Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 15 (2022)

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Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 15 (2022)

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Research Articles

Article
Bioactive platinum complex of ligand bearing pyrimidine skeleton: DNA/BSA binding, molecular docking, anticancer, antioxidant and antimicrobial activities
Murugesan Sankarganesh, Paul Raj Adwin Jose, Jeyaraj Dhaveethu Raja, Rajadurai Vijay Solomon, Clarence Dorothy Sheela & Shunmugasundaram Gurusamy
Pages: 6683-6696
Published online: 26 Feb 2021
AbstractforBioactive platinum complex of ligand bearing pyrimidine skeleton: DNA/BSA binding, molecular docking, anticancer, antioxidant and antimicrobial activities | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 333 Views
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Article
Structural stability predictions and molecular dynamics simulations of RBD and HR1 mutations associated with SARS-CoV-2 spike glycoprotein
Shahzaib Ahamad, Kanipakam Hema & Dinesh Gupta
Pages: 6697-6709
Published online: 23 Feb 2021
AbstractforStructural stability predictions and molecular dynamics simulations of RBD and HR1 mutations associated with SARS-CoV-2 spike glycoprotein | Full Text | References | PDF (4.3 MB) | EPUB | Supplemental
  • 418 Views
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Article
Insilico evaluation of isatin-based derivatives with RNA-dependent RNA polymerase of the novel coronavirus SARS-CoV-2
Rajesh Kumar M.Daniel A. Gideon, Richard Mariadasse, Vijay Nirusimhan, Sherlin Rosita A.Jesu Castin Edward, Jeyakanthan Jeyaraman & Violet Dhayabaran V.
Pages: 6710-6724
Published online: 22 Feb 2021
AbstractforInsilico evaluation of isatin-based derivatives with RNA-dependent RNA polymerase of the novel coronavirus SARS-CoV-2 | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 340 Views
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Article
Insilico design of novel tubulin binding 9-arylimino derivatives of noscapine, their chemical synthesis and cellular activity as potent anticancer agents against breast cancer
Rajesh Kumar Meher, Praveen Kumar Reddy Nagireddy, Pratyush Pragyandipta, Srinivas Kantevari, Satyandra Kumar Singh, Vijay Kumar & Pradeep K. Naik
Pages: 6725-6736
Published online: 25 Feb 2021
AbstractforInsilico design of novel tubulin binding 9-arylimino derivatives of noscapine, their chemical synthesis and cellular activity as potent anticancer agents against breast cancer | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 181 Views
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Article
In silico identification of epitope-based vaccine candidates against HTLV-1
Hamid Reza Jahantigh, Angela Stufano, Piero Lovreglio, Seyed Abdolrahim Rezaee & Khadijeh Ahmadi
Pages: 6737-6754
Published online: 02 Mar 2021
AbstractforIn silico identification of epitope-based vaccine candidates against HTLV-1 | Full Text | References | PDF (5.1 MB) | EPUB | Supplemental
  • 298 Views
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Article
Investigation of the inhibitory activity of some dietary bioactive flavonoids against SARS-CoV-2 using molecular dynamics simulations and MM-PBSA calculations
Jibin K. Varughese, K. L. Joseph Libin, K. S. Sindhu, A. V. Rosily & T. G. Abi
Pages: 6755-6770
Published online: 23 Feb 2021
AbstractforInvestigation of the inhibitory activity of some dietary bioactive flavonoids against SARS-CoV-2 using molecular dynamics simulations and MM-PBSA calculations | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 282 Views
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Article
Identifying novel putative ERK1/2 inhibitors via hybrid scaffold hopping –FBDD approach
Shelly Pathania, Pankaj Kumar Singh, Raj Kumar Narang & Ravindra K. Rawal
Pages: 6771-6786
Published online: 22 Feb 2021
AbstractforIdentifying novel putative ERK1/2 inhibitors via hybrid scaffold hopping –FBDD approach | Full Text | References | PDF (3.1 MB) | EPUB
  • 347 Views
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Article
Homology modeling, docking, molecular dynamics and in vitro studies to identify Rhipicephalus microplus acetylcholinesterase inhibitors
Amanda Ponce Morais Cerqueira, Isis Bugia Santana, Janay Stefany Carneiro Araújo, Hélimar Gonçalves Lima, Maria José Moreira Batatinha, Alexsandro Branco, Manoelito Coelho dos Santos Junior & Mariana Borges Botura
Pages: 6787-6797
Published online: 01 Mar 2021
AbstractforHomology modeling, docking, molecular dynamics and in vitro studies to identify Rhipicephalus microplus acetylcholinesterase inhibitors | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 406 Views
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Article
Insilico exploration of hydroxylated polychlorinated biphenyls as estrogen receptor β ligands by 3D-QSAR, molecular docking and molecular dynamics simulations
Fangfang Wang, Yingchao Qiu & Bo Zhou
Pages: 6798-6809
Published online: 01 Mar 2021
AbstractforInsilico exploration of hydroxylated polychlorinated biphenyls as estrogen receptor β ligands by 3D-QSAR, molecular docking and molecular dynamics simulations | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 144 Views
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Article
Synthesis, characterization, biological evaluation and molecular docking of a new quinazolinone-based derivative as a potent dual inhibitor for VEGFR-2 and EGFR tyrosine kinases
Yassine Riadi, Mubarak A. Alamri, Mohammed H. Geesi, El Hassane Anouar, Oussama Ouerghi, Alhumaidi B. Alabbas, Manal A. Alossaimi, Ali Altharawi, Oussama Dehbi & Safar M. Alqahtani
Pages: 6810-6816
Published online: 08 Mar 2021
AbstractforSynthesis, characterization, biological evaluation and molecular docking of a new quinazolinone-based derivative as a potent dual inhibitor for VEGFR-2 and EGFR tyrosine kinases | Full Text | References | PDF (1.3 MB) | EPUB | Supplemental
  • 393 Views
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Article
In depth analysis on the carbohydrate-binding properties of a vasorelaxant lectin from Dioclea lasiophylla Mart Ex. Benth seeds
Benildo Sousa Cavada, Vanir Reis Pinto-Junior, Vinicius Jose Silva Osterne, Messias Vital Oliveira, Ivanice Bezerra Silva, Eva Pollyanna Peixe Laranjeira, Alana Freitas Pires, Jorge Luiz Coelho Domingos, Wandemberg Paiva Ferreira, Jeanlex Soares Sousa, Ana Maria Sampaio Assreuy & Kyria Santiago Nascimento
Pages: 6817-6830
Published online: 22 Feb 2021
AbstractforIn depth analysis on the carbohydrate-binding properties of a vasorelaxant lectin from Dioclea lasiophylla Mart Ex. Benth seeds | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 238 Views
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Article
Understanding the binding affinities between SFRP1CRD, SFRP1Netrin, Wnt5B and frizzled receptors 2, 3 and 7 using MD simulations
Raghava R. Sunkara, Shruti Koulgi, Vinod Jani, Nikhil Gadewal, Uddhavesh Sonavane, Rajendra Joshi & Sanjeev K. Waghmare
Pages: 6831-6844
Published online: 05 Mar 2021
AbstractforUnderstanding the binding affinities between SFRP1CRD, SFRP1Netrin, Wnt5B and frizzled receptors 2, 3 and 7 using MD simulations | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 182 Views
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Article
Anti-quorum sensing activity in Pseudomonas aeruginosa PA01 of benzimidazolium salts: electronic, spectral and structural investigations as theoretical approach
Ebru Önem, Burak Tüzün & Senem Akkoç
Pages: 6845-6856
Published online: 01 Mar 2021
AbstractforAnti-quorum sensing activity in Pseudomonas aeruginosa PA01 of benzimidazolium salts: electronic, spectral and structural investigations as theoretical approach | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 456 Views
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Article
In-silico based identification of phytochemicals from Houttuynia cordata Thunb. as potential inhibitors for overexpressed HER2 and VEGFR2 cancer genes
Sanjib Kumar Das, Suman Jyoti Deka, Dipayan Paul, Debmalya Das Gupta, Tridip Jyoti Das, Devendra Kumar Maravi, Hui Tag & Pallabi Kalita Hui
Pages: 6857-6867
Published online: 24 Feb 2021
AbstractforIn-silico based identification of phytochemicals from Houttuynia cordata Thunb. as potential inhibitors for overexpressed HER2 and VEGFR2 cancer genes | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 272 Views
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Article
Investigations of the molecular mechanism of diltiazem binding to human serum albumin in the presence of metal ions, glucose and urea
Sara Asadi Farsad, Hossein Haghaei, Mina Shaban, Mostafa Zakariazadeh & Somaieh Soltani
Pages: 6868-6879
Published online: 05 Mar 2021
AbstractforInvestigations of the molecular mechanism of diltiazem binding to human serum albumin in the presence of metal ions, glucose and urea | Full Text | References | PDF (2.9 MB) | EPUB
  • 142 Views
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Article
Role of Cys-298 in specific recognition of glutathione by aldose reductase
Gurprit Sekhon, Balvinder Singh & Ranvir Singh
Pages: 6880-6888
Published online: 25 Feb 2021
AbstractforRole of Cys-298 in specific recognition of glutathione by aldose reductase | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 144 Views
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Article
Identification of novel allosteric binding sites and multi-targeted allosteric inhibitors of receptor and non-receptor tyrosine kinases using a computational approach
Kavita Kumari Kakarala & Kaiser Jamil
Pages: 6889-6909
Published online: 08 Mar 2021
AbstractforIdentification of novel allosteric binding sites and multi-targeted allosteric inhibitors of receptor and non-receptor tyrosine kinases using a computational approach | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
  • 386 Views
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Article
New anticancer Pd and Pt complexes of tertamyl dithiocarbamate and DACH ligands against HT29 and Panc1 cell lines
Soudeh Hosseinzadeh, Mahboube Eslami Moghadam, Shabnam Sheshmani & Ashraf S. Shahvelayati
Pages: 6910-6920
Published online: 01 Mar 2021
AbstractforNew anticancer Pd and Pt complexes of tertamyl dithiocarbamate and DACH ligands against HT29 and Panc1 cell lines | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 150 Views
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Article
Structure-based virtual screening, molecular dynamics and binding affinity calculations of some potential phytocompounds against SARS-CoV-2
Shiv Rakesh Naik, Prashant Bharadwaj, Nadia Dingelstad, Subha Kalyaanamoorthy, Subhash C Mandal, Aravindhan Ganesan, Debprasad Chattopadhyay & Partha Palit
Pages: 6921-6938
Published online: 08 Mar 2021
AbstractforStructure-based virtual screening, molecular dynamics and binding affinity calculations of some potential phytocompounds against SARS-CoV-2 | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 499 Views
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Article
Molecular docking and molecular dynamics simulation identify a novel Radicicol derivative that predicts exclusive binding to Plasmodium falciparum Topoisomerase VIB
Shephali Bansod, Navya Raj, Amjesh R, Achuthsankar S. Nair & Sunanda Bhattacharyya
Pages: 6939-6951
Published online: 02 Mar 2021
AbstractforMolecular docking and molecular dynamics simulation identify a novel Radicicol derivative that predicts exclusive binding to Plasmodium falciparum Topoisomerase VIB | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 220 Views
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Article
Spectroscopic investigations, concentration dependent SERS, and molecular docking studies of a hydroxybenzylidene derivative
Veena S. Kumar, Y. Sheena Mary, Y. Shyma Mary, Martin Krátký, Jarmila Vinsova, Cecilia Baraldi, M. S. Roxy & Maria Cristina Gamberini
Pages: 6952-6964
Published online: 01 Mar 2021
AbstractforSpectroscopic investigations, concentration dependent SERS, and molecular docking studies of a hydroxybenzylidene derivative | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 179 Views
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Article
Investigation of in vitro and in silico effects of some novel carbazole Schiff bases on human carbonic anhydrase isoforms I and II
Yasemin Camadan, Baki Çiçek, Şevki Adem, Ümit Çalişir & Ebru Akkemik
Pages: 6965-6973
Published online: 01 Mar 2021
AbstractforInvestigation of in vitro and in silico effects of some novel carbazole Schiff bases on human carbonic anhydrase isoforms I and II | Full Text | References | PDF (2.3 MB) | EPUB
  • 574 Views
  • 5 CrossRef citations
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Article
Ligand and structure-based computational designing of multi-target molecules directing FFAR-1, FFAR-4 and PPAR-G as modulators of insulin receptor activity
Shweta Mishra, Mithun Singh Rajput, Devashish Rathore & Rashmi Dahima
Pages: 6974-6988
Published online: 02 Mar 2021
AbstractforLigand and structure-based computational designing of multi-target molecules directing FFAR-1, FFAR-4 and PPAR-G as modulators of insulin receptor activity | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 192 Views
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Article
Flavonoids as potential therapeutics against novel coronavirus disease-2019 (nCOVID-19)
Gourav Rakshit, Pankaj Dagur, Swaha Satpathy, Arjun Patra, Alok Jain & Manik Ghosh
Pages: 6989-7001
Published online: 08 Mar 2021
AbstractforFlavonoids as potential therapeutics against novel coronavirus disease-2019 (nCOVID-19) | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 342 Views
  • 9 CrossRef citations
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Article
Metadynamics-based enhanced sampling protocol for virtual screening: case study for 3CLpro protein for SARS-CoV-2
Sadanandam Namsani, Debabrata Pramanik, Mohd Aamir Khan, Sudip Roy & Jayant Kumar Singh
Pages: 7002-7017
Published online: 04 Mar 2021
AbstractforMetadynamics-based enhanced sampling protocol for virtual screening: case study for 3CLpro protein for SARS-CoV-2 | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 355 Views
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Article
Invitro and in silico anti-leukemic activity of 2-amino-6-nitro-4-(4-oxo-2-thioxothiazolidin-5-yl)-4H-chromene-3-carbonitrile (ANC) through inhibition of anti-apoptotic Bcl-2 proteins
Vijay Kumar Veena, Ahana Roy Choudhury & Adhikesavan Harikrishnan
Pages: 7018-7026
Published online: 08 Mar 2021
AbstractforInvitro and in silico anti-leukemic activity of 2-amino-6-nitro-4-(4-oxo-2-thioxothiazolidin-5-yl)-4H-chromene-3-carbonitrile (ANC) through inhibition of anti-apoptotic Bcl-2 proteins | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 89 Views
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Article
Imperative role of glycosylation in human MOG-HLA interaction: molecular insights of MOG-Ab associated demyelination
P. Jayananth, R. Madhumitha & L. Ramya
Pages: 7027-7037
Published online: 04 Mar 2021
AbstractforImperative role of glycosylation in human MOG-HLA interaction: molecular insights of MOG-Ab associated demyelination | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 199 Views
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Article
Designing a natural inhibitor against human kynurenine aminotransferase type II and a comparison with PF-04859989: a computational effort against schizophrenia
Akbar Noorbakhsh, Elnaz Hosseininezhadian Koushki, Chiako Farshadfar & Noeman Ardalan
Pages: 7038-7051
Published online: 01 Mar 2021
AbstractforDesigning a natural inhibitor against human kynurenine aminotransferase type II and a comparison with PF-04859989: a computational effort against schizophrenia | Full Text | References | PDF (4.1 MB) | EPUB
  • 292 Views
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Article
Isoleucine with secondary sulfonamide functionality as anticancer, antibacterial and antifungal agents
Kirna Devi & Pamita Awasthi
Pages: 7052-7069
Published online: 11 Mar 2021
AbstractforIsoleucine with secondary sulfonamide functionality as anticancer, antibacterial and antifungal agents | Full Text | References | PDF (5 MB) | EPUB | Supplemental
  • 183 Views
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Article
Phenothiazine as novel human superoxide dismutase modulators: discovery, optimization, and biological evaluation
Homa Azizian, Simin Forooghian, Arash Amanlou, Horacio Pérez-Sánchez & Massoud Amanlou
Pages: 7070-7083
Published online: 04 Mar 2021
AbstractforPhenothiazine as novel human superoxide dismutase modulators: discovery, optimization, and biological evaluation | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 196 Views
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Article
Mn3O4 nanoparticles bearing 5-amino-2-mercapto benzimidazole moiety as antibacterial and antifungal agents
S. Philip Raja, K. Jayamoorthy, K. I. Dhanalekshmi & S. Suresh
Pages: 7084-7090
Published online: 10 Mar 2021
AbstractforMn3O4 nanoparticles bearing 5-amino-2-mercapto benzimidazole moiety as antibacterial and antifungal agents | Full Text | References | PDF (1.9 MB) | EPUB
  • 156 Views
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Article
Molecular docking and molecular dynamics studies of bioactive compounds contained in noni fruit (Morinda citrifolia L.) against human pancreatic α-amylase
Nikeherpianti Lolok, Sri Adi Sumiwi, Ahmad Muhtadi, Yasmiwar Susilawati, Rini Hendriani, Dwi Syah Fitra Ramadhan, Jutti Levita & Idin Sahidin
Pages: 7091-7098
Published online: 08 Mar 2021
AbstractforMolecular docking and molecular dynamics studies of bioactive compounds contained in noni fruit (Morinda citrifolia L.) against human pancreatic α-amylase | Full Text | References | PDF (1.7 MB) | EPUB
  • 474 Views
  • 6 CrossRef citations
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Article
A rational design of a multi-epitope vaccine against SARS-CoV-2 which accounts for the glycan shield of the spike glycoprotein
William R. Martin & Feixiong Cheng
Pages: 7099-7113
Published online: 10 Mar 2021
AbstractforA rational design of a multi-epitope vaccine against SARS-CoV-2 which accounts for the glycan shield of the spike glycoprotein | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 294 Views
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Article
Discovery of novel heterocyclic amide-based inhibitors: an integrative in-silico approach to targeting soluble epoxide hydrolase
Zeynab Fakhar, Leila Hejazi, Sayyed Abbas Tabatabai & Orde Q. Munro
Pages: 7114-7128
Published online: 02 Mar 2021
AbstractforDiscovery of novel heterocyclic amide-based inhibitors: an integrative in-silico approach to targeting soluble epoxide hydrolase | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 270 Views
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Article
Molecular modeling of potent novel sulfonamide derivatives as non-peptide small molecule anti-COVID 19 agents
Sayantan Pradhan, Ramesh Prasad, Chittaranjan Sinha & Prosenjit Sen
Pages: 7129-7142
Published online: 01 Jun 2021
AbstractforMolecular modeling of potent novel sulfonamide derivatives as non-peptide small molecule anti-COVID 19 agents | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 1139 Views
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Article
Black tea bioactives as inhibitors of multiple targets of SARS-CoV-2 (3CLpro, PLpro and RdRp): a virtual screening and molecular dynamic simulation study
Madhurjya Gogoi, Meghali Borkotoky, Sangeeta Borchetia, Pritom Chowdhury, Saurov Mahanta & Anoop Kumar Barooah
Pages: 7143-7166
Published online: 10 Mar 2021
AbstractforBlack tea bioactives as inhibitors of multiple targets of SARS-CoV-2 (3CLpro, PLpro and RdRp): a virtual screening and molecular dynamic simulation study | Full Text | References | PDF (6.4 MB) | EPUB | Supplemental
  • 558 Views
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Article
Inhibition of SARS-CoV-2 main protease: a repurposing study that targets the dimer interface of the protein
Hanife Pekel, Metehan Ilter & Ozge Sensoy
Pages: 7167-7182
Published online: 13 Apr 2021
AbstractforInhibition of SARS-CoV-2 main protease: a repurposing study that targets the dimer interface of the protein | Full Text | References | PDF (4.9 MB) | EPUB | Supplemental
  • 1285 Views
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