Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 11 (2023)

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Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 11 (2023)

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Research Articles

Article
In silico insights into the dimer structure and deiodinase activity of type III iodothyronine deiodinase from bioinformatics, molecular dynamics simulations, and QM/MM calculations
Eric S. Marsan, Ana Dreab & Craig A. Bayse
Pages: 4819-4829
Published online: 17 May 2022
AbstractforIn silico insights into the dimer structure and deiodinase activity of type III iodothyronine deiodinase from bioinformatics, molecular dynamics simulations, and QM/MM calculations | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 208 Views
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Article
Molecular insights into binding dynamics of tandem RNA recognition motifs (tRRMs) of human antigen R (HuR) with mRNA and the effect of point mutations in impaired HuR-mRNA recognition
Ankita Agarwal, Suresh Alagar, Shri Kant & Ranjit Prasad Bahadur
Pages: 4830-4846
Published online: 10 May 2022
AbstractforMolecular insights into binding dynamics of tandem RNA recognition motifs (tRRMs) of human antigen R (HuR) with mRNA and the effect of point mutations in impaired HuR-mRNA recognition | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 363 Views
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Article
Prediction of binding affinity of 1,2-diphenyline ketone analogues at adenosine triphosphate binding site of glycogen synthase kinase-3β: a molecular docking and dynamic simulation study
Subramaniyan Dinakar, Mani Gurubarath & Karthik Dhananjayan
Pages: 4847-4862
Published online: 11 May 2022
AbstractforPrediction of binding affinity of 1,2-diphenyline ketone analogues at adenosine triphosphate binding site of glycogen synthase kinase-3β: a molecular docking and dynamic simulation study | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 157 Views
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Article
Computational analysis of marine algal compounds for obesity management against pancreatic lipase
Lavanya Prabhakar, Davis G. Dicky John, Satya Ranjan Singh & Ayaluru Murali
Pages: 4863-4872
Published online: 16 May 2022
AbstractforComputational analysis of marine algal compounds for obesity management against pancreatic lipase | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 308 Views
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Article
Finding alternatives to 5-fluorouracil: application of ensemble-based virtual screening for drug repositioning against human thymidylate synthase
Denis Mteremko, Daniel M. Shadrack, Fidele Ntie-Kang, Jaffu Chilongola & Musa Chacha
Pages: 4873-4889
Published online: 10 May 2022
AbstractforFinding alternatives to 5-fluorouracil: application of ensemble-based virtual screening for drug repositioning against human thymidylate synthase | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 191 Views
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Article
Inside the cracked kernel: establishing the molecular basis of AMG510 and MRTX849 in destabilising KRASG12C mutant switch I and II in cancer treatment
Abdul Rashid Issahaku, Elliasu Y. Salifu & Mahmoud E. S. Soliman
Pages: 4890-4902
Published online: 11 May 2022
AbstractforInside the cracked kernel: establishing the molecular basis of AMG510 and MRTX849 in destabilising KRASG12C mutant switch I and II in cancer treatment | Full Text | References | PDF (3.8 MB) | EPUB
  • 285 Views
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Article
Computational assessment of Withania somnifera phytomolecules as putative inhibitors of Mycobacterium tuberculosis CTP synthase PyrG
Ankita Singh, Sanjay Kumar, Vivek Kumar Gupta, Shailja Singh, Vivek Dhar Dwivedi & Usha Mina
Pages: 4903-4916
Published online: 12 May 2022
AbstractforComputational assessment of Withania somnifera phytomolecules as putative inhibitors of Mycobacterium tuberculosis CTP synthase PyrG | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 318 Views
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Article
Reverse vaccinology-based prediction of a multi-epitope SARS-CoV-2 vaccine and its tailoring to new coronavirus variants
Wahiba Ezzemani, Anass Kettani, Subrahmanyam Sappati, Kavya Kondaka, Hicham El Ossmani, Kyoko Tsukiyama-Kohara, Haya Altawalah, Rachid Saile, Michinori Kohara, Soumaya Benjelloun & Sayeh Ezzikouri
Pages: 4917-4938
Published online: 13 May 2022
AbstractforReverse vaccinology-based prediction of a multi-epitope SARS-CoV-2 vaccine and its tailoring to new coronavirus variants | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
  • 339 Views
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Article
Estrogen receptor potentially stable conformations from molecular dynamics as a structure-based pharmacophore model for mapping, screening, and identifying ligands—a new paradigm shift in pharmacophore screening
Dhivya Shanmugarajan & Charles David
Pages: 4939-4948
Published online: 11 May 2022
AbstractforEstrogen receptor potentially stable conformations from molecular dynamics as a structure-based pharmacophore model for mapping, screening, and identifying ligands—a new paradigm shift in pharmacophore screening | Full Text | References | PDF (2.1 MB) | EPUB
  • 243 Views
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Article
Evidence for a high pKa of an aspartic acid residue in the active site of CALB by a fully atomistic multiscale approach
Matteo Capone, Laura Zanetti-Polzi, Ilenia Leonzi, Nicoletta Spreti & Isabella Daidone
Pages: 4949-4956
Published online: 20 May 2022
AbstractforEvidence for a high pKa of an aspartic acid residue in the active site of CALB by a fully atomistic multiscale approach | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 190 Views
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Article
Copper(II) Schiff base complex derived from salen ligand: structural investigation, Hirshfeld surface analysis, anticancer and anti-SARS-CoV-2
Sunil Kumar & Mukesh Choudhary
Pages: 4957-4980
Published online: 23 May 2022
AbstractforCopper(II) Schiff base complex derived from salen ligand: structural investigation, Hirshfeld surface analysis, anticancer and anti-SARS-CoV-2 | Full Text | References | PDF (8.3 MB) | EPUB | Supplemental
  • 325 Views
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Article
Computational attributes of protein kinase-C gamma C2-domain & virtual screening for small molecules: elucidation from meta-dynamics simulations & free-energy calculations
Harvinder Singh, Anupam Raja, Nishant Shekhar, Arushi Chauhan, Ajay Prakash, Pramod Avti & Bikash Medhi
Pages: 4981-4992
Published online: 23 May 2022
AbstractforComputational attributes of protein kinase-C gamma C2-domain & virtual screening for small molecules: elucidation from meta-dynamics simulations & free-energy calculations | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 222 Views
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Article
Isolation and structure elucidation of a steroidal moiety from Withania somnifera and in silico evaluation of antimalarial efficacy against artemisinin resistance Plasmodium falciparum kelch 13 protein
Deepak Pradhan, Prativa Biswasroy, Dipak Kumar Sahu, Goutam Ghosh & Goutam Rath
Pages: 4993-5006
Published online: 18 May 2022
AbstractforIsolation and structure elucidation of a steroidal moiety from Withania somnifera and in silico evaluation of antimalarial efficacy against artemisinin resistance Plasmodium falciparum kelch 13 protein | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 204 Views
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Article
In-silico study of the interactions between acylated glucagon like-peptide-1 analogues and the native receptor
Tine Maja Frimann, Suk Kyu Ko, Pernille Harris, Jens Thostrup Bukrinski & Günther H. J. Peters
Pages: 5007-5021
Published online: 25 May 2022
AbstractforIn-silico study of the interactions between acylated glucagon like-peptide-1 analogues and the native receptor | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 320 Views
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Article
Antimalarial phytochemicals as potential inhibitors of SARS-CoV-2 guanine N7-methyltransferase (nsp 14): an integrated computational approach
Gideon A. Gyebi, Oludare M. Ogunyemi, Adedotun A. Adefolalu, Juan F. López-Pastor, Antonio J. Banegas-Luna, Alejandro Rodríguez-Martínez, Horacio Pérez-Sánchez, Adegbenro P. Adegunloye, Olalekan B. Ogunro, Saheed O. Afolabi, Alaa Baazeem, Saqer S. Alotaibi & Gaber El-Saber Batiha
Pages: 5022-5044
Published online: 28 May 2022
AbstractforAntimalarial phytochemicals as potential inhibitors of SARS-CoV-2 guanine N7-methyltransferase (nsp 14): an integrated computational approach | Full Text | References | PDF (5.8 MB) | EPUB | Supplemental
  • 285 Views
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Article
In-silico validation of novel therapeutic activities of withaferin a using molecular docking and dynamics studies
Rutwick Surya Ulhas & Alok Malaviya
Pages: 5045-5056
Published online: 24 May 2022
AbstractforIn-silico validation of novel therapeutic activities of withaferin a using molecular docking and dynamics studies | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 307 Views
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Article
Repurposing antiviral drugs against HTLV-1 protease by molecular docking and molecular dynamics simulation
Hamidreza Jahantigh, Nahid Ahmadi, Piero Lovreglio, Angela Stufano, Maryam Enayatkhani, Behzad Shahbazi & Khadijeh Ahmadi
Pages: 5057-5066
Published online: 25 May 2022
AbstractforRepurposing antiviral drugs against HTLV-1 protease by molecular docking and molecular dynamics simulation | Full Text | References | PDF (2.7 MB) | EPUB
  • 287 Views
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Article
Synthesis, characterisation, DNA binding, acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) activities and molecular docking studies of metal(II) complexes with 1,10-phenanthroline scaffold
E. H. Edinsha Gladis, K. Nagashri, M. Anisha & J. Joseph
Pages: 5067-5085
Published online: 14 Jun 2022
AbstractforSynthesis, characterisation, DNA binding, acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) activities and molecular docking studies of metal(II) complexes with 1,10-phenanthroline scaffold | Full Text | References | PDF (3.8 MB) | EPUB
  • 183 Views
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Article
Virtually screened novel sulfathiazole derivatives as a potential drug candidate for methicillin-resistant Staphylococcus aureus and multidrug-resistant tuberculosis
Saraswathy Nagendran, Sakthivel Balasubramaniyan & Navabshan Irfan
Pages: 5086-5095
Published online: 28 May 2022
AbstractforVirtually screened novel sulfathiazole derivatives as a potential drug candidate for methicillin-resistant Staphylococcus aureus and multidrug-resistant tuberculosis | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 202 Views
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Article
Structure-guided pharmacophore based virtual screening, docking, and molecular dynamics to discover repurposed drugs as novel inhibitors against endoribonuclease Nsp15 of SARS-CoV-2
Prakash Jha, Daman Saluja & Madhu Chopra
Pages: 5096-5106
Published online: 02 Jun 2022
AbstractforStructure-guided pharmacophore based virtual screening, docking, and molecular dynamics to discover repurposed drugs as novel inhibitors against endoribonuclease Nsp15 of SARS-CoV-2 | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 228 Views
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Article
Prospects for the use of macrocyclic photosensitizers for inactivation of SARS-CoV-2: selection of compounds leaders based on the molecular docking data
Yury A. Gubarev, Natalia Sh. Lebedeva, Elena S. Yurina, Galina M. Mamardashvili, Svetlana V. Zaitceva, Sergey A. Zdanovich & Oskar I. Koifman
Pages: 5107-5116
Published online: 08 Jun 2022
AbstractforProspects for the use of macrocyclic photosensitizers for inactivation of SARS-CoV-2: selection of compounds leaders based on the molecular docking data | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 110 Views
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Article
Identification and validation of potent inhibitor of Escherichia coli DHFR from MMV pathogen box
Shingini Sharma, Rashmi Tyagi, Mitul Srivastava, Kusum Rani, Dhruv Kumar, Shailendra Asthana & V. Samuel Raj
Pages: 5117-5126
Published online: 02 Jun 2022
AbstractforIdentification and validation of potent inhibitor of Escherichia coli DHFR from MMV pathogen box | Full Text | References | PDF (2.4 MB) | EPUB
  • 286 Views
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Article
Phthalide derivatives as dihydrofolate reductase inhibitors for malaria: molecular docking and molecular dynamics studies
Walaa Ibraheem, Alaa A. Makki & Abdulrahim Altoam Alzain
Pages: 5127-5137
Published online: 28 May 2022
AbstractforPhthalide derivatives as dihydrofolate reductase inhibitors for malaria: molecular docking and molecular dynamics studies | Full Text | References | PDF (2.4 MB) | EPUB
  • 233 Views
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Article
Characterization and activity-folding relationship of serine protease from Antarctic krill (Euphausia superba)
Shang-Jun Yin, Ho-Yeon Lee, Wei Wang, Jinhyuk Lee & Yong-Doo Park
Pages: 5138-5151
Published online: 25 May 2022
AbstractforCharacterization and activity-folding relationship of serine protease from Antarctic krill (Euphausia superba) | Full Text | References | PDF (2.9 MB) | EPUB
  • 105 Views
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Article
Drug repurposing against the RNA-dependent RNA polymerase domain of dengue serotype 3 by virtual screening and molecular dynamics simulations
Aditi Gangopadhyay & Achintya Saha
Pages: 5152-5165
Published online: 31 May 2022
AbstractforDrug repurposing against the RNA-dependent RNA polymerase domain of dengue serotype 3 by virtual screening and molecular dynamics simulations | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 188 Views
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Article
Targeting new N-furfurylated 4-chlorophenyl-1,2,4-triazolepropionamide hybrids as potential 15-lipoxygenase inhibitors supported with in vitro and in silico studies
Muhammad Yasin, Wardah Shahid, Muhammad Ashraf, Muhammad Saleem, Saima Muzaffar, Aziz-ur-Rehman  , Syeda Abida Ejaz, Hafiz Mohammad Kashif Mahmood, Keshab Bhattarai & Naheed Riaz
Pages: 5166-5182
Published online: 14 Jun 2022
AbstractforTargeting new N-furfurylated 4-chlorophenyl-1,2,4-triazolepropionamide hybrids as potential 15-lipoxygenase inhibitors supported with in vitro and in silico studies | Full Text | References | PDF (3 MB) | EPUB
  • 124 Views
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Article
Unique mutations in mitochondrial DNA and associated pathways involved in high altitude pulmonary edema susceptibility in Indian lowlanders
Swati Sharma, Rajat Sandhir, Lilly Ganju, Bhuvnesh Kumar & Yamini Singh
Pages: 5183-5198
Published online: 06 Jun 2022
AbstractforUnique mutations in mitochondrial DNA and associated pathways involved in high altitude pulmonary edema susceptibility in Indian lowlanders | Full Text | References | PDF (3.1 MB) | EPUB
  • 196 Views
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Article
Synthesis, structural characterization, DFT calculations, molecular docking, and molecular dynamics simulations of a novel ferrocene derivative to unravel its potential antitumor activity
Mohamed M. Hammoud, Muhammad Khattab, Marwa Abdel-Motaal, Johan Van der Eycken, Radwan Alnajjar, Hamada S. Abulkhair & Ahmed Ali Al‐Karmalawy
Pages: 5199-5216
Published online: 08 Jun 2022
AbstractforSynthesis, structural characterization, DFT calculations, molecular docking, and molecular dynamics simulations of a novel ferrocene derivative to unravel its potential antitumor activity | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 786 Views
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Article
Investigation on anti-Corona viral potential of Yarrow tea
Komal Tilwani, Abhishek Patel, Hirak Parikh, Dr Janki Thakker & Gayatri Dave
Pages: 5217-5229
Published online: 31 May 2022
AbstractforInvestigation on anti-Corona viral potential of Yarrow tea | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 335 Views
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Article
Evaluation of implicit solvent models in molecular dynamics simulation of α-Synuclein
Loizos Savva & James A. Platts
Pages: 5230-5245
Published online: 07 Jun 2022
AbstractforEvaluation of implicit solvent models in molecular dynamics simulation of α-Synuclein | Full Text | References | PDF (7.9 MB) | EPUB | Supplemental
  • 375 Views
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Article
Antiproliferative efficacy of the antioxidant bioactive compounds of defatted seeds of Azadirachta indica and Momordica charantia against the regulatory function of tumor suppressor gene inducing oral carcinoma
Yash Sharma, Amritpal Kaur, Rupa Mishra, Sharvari Kulkarni, Mausumi Bharadwaj & Kumud Bala
Pages: 5246-5260
Published online: 08 Jun 2022
AbstractforAntiproliferative efficacy of the antioxidant bioactive compounds of defatted seeds of Azadirachta indica and Momordica charantia against the regulatory function of tumor suppressor gene inducing oral carcinoma | Full Text | References | PDF (3.5 MB) | EPUB
  • 184 Views
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Article
Identification of dual active sites in Caenorhabditis elegans GANA-1 protein: an ortholog of the human α-GAL a and α-NAGA enzymes
Clerance Su Yee Cheong, Shafi Ullah Khan, Nafees Ahmed & Kumaran Narayanan
Pages: 5261-5276
Published online: 11 Jun 2022
AbstractforIdentification of dual active sites in Caenorhabditis elegans GANA-1 protein: an ortholog of the human α-GAL a and α-NAGA enzymes | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 224 Views
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Article
Synthesis, virtual screening and computational approach of a quinoxaline derivative as potent anti-HIV agent targeting the reverse transcriptase enzyme
Youness El Bakri, Kandasamy Saravanan, Sajjad Ahmad & Joel T. Mague
Pages: 5277-5290
Published online: 06 Jun 2022
AbstractforSynthesis, virtual screening and computational approach of a quinoxaline derivative as potent anti-HIV agent targeting the reverse transcriptase enzyme | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 132 Views
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Article
“Mango in all her majesty”—the potential of mangiferin and its analogues in the inhibition of Eimeria tenella hexokinase—a computational approach
Kehinde F. Paul-Odeniran, Paul O. Odeniran, Isaiah O. Ademola & Hezekiel Kumalo
Pages: 5291-5304
Published online: 11 Jun 2022
Abstractfor“Mango in all her majesty”—the potential of mangiferin and its analogues in the inhibition of Eimeria tenella hexokinase—a computational approach | Full Text | References | PDF (3.5 MB) | EPUB
  • 129 Views
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Article
Experimental and theoretical evaluation of N-pyridoxal-salicylic acid hydrazide derived copper(II) complex with 2-methylimidazole
Pradeep Kumar Vishwakarma, Pushpendra Singh Jaget, Mahendra Kumar Parte, Ram Charitra Maurya, Deepak Kumar Rajak, Aniteshma Chanpuria, Abhilasha Shukla & Ahad Ali
Pages: 5305-5316
Published online: 13 Jun 2022
AbstractforExperimental and theoretical evaluation of N-pyridoxal-salicylic acid hydrazide derived copper(II) complex with 2-methylimidazole | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 197 Views
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Article
Computational, biochemical and ex vivo evaluation of xanthine derivatives against phosphodiesterases to enhance the sperm motility
Mutyala Satish, Kumari Sandhya, Kulhar Nitin, Ninjoor Yashas Kiran, Babu Aleena, Adiga Satish Kumar, Kalthur G & Eerappa Rajakumara
Pages: 5317-5327
Published online: 13 Jun 2022
AbstractforComputational, biochemical and ex vivo evaluation of xanthine derivatives against phosphodiesterases to enhance the sperm motility | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 256 Views
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Article
Identification of phytochemicals from Eclipta alba and assess their potentiality against Hepatitis C virus envelope glycoprotein: virtual screening, docking, and molecular dynamics simulation study
Maheswata Moharana, Subrat Kumar Pattanayak & Fahmida Khan
Pages: 5328-5344
Published online: 11 Jun 2022
AbstractforIdentification of phytochemicals from Eclipta alba and assess their potentiality against Hepatitis C virus envelope glycoprotein: virtual screening, docking, and molecular dynamics simulation study | Full Text | References | PDF (4.7 MB) | EPUB | Supplemental
  • 263 Views
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Article
Computational discovery of small drug-like compounds as potential inhibitors of PD-1/PD-L1 interactions
Viktor A. Urban, Alexander I. Davidovskii & Valery G. Veresov
Pages: 5345-5361
Published online: 13 Jun 2022
AbstractforComputational discovery of small drug-like compounds as potential inhibitors of PD-1/PD-L1 interactions | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 292 Views
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Letter to the Editor

Letter
Functional identification of ‘hypothetical protein’ structures with unknown function
Y. N. Chirgadze, E. A. Boshkova, A. M. Kargatov & N. Y. Chirgadze
Pages: 5362-5366
Published online: 11 Jun 2022
First Page PreviewforFunctional identification of ‘hypothetical protein’ structures with unknown function | Full Text | References | PDF (1.1 MB) | EPUB
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