, antibacterial activities and their inhibitory effects on some metabolic enzymes with molecular docking studies
Parham Taslimi, Fikret Türkan, Derya Güngördü Solğun, Abdülmelik Aras, Yavuz Erden, Hasan Ufuk Celebioglu, Burak Tuzun, Mehmet Salih Ağırtaş, Sevilay Günay & Ilhami Gulcin
Pages: 2991-3002
Published online: 24 Nov 2020
AbstractforMetal contained Phthalocyanines with 3,4-Dimethoxyphenethoxy substituents: their anticancer, antibacterial activities and their inhibitory effects on some metabolic enzymes with molecular docking studies | Full Text | References | PDF (3.2 MB) | EPUB
  • 608 Views
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Article
In-silico drug repurposing for targeting SARS-CoV-2 main protease (Mpro)
Shilpa Sharma & Shashank Deep
Pages: 3003-3010
Published online: 12 Nov 2020
AbstractforIn-silico drug repurposing for targeting SARS-CoV-2 main protease (Mpro) | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 2021 Views
  • 18 CrossRef citations
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Article
Structural mechanism of the Tanford transition of bovine β-lactoglobulin through microsecond molecular dynamics simulations
Martiniano Bello
Pages: 3011-3023
Published online: 06 Nov 2020
AbstractforStructural mechanism of the Tanford transition of bovine β-lactoglobulin through microsecond molecular dynamics simulations | Full Text | References | PDF (5.1 MB) | EPUB | Supplemental
  • 257 Views
  • 3 CrossRef citations
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Article
Molecular modeling, docking and dynamic simulations of growth hormone receptor (GHR) of Labeo rohita
Bhushan C. Dhandare, Mohd Ashraf Rather, B. P. Bhosale, Ravindra Pawar, Praveen Kumar Guttula & A.U Pagarkar
Pages: 3024-3037
Published online: 12 Nov 2020
AbstractforMolecular modeling, docking and dynamic simulations of growth hormone receptor (GHR) of Labeo rohita | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 265 Views
  • 8 CrossRef citations
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Article
A new molecular mechanism of RNA circularization and the microRNA sponge formation
Agnieszka Belter, Mariusz Popenda, Marcin Sajek, Tomasz Woźniak, Mirosława Z. Naskręt-Barciszewska, Marta Szachniuk, Stefan Jurga & Jan Barciszewski
Pages: 3038-3045
Published online: 17 Nov 2020
AbstractforA new molecular mechanism of RNA circularization and the microRNA sponge formation | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 1931 Views
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Open Access
Article
p38α MAP kinase inhibitors to overcome EGFR tertiary C797S point mutation associated with osimertinib in non-small cell lung cancer (NSCLC): emergence of fourth-generation EGFR inhibitor
Iqrar Ahmad, Matin Shaikh, Sanjay Surana, Arabinda Ghosh & Harun Patel
Pages: 3046-3059
Published online: 11 Nov 2020
Abstractforp38α MAP kinase inhibitors to overcome EGFR tertiary C797S point mutation associated with osimertinib in non-small cell lung cancer (NSCLC): emergence of fourth-generation EGFR inhibitor | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 472 Views
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Article
Discovery of new promising USP14 inhibitors: computational evaluation of the thumb-palm pocket
Niyi Adelakun, Ikponwmosa Obaseki, Ayobami Adeniyi, Oluwaseun Fapohunda, Eseiwi Obaseki & Olaposi Omotuyi
Pages: 3060-3070
Published online: 10 Nov 2020
AbstractforDiscovery of new promising USP14 inhibitors: computational evaluation of the thumb-palm pocket | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 451 Views
  • 7 CrossRef citations
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Article
Computational investigation of binding of chloroquinone and hydroxychloroquinone against PLPro of SARS-CoV-2
Dhaval Patel, Mohd Athar & P. C Jha
Pages: 3071-3081
Published online: 17 Nov 2020
AbstractforComputational investigation of binding of chloroquinone and hydroxychloroquinone against PLPro of SARS-CoV-2 | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 1590 Views
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Article
LRH-1 (liver receptor homolog-1) derived affinity peptide ligand to inhibit interactions between β-catenin and LRH-1 in pancreatic cancer cells: from computational design to experimental validation
Khadijeh Pouraghajan, Hamid Mahdiuni, Sirous Ghobadi & Reza Khodarahmi
Pages: 3082-3097
Published online: 13 Nov 2020
AbstractforLRH-1 (liver receptor homolog-1) derived affinity peptide ligand to inhibit interactions between β-catenin and LRH-1 in pancreatic cancer cells: from computational design to experimental validation | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 284 Views
  • 6 CrossRef citations
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Article
Development of multi-epitope subunit vaccine for protection against the norovirus’ infections based on computational vaccinology
Irfan Ahmad, Syed Shujait Ali, Bisma Zafar, Huma Farooque Hashmi, Ismail Shah, Shahzeb Khan, Muhammad Suleman, Mazhar Khan, Saif Ullah, Shahid Ali, Jafar Khan, Mohammad Ali, Abbas Khan & Dong-Qing Wei
Pages: 3098-3109
Published online: 10 Nov 2020
AbstractforDevelopment of multi-epitope subunit vaccine for protection against the norovirus’ infections based on computational vaccinology | Full Text | References | PDF (2.6 MB) | EPUB
  • 397 Views
  • 8 CrossRef citations
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Article
Determination of potential inhibitors based on isatin derivatives against SARS-CoV-2 main protease (mpro): a molecular docking, molecular dynamics and structure-activity relationship studies
Vishnu Nayak Badavath, Akhil Kumar, Pralok K. Samanta, Siddhartha Maji, Anik Das, Galia Blum, Anjali Jha & Anik Sen
Pages: 3110-3128
Published online: 17 Nov 2020
AbstractforDetermination of potential inhibitors based on isatin derivatives against SARS-CoV-2 main protease (mpro): a molecular docking, molecular dynamics and structure-activity relationship studies | Full Text | References | PDF (4.7 MB) | EPUB | Supplemental
  • 3443 Views
  • 25 CrossRef citations
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Article
Nanobodies: an unexplored opportunity to combat COVID-19
Sayeh Ezzikouri, Jalal Nourlil, Kyoko Tsukiyama-Kohara, Michinori Kohara, Hicham El Ossmani, Marc P. Windisch & Soumaya Benjelloun
Pages: 3129-3131
Published online: 10 Nov 2020
AbstractforNanobodies: an unexplored opportunity to combat COVID-19 | Full Text | References | PDF (1 MB) | EPUB
  • 2307 Views
  • 2 CrossRef citations
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Article
Molecular dynamic study on PTEN frameshift mutations in breast cancer provide c2 domain as a potential biomarker
Rohit Karn & Isaac Arnold Emerson
Pages: 3132-3143
Published online: 13 Nov 2020
AbstractforMolecular dynamic study on PTEN frameshift mutations in breast cancer provide c2 domain as a potential biomarker | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 181 Views
  • 3 CrossRef citations
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Article
Design and development of 5-(4H)-oxazolones as potential inhibitors of human carbonic anhydrase VA: towards therapeutic management of diabetes and obesity
Amarjyoti Das Mahapatra, Aarfa Queen, Mohd Yousuf, Parvez Khan, Afzal Hussain, Md. Tabish Rehman, Mohamed F. Alajmi, Bhaskar Datta & Md. Imtaiyaz Hassan
Pages: 3144-3154
Published online: 13 Nov 2020
AbstractforDesign and development of 5-(4H)-oxazolones as potential inhibitors of human carbonic anhydrase VA: towards therapeutic management of diabetes and obesity | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 271 Views
  • 5 CrossRef citations
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Article
In silico screening and molecular dynamics of phytochemicals from Indian cuisine against SARS-CoV-2 MPro
Mala Rajendran, Sudeep Roy, Keerthana Ravichandran, Bagdevi Mishra, Deepak K. Gupta, Subash Nagarajan, Ruby Celsia Arul Selvaraj & Ivo Provaznik
Pages: 3155-3169
Published online: 17 Nov 2020
AbstractforIn silico screening and molecular dynamics of phytochemicals from Indian cuisine against SARS-CoV-2 MPro | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 1756 Views
  • 5 CrossRef citations
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Article
Reprofiling of approved drugs against SARS-CoV-2 main protease: an in-silico study
Prateek Kumar, Taniya Bhardwaj, Ankur Kumar, Bhuvaneshwari R. Gehi, Shivani K. Kapuganti, Neha Garg, Gopal Nath & Rajanish Giri
Pages: 3170-3184
Published online: 12 Nov 2020
AbstractforReprofiling of approved drugs against SARS-CoV-2 main protease: an in-silico study | Full Text | References | PDF (4.1 MB) | EPUB
  • 2058 Views
  • 9 CrossRef citations
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Article
Structure-activity relationship, molecular docking, and molecular dynamic studies of diterpenes from marine natural products with anti-HIV activity
N. L. vonRanke, M. M. J. Ribeiro, L. A. Miceli, N. P. de Souza, B. A. Abrahim-Vieira, H. C. Castro, V. L. Teixeira, C. R. Rodrigues & A. M. T. Souza
Pages: 3185-3195
Published online: 13 Nov 2020
AbstractforStructure-activity relationship, molecular docking, and molecular dynamic studies of diterpenes from marine natural products with anti-HIV activity | Full Text | References | PDF (2.6 MB) | EPUB
  • 407 Views
  • 3 CrossRef citations
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Research Article

Article
In silico design of influenza a virus artificial epitope-based T-cell antigens and the evaluation of their immunogenicity in mice
Sergei I. Bazhan, Denis V. Antonets, Ekaterina V. Starostina, Tatyana N. Ilyicheva, Olga N. Kaplina, Vasiliy Yu. Marchenko, Olga Yu. Volkova, Anastasiya Yu. Bakulina & Larisa I. Karpenko
Pages: 3196-3212
Published online: 23 Nov 2020
AbstractforIn silico design of influenza a virus artificial epitope-based T-cell antigens and the evaluation of their immunogenicity in mice | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 501 Views
  • 3 CrossRef citations
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Research Articles

Article
Thiohydantoins as anti-leishmanial agents: n vitro biological evaluation and multi-target investigation by molecular docking studies
Priscila Goes Camargo, Bruna Taciane da Silva Bortoleti, Marcieli Fabris, Manoela Daiele Gonçalves, Fernanda Tomiotto-Pellissier, Idessania Nazareth Costa, Ivete Conchon-Costa, Camilo Henrique da Silva Lima, Wander Rogério Pavanelli, Marcelle de Lima Ferreira Bispo & Fernando Macedo Jr
Pages: 3213-3222
Published online: 13 Nov 2020
AbstractforThiohydantoins as anti-leishmanial agents: n vitro biological evaluation and multi-target investigation by molecular docking studies | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 303 Views
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Article
Molecular evolution, binding site interpretation and functional divergence of aspartate semialdehyde dehydrogenase
Mathimaran Amala, Mariadasse Richard, Poopandi Saritha, Dhamodharan Prabhu, Malaisamy Veerapandiyan, Kangarajan Surekha & Jeyaraman Jeyakanthan
Pages: 3223-3241
Published online: 23 Nov 2020
AbstractforMolecular evolution, binding site interpretation and functional divergence of aspartate semialdehyde dehydrogenase | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
  • 150 Views
  • 1 CrossRef citations
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Article
Molecular modeling approach to identify inhibitors of Rv2004c (rough morphology and virulent strain gene), a DosR (dormancy survival regulator) regulon protein from Mycobacterium tuberculosis
V. G. Shanmuga Priya, Vishwambhar Bhandare, Uday M. Muddapur, Priya Swaminathan, Prayagraj M. Fandilolu & Kailas D. Sonawane
Pages: 3242-3257
Published online: 13 Nov 2020
AbstractforMolecular modeling approach to identify inhibitors of Rv2004c (rough morphology and virulent strain gene), a DosR (dormancy survival regulator) regulon protein from Mycobacterium tuberculosis | Full Text | References | PDF (5.1 MB) | EPUB | Supplemental
  • 214 Views
  • 1 CrossRef citations
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Article
Synthesis and spectroscopic characterizations of hexakis[(1-(4′-oxyphenyl)-3-(substituted-phenyl)prop-2-en-1-one)]cyclotriphosphazenes: their in vitro cytotoxic activity, theoretical analysis and molecular docking studies
Hacer Doğan, Mehmet Refik Bahar, Eray Çalışkan, Suat Tekin, Harun Uslu, Feride Akman, Kenan Koran, Süleyman Sandal & Ahmet Orhan Görgülü
Pages: 3258-3272
Published online: 19 Nov 2020
AbstractforSynthesis and spectroscopic characterizations of hexakis[(1-(4′-oxyphenyl)-3-(substituted-phenyl)prop-2-en-1-one)]cyclotriphosphazenes: their in vitro cytotoxic activity, theoretical analysis and molecular docking studies | Full Text | References | PDF (3.2 MB) | EPUB
  • 761 Views
  • 7 CrossRef citations
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Article
Antimicrobial activity of Plumbago indica and ligand screening of plumbagin against methicillin-resistant Staphylococcus aureus
D. M. I. H. Dissanayake, D. D. B. D. Perera, L. R. Keerthirathna, Saumya Heendeniya, Raymond J. Anderson, David E. Williams & L. Dinithi C. Peiris
Pages: 3273-3284
Published online: 19 Nov 2020
AbstractforAntimicrobial activity of Plumbago indica and ligand screening of plumbagin against methicillin-resistant Staphylococcus aureus | Full Text | References | PDF (1.8 MB) | EPUB
  • 416 Views
  • 12 CrossRef citations
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Article
Modeling and simulation of atrazine biodegradation in bacteria and its effect in other living systems
Pankaj Bhatt, Kanika Sethi, Saurabh Gangola, Geeta Bhandari, Amit Verma, Muhammad Adnan, Yashpal Singh & Shshank Chaube
Pages: 3285-3295
Published online: 12 Nov 2020
AbstractforModeling and simulation of atrazine biodegradation in bacteria and its effect in other living systems | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 663 Views
  • 22 CrossRef citations
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Article
Identification of natural inhibitors against prime targets of SARS-CoV-2 using molecular docking, molecular dynamics simulation and MM-PBSA approaches
Abhilasha Sharma, Jaykant Vora, Dhaval Patel, Sonam Sinha, Prakash C. Jha & Neeta Shrivastava
Pages: 3296-3311
Published online: 13 Nov 2020
AbstractforIdentification of natural inhibitors against prime targets of SARS-CoV-2 using molecular docking, molecular dynamics simulation and MM-PBSA approaches | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 3281 Views
  • 20 CrossRef citations
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Article
Designing a novel multiepitope peptide vaccine against melanoma using immunoinformatics approach
Zahra Yazdani, Alireza Rafiei, Hamid Irannejad, Mohammadreza Yazdani & Reza Valadan
Pages: 3312-3324
Published online: 23 Nov 2020
AbstractforDesigning a novel multiepitope peptide vaccine against melanoma using immunoinformatics approach | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 207 Views
  • 6 CrossRef citations
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Review Article

Review Article
G protein-coupled estrogen receptor-1: homology modeling approaches and application in screening new GPER-1 modulators
Shafi Ullah Khan, Nafees Ahemad, Lay-Hong Chuah, Rakesh Naidu & Thet Thet Htar
Pages: 3325-3335
Published online: 08 Nov 2020
AbstractforG protein-coupled estrogen receptor-1: homology modeling approaches and application in screening new GPER-1 modulators | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 312 Views
  • 4 CrossRef citations
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Letter to the Editor

Letter
SARS-CoV-2 mutations and where to find them: an in silico perspective of structural changes and antigenicity of the spike protein
Ricardo Lemes Gonçalves, Túlio César Rodrigues Leite, Bruna de Paula Dias, Camila Carla da Silva Caetano, Ana Clara Gomes de Souza, Ubiratan da Silva Batista, Camila Cavadas Barbosa, Arturo Reyes-Sandoval, Luiz Felipe Leomil Coelho & Breno de Mello Silva
Pages: 3336-3346
Published online: 06 Nov 2020
AbstractforSARS-CoV-2 mutations and where to find them: an in silico perspective of structural changes and antigenicity of the spike protein | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 964 Views
  • 1 CrossRef citations
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