Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 8 (2022)

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Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 8 (2022)

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Research Articles

Article
Multiple epitope-based vaccine prediction against SARS-CoV-2 spike glycoprotein
Preeti Rana Sirohi, Jyoti Gupta, Pallavi Somvanshi, Vijay Kumar Prajapati & Abhinav Grover
Pages: 3347-3358
Published online: 27 Nov 2020
AbstractforMultiple epitope-based vaccine prediction against SARS-CoV-2 spike glycoprotein | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
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Article
Novel quinazolin–sulfonamid derivatives: synthesis, characterization, biological evaluation, and molecular docking studies
Nima Sepehri, Maryam Mohammadi-Khanaposhtani, Nafise Asemanipoor, Samanesadat Hosseini, Mahmood Biglar, Bagher Larijani, Mohammad Mahdavi, Haleh Hamedifar, Parham Taslimi, Nastaran Sadeghian, Mostafa Norizadehtazehkand & Ilhami Gulcin
Pages: 3359-3370
Published online: 23 Nov 2020
AbstractforNovel quinazolin–sulfonamid derivatives: synthesis, characterization, biological evaluation, and molecular docking studies | Full Text | References | PDF (2.2 MB) | EPUB
  • 508 Views
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Article
In-silico studies on Myo inositol-1-phosphate synthase of Leishmania donovani in search of anti-leishmaniasis
Mousumi Sinha, Rahul Jagadeesan, Neeraj Kumar, Satabdi Saha, Gugan Kothandan & Diwakar Kumar
Pages: 3371-3384
Published online: 17 Nov 2020
AbstractforIn-silico studies on Myo inositol-1-phosphate synthase of Leishmania donovani in search of anti-leishmaniasis | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 464 Views
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Article
Pharmacophore based virtual screening, molecular docking and molecular dynamic simulation studies for finding ROS1 kinase inhibitors as potential drug molecules
Ramar Vanajothi, Hemamalini Vedagiri, Mysoon M. Al-Ansari, Latifah A. Al-Humaid & Premkumar Kumpati
Pages: 3385-3399
Published online: 17 Nov 2020
AbstractforPharmacophore based virtual screening, molecular docking and molecular dynamic simulation studies for finding ROS1 kinase inhibitors as potential drug molecules | Full Text | References | PDF (3.3 MB) | EPUB
  • 258 Views
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Article
Plausible computational insights and new atomic-level perspective of epicathechin gallate from Crataegus oxycantha extract in preventing caspase 3 activation in conditions like post-myocardial infarction
Arul Salomee Kamalabai Ravindran, Sivaramakrishnan Venkatabalasubramanian, Ranjani Manickam, Muthuswamy Anusuyadevi & Jayachandran K. Swaminathan
Pages: 3400-3415
Published online: 17 Nov 2020
AbstractforPlausible computational insights and new atomic-level perspective of epicathechin gallate from Crataegus oxycantha extract in preventing caspase 3 activation in conditions like post-myocardial infarction | Full Text | References | PDF (3.6 MB) | EPUB
  • 142 Views
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Article
Inhibitory potential of repurposed drugs against the SARS-CoV-2 main protease: a computational-aided approach
Adewale Oluwaseun Fadaka, Raphael Taiwo Aruleba, Nicole Remaliah Samantha Sibuyi, Ashwil Klein, Abram Madimabe Madiehe & Mervin Meyer
Pages: 3416-3427
Published online: 17 Nov 2020
AbstractforInhibitory potential of repurposed drugs against the SARS-CoV-2 main protease: a computational-aided approach | Full Text | References | PDF (3.4 MB) | EPUB
  • 1693 Views
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Article
Role of cardiac drugs and flavonoids on the IRE1–JNK pathway as revealed by re-ranked molecular docking scores, MM/PBSA and umbrella sampling
Zekeriya Duzgun & Zuhal Eroglu
Pages: 3428-3450
Published online: 30 Nov 2020
AbstractforRole of cardiac drugs and flavonoids on the IRE1–JNK pathway as revealed by re-ranked molecular docking scores, MM/PBSA and umbrella sampling | Full Text | References | PDF (6.1 MB) | EPUB | Supplemental
  • 342 Views
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Article
Identification of novel human neutrophil elastase inhibitors from dietary phytochemicals using in silico and in vitro studies
Ramachandran Vidhya, Velmurugan Ilavarasi Anbumani, Ampasala Dinakara Rao & Carani Venkatraman Anuradha
Pages: 3451-3461
Published online: 23 Nov 2020
AbstractforIdentification of novel human neutrophil elastase inhibitors from dietary phytochemicals using in silico and in vitro studies | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 233 Views
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Article
Chemical composition variability and vascular endothelial growth factor receptors inhibitory activity of Inulaviscosa essential oils from Algeria
Bouhassane Nadia, Fouzia Mesli, Benomari Fatima Zahra, Nouria Merad-Boussalah, Achiri Radja, Alain Muselli, Nassim Djabou & Mohammed El Amine Dib
Pages: 3462-3480
Published online: 23 Nov 2020
AbstractforChemical composition variability and vascular endothelial growth factor receptors inhibitory activity of Inulaviscosa essential oils from Algeria | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 153 Views
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Article
Development of parameters compatible with the CHARMM36 force field for [Fe4S4]2+ clusters and molecular dynamics simulations of adenosine-5’-phosphosulfate reductase in GROMACS 2019
Talis Uelisson da Silva, Karina de Carvalho Pougy, Magaly Girão Albuquerque, Camilo Henrique da Silva Lima & Sérgio de Paula Machado
Pages: 3481-3491
Published online: 13 Nov 2020
AbstractforDevelopment of parameters compatible with the CHARMM36 force field for [Fe4S4]2+ clusters and molecular dynamics simulations of adenosine-5’-phosphosulfate reductase in GROMACS 2019 | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 962 Views
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Article
Computational investigation for identification of potential phytochemicals and antiviral drugs as potential inhibitors for RNA-dependent RNA polymerase of COVID-19
Jitender Singh, Deepti Malik & Ashvinder Raina
Pages: 3492-3507
Published online: 17 Nov 2020
AbstractforComputational investigation for identification of potential phytochemicals and antiviral drugs as potential inhibitors for RNA-dependent RNA polymerase of COVID-19 | Full Text | References | PDF (5.6 MB) | EPUB
  • 1548 Views
  • 7 CrossRef citations
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Article
Druggability assessment of precursor membrane protein as a target for inhibiting the Zika virus
Nirmitee Mulgaonkar, Haoqi Wang, Maria King & Sandun Fernando
Pages: 3508-3524
Published online: 01 Dec 2020
AbstractforDruggability assessment of precursor membrane protein as a target for inhibiting the Zika virus | Full Text | References | PDF (5 MB) | EPUB
  • 255 Views
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Article
Design, synthesis and antiproliferative activity evaluation of fluorine-containing chalcone derivatives
Serdar Burmaoglu, Derya Aktas Anil, Arzu Gobek, Deryanur Kilic, Derya Yetkin, Nizami Duran & Oztekin Algul
Pages: 3525-3550
Published online: 17 Nov 2020
AbstractforDesign, synthesis and antiproliferative activity evaluation of fluorine-containing chalcone derivatives | Full Text | References | PDF (5.8 MB) | EPUB | Supplemental
  • 689 Views
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Article
Structural stability of antimicrobial peptides rich in tryptophan, proline and arginine: a computational study
Sathish Kumar Marimuthu, Krishnanand Nagarajan, Sathish Kumar Perumal, Selvamani Palanisamy & Latha Subbiah
Pages: 3551-3559
Published online: 19 Nov 2020
AbstractforStructural stability of antimicrobial peptides rich in tryptophan, proline and arginine: a computational study | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 583 Views
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Article
In vitro assessment of dual (antiviral and antitumor) activity of a novel lectin produced by the newly cyanobacterium isolate, Oscillatoria acuminate MHM-632 MK014210.1
Mabroka H. Saad, Esmail M. El-Fakharany, Marwa S. Salem & Nagwa M. Sidkey
Pages: 3560-3580
Published online: 17 Nov 2020
AbstractforIn vitro assessment of dual (antiviral and antitumor) activity of a novel lectin produced by the newly cyanobacterium isolate, Oscillatoria acuminate MHM-632 MK014210.1 | Full Text | References | PDF (3.4 MB) | EPUB
  • 189 Views
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Article
Exploring the structural basis of conformational alterations of myoglobin in the presence of spermine through computational modeling, molecular dynamics simulations, and spectroscopy methods
Rasoul Eslami-Farsani, Sadegh Farhadian & Behzad Shareghi
Pages: 3581-3594
Published online: 14 Dec 2020
AbstractforExploring the structural basis of conformational alterations of myoglobin in the presence of spermine through computational modeling, molecular dynamics simulations, and spectroscopy methods | Full Text | References | PDF (2.8 MB) | EPUB
  • 128 Views
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Article
Structure-based identification of potential SARS-CoV-2 main protease inhibitors
Shama Khan, Zeynab Fakhar, Afzal Hussain, Aijaz Ahmad, Deeba Shamim Jairajpuri, Mohamed F. Alajmi & Md. Imtaiyaz Hassan
Pages: 3595-3608
Published online: 19 Nov 2020
AbstractforStructure-based identification of potential SARS-CoV-2 main protease inhibitors | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 1960 Views
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Article
Targeting SARS-CoV-2 main protease: structure based virtual screening, in silico ADMET studies and molecular dynamics simulation for identification of potential inhibitors
Ankit Uniyal, Manoj Kumar Mahapatra, Vinod Tiwari, Rajat Sandhir & Rajnish Kumar
Pages: 3609-3625
Published online: 23 Nov 2020
AbstractforTargeting SARS-CoV-2 main protease: structure based virtual screening, in silico ADMET studies and molecular dynamics simulation for identification of potential inhibitors | Full Text | References | PDF (4.6 MB) | EPUB
  • 2740 Views
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Article
The comparative analysis of the properties and structures of purine nucleoside phosphorylases from thermophilic bacterium Thermus thermophilus HB27
Vladimir I. Timofeev, Ilya V. Fateev, Maria A. Kostromina, Yuliya A. Abramchik, Irina D. Konstantinova, Vladimir V. Volkov, Dmitry D. Lykoshin, Olga O. Mikheeva, Tatiana I. Muravieva, Roman S. Esipov & Inna P. Kuranova
Pages: 3626-3641
Published online: 23 Nov 2020
AbstractforThe comparative analysis of the properties and structures of purine nucleoside phosphorylases from thermophilic bacterium Thermus thermophilus HB27 | Full Text | References | PDF (5.3 MB) | EPUB | Supplemental
  • 125 Views
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Article
Cyclic peptide engineered from phytocystatin inhibitory hairpin loop as an effective modulator of falcipains and potent antimalarial
Manasi Mishra, Vigyasa Singh, Meenakshi B. Tellis, Rakesh S. Joshi, Kailash C. Pandey & Shailja Singh
Pages: 3642-3654
Published online: 09 Dec 2020
AbstractforCyclic peptide engineered from phytocystatin inhibitory hairpin loop as an effective modulator of falcipains and potent antimalarial | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 261 Views
  • 5 CrossRef citations
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Article
Virtual screening and molecular simulation study of natural products database for lead identification of novel coronavirus main protease inhibitors
Nancy Tripathi, Bharat Goel, Nivedita Bhardwaj, Bharat Sahu, Hemant Kumar & Shreyans K. Jain
Pages: 3655-3667
Published online: 19 Nov 2020
AbstractforVirtual screening and molecular simulation study of natural products database for lead identification of novel coronavirus main protease inhibitors | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 1597 Views
  • 11 CrossRef citations
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Article
In vitro antimicrobial, physicochemical, pharmacokinetics and molecular docking studies of benzoyl uridine esters against SARS-CoV-2 main protease
Mohammed Mahbubul Matin, Monir Uzzaman, Shagir Ahammad Chowdhury & Md. Mosharef Hossain Bhuiyan
Pages: 3668-3680
Published online: 10 Dec 2020
AbstractforIn vitro antimicrobial, physicochemical, pharmacokinetics and molecular docking studies of benzoyl uridine esters against SARS-CoV-2 main protease | Full Text | References | PDF (2.4 MB) | EPUB
  • 2754 Views
  • 21 CrossRef citations
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Article
Computational gene expression profiling in the exploration of biomarkers, non-coding functional RNAs and drug perturbagens for COVID-19
S. Aishwarya, K. Gunasekaran & A. Anita Margret
Pages: 3681-3696
Published online: 23 Nov 2020
AbstractforComputational gene expression profiling in the exploration of biomarkers, non-coding functional RNAs and drug perturbagens for COVID-19 | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 2279 Views
  • 8 CrossRef citations
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Article
In silico inhibition of SGTP4 as a therapeutic target for the treatment of schistosomiasis
Tayo A. Adekiya, Raphael Taiwo Aruleba, Ashwil Klein & Adewale O. Fadaka
Pages: 3697-3705
Published online: 23 Nov 2020
AbstractforIn silico inhibition of SGTP4 as a therapeutic target for the treatment of schistosomiasis | Full Text | References | PDF (2.8 MB) | EPUB
  • 437 Views
  • 11 CrossRef citations
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Article
In silico screening predicts common cold drug Dextromethorphan along with Prednisolone and Dexamethasone can be effective against novel Coronavirus disease (COVID-19)
Indrani Sarkar & Arnab Sen
Pages: 3706-3710
Published online: 23 Nov 2020
AbstractforIn silico screening predicts common cold drug Dextromethorphan along with Prednisolone and Dexamethasone can be effective against novel Coronavirus disease (COVID-19) | Full Text | References | PDF (1.3 MB) | EPUB
  • 2244 Views
  • 6 CrossRef citations
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Article
Combination of QSAR, molecular docking, molecular dynamic simulation and MM-PBSA: analogues of lopinavir and favipiravir as potential drug candidates against COVID-19
Md. Oliullah Rafi, Gourab Bhattacharje, Khattab Al-Khafaji, Tugba Taskin-Tok, Md. Almujaddade Alfasane, Amit Kumar Das, Md. Anowar Khasru Parvez & Md. Shahedur Rahman
Pages: 3711-3730
Published online: 30 Nov 2020
AbstractforCombination of QSAR, molecular docking, molecular dynamic simulation and MM-PBSA: analogues of lopinavir and favipiravir as potential drug candidates against COVID-19 | Full Text | References | PDF (5.8 MB) | EPUB | Supplemental
  • 5108 Views
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Article
Repurposing of FDA approved drugs against Salmonella enteric serovar Typhi by targeting dihydrofolate reductase: an in silico study
Tushar Joshi, Priyanka Sharma, Tanuja Joshi, Shalini Mathpal, Veena Pande & Subhash Chandra
Pages: 3731-3744
Published online: 30 Nov 2020
AbstractforRepurposing of FDA approved drugs against Salmonella enteric serovar Typhi by targeting dihydrofolate reductase: an in silico study | Full Text | References | PDF (5.6 MB) | EPUB | Supplemental
  • 281 Views
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Article
Cordycepin: a bioactive metabolite of Cordyceps militaris and polyadenylation inhibitor with therapeutic potential against COVID-19
Akalesh Kumar Verma
Pages: 3745-3752
Published online: 23 Nov 2020
AbstractforCordycepin: a bioactive metabolite of Cordyceps militaris and polyadenylation inhibitor with therapeutic potential against COVID-19 | Full Text | References | PDF (1.7 MB) | EPUB
  • 9660 Views
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Article
Core amino acid substitutions in HCV-3a isolates from Pakistan and opportunities for multi-epitopic vaccines
Ayyaz Khan, Mehboob Nawaz, Saeed Ullah, Irshad Ur Rehman, Abbas Khan, Shoaib Saleem, Nasib Zaman, Zabta Khan Shinwari, Muhammad Ali & Dong-Qing Wei
Pages: 3753-3768
Published online: 27 Nov 2020
AbstractforCore amino acid substitutions in HCV-3a isolates from Pakistan and opportunities for multi-epitopic vaccines | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 220 Views
  • 3 CrossRef citations
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Article
Deciphering LncRNA–protein interactions using docking complexes
Renuka Suravajhala, Sonal Gupta, Narayan Kumar & Prashanth Suravajhala
Pages: 3769-3776
Published online: 07 Dec 2020
AbstractforDeciphering LncRNA–protein interactions using docking complexes | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 440 Views
  • 4 CrossRef citations
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Article
Synthetic flavonoids as potential antiviral agents against SARS-CoV-2 main protease
Farwa Batool, Ehsan Ullah Mughal, Komal Zia, Amina Sadiq, Nafeesa Naeem, Asif Javid, Zaheer Ul-Haq & Muhammad Saeed
Pages: 3777-3788
Published online: 30 Nov 2020
AbstractforSynthetic flavonoids as potential antiviral agents against SARS-CoV-2 main protease | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 2566 Views
  • 10 CrossRef citations
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Article
Molecular docking studies of phytocompounds of Rheum emodi Wall with proteins responsible for antibiotic resistance in bacterial and fungal pathogens: in silico approach to enhance the bio-availability of antibiotics
Rajan Rolta, Deeksha Salaria, Vikas Kumar, Chirag N. Patel, Anuradha Sourirajan, David J. Baumler & Kamal Dev
Pages: 3789-3803
Published online: 23 Nov 2020
AbstractforMolecular docking studies of phytocompounds of Rheum emodi Wall with proteins responsible for antibiotic resistance in bacterial and fungal pathogens: in silico approach to enhance the bio-availability of antibiotics | Full Text | References | PDF (4.9 MB) | EPUB | Supplemental
  • 482 Views
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Review Article

Review Article
Comparative structural insight into prefoldin subunints of archaea and eukaryotes with special emphasis on unexplored prefoldin of Plasmodium falciparum
Vikash Kumar, Ankita Behl, Rumaisha Shoaib, Mohammad Abid, Maxim Shevtsov & Shailja Singh
Pages: 3804-3818
Published online: 04 Dec 2020
AbstractforComparative structural insight into prefoldin subunints of archaea and eukaryotes with special emphasis on unexplored prefoldin of Plasmodium falciparum | Full Text | References | PDF (3.3 MB) | EPUB
  • 450 Views
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