Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 9 (2023)

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Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 9 (2023)

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Research Articles

Article
Mannose 2, 3, 4, 5, 6-O-pentasulfate (MPS): a partial activator of human heparin cofactor II with anticoagulation potential
Shadabi Bano, Abdul Burhan Khan, Sana Fatima, Qudsia Rashid, Amresh Prakash, Neha Gupta, Irshad Ahmad, Shoyab Ansari, Andrew M. Lynn, Mohammad Abid & Mohamad Aman Jairajpuri
Pages: 3717-3727
Published online: 28 Mar 2022
AbstractforMannose 2, 3, 4, 5, 6-O-pentasulfate (MPS): a partial activator of human heparin cofactor II with anticoagulation potential | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 220 Views
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Article
Mode of interaction of altretamine with calf thymus DNA: biophysical insights
Sathi Goswami, Ritutama Ghosh, Pooja Prasanthan & Nand Kishore
Pages: 3728-3740
Published online: 28 Mar 2022
AbstractforMode of interaction of altretamine with calf thymus DNA: biophysical insights | Full Text | References | PDF (2.4 MB) | EPUB
  • 482 Views
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Article
Computational studies on the design of NCI natural products as inhibitors to SARS-CoV-2 main protease
Laxman Durgam & Lalitha Guruprasad
Pages: 3741-3751
Published online: 25 Mar 2022
AbstractforComputational studies on the design of NCI natural products as inhibitors to SARS-CoV-2 main protease | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 266 Views
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Article
Crystal structure analysis of phycoerythrin from marine cyanobacterium Halomicronema
Stuti N. Patel, Ravi R. Sonani, Gagan D. Gupta, Niraj Kumar Singh, Vinay Kumar & Datta Madamwar
Pages: 3752-3761
Published online: 31 Mar 2022
AbstractforCrystal structure analysis of phycoerythrin from marine cyanobacterium Halomicronema | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 229 Views
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Article
Design of a multi-epitope Zika virus vaccine candidate – an in-silico study
Wahiba Ezzemani, Marc P. Windisch, Haya Altawalah, Fadila Guessous, Rachid Saile, Soumaya Benjelloun, Anass Kettani & Sayeh Ezzikouri
Pages: 3762-3771
Published online: 23 Mar 2022
AbstractforDesign of a multi-epitope Zika virus vaccine candidate – an in-silico study | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 420 Views
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Article
MIA-QSAR study of the structural merging of (thio)benzamide herbicides with photosynthetic system II inhibitory activities
Ingrid V. Pereira, Joyce K. Daré, Elaine F. F. da Cunha & Matheus P. Freitas
Pages: 3772-3778
Published online: 28 Mar 2022
AbstractforMIA-QSAR study of the structural merging of (thio)benzamide herbicides with photosynthetic system II inhibitory activities | Full Text | References | PDF (1.3 MB) | EPUB | Supplemental
  • 111 Views
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Article
Biophysical and molecular modeling evidences for the binding of sulfa molecules with hemoglobin
A. Mavani, Aben Ovung, Soching Luikham, Gopinatha Suresh Kumar, Abhi Das, Debes Ray, Vinod K. Aswal & Jhimli Bhattacharyya
Pages: 3779-3790
Published online: 05 Apr 2022
AbstractforBiophysical and molecular modeling evidences for the binding of sulfa molecules with hemoglobin | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 236 Views
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Article
Differential interaction of Fluorescein-β-cyclodextrin conjugate to quadruplex kit22 DNA: Inclusion of Berberine and modulation of binding
Suganthi Soundarapandian, Aleyamma Alexander, Archana Sumohan Pillai, Varnitha Manikandan, Israel V. M. V. Enoch & Sameena Yousuf
Pages: 3791-3799
Published online: 01 Apr 2022
AbstractforDifferential interaction of Fluorescein-β-cyclodextrin conjugate to quadruplex kit22 DNA: Inclusion of Berberine and modulation of binding | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 168 Views
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Article
Synthesis, characterization, in vitro, in silico and in vivo investigations and biological assessment of Knoevenagel condensate β-diketone Schiff base transition metal complexes
Bhuvaneswari Marimuthu, Sakthiveni Saravanaselvam, Samuel Michael, Porkodi Jeyaraman & Xavier Arulannandham
Pages: 3800-3820
Published online: 11 Apr 2022
AbstractforSynthesis, characterization, in vitro, in silico and in vivo investigations and biological assessment of Knoevenagel condensate β-diketone Schiff base transition metal complexes | Full Text | References | PDF (5.4 MB) | EPUB | Supplemental
  • 307 Views
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Article
Genome sequencing and in silico analysis of isoprene degrading monooxygenase enzymes of Sphingobium sp. BHU LFT2
Abhishek Singh, Anand Kumar Pandey & Suresh Kumar Dubey
Pages: 3821-3834
Published online: 05 Apr 2022
AbstractforGenome sequencing and in silico analysis of isoprene degrading monooxygenase enzymes of Sphingobium sp. BHU LFT2 | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 173 Views
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Article
Identification of potential Staphylococcus aureus dihydrofolate reductase inhibitors using QSAR, molecular docking, dynamics simulations and free energy calculation
Isaac de Araujo Matos, Ana Carolina Goes Pinto, Matheus Vitor Ferreira Ferraz, Wenny Camilla Santos Adan, Ricardo Pereira Rodrigues, Juliane Xavier dos Santos, Rodrigo Rezende Kitagawa, Roberto Dias Lins, Tiago Branquinho Oliveira & Nivan Bezerra da Costa Junior
Pages: 3835-3846
Published online: 31 Mar 2022
AbstractforIdentification of potential Staphylococcus aureus dihydrofolate reductase inhibitors using QSAR, molecular docking, dynamics simulations and free energy calculation | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 226 Views
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Article
Alpha-cadinol as a potential ACE-inhibitory volatile compound identified from Phaseolus vulgaris L. through in vitro and in silico analysis
Jyoti Tripathi, Sumit Gupta & Satyendra Gautam
Pages: 3847-3861
Published online: 05 Apr 2022
AbstractforAlpha-cadinol as a potential ACE-inhibitory volatile compound identified from Phaseolus vulgaris L. through in vitro and in silico analysis | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 187 Views
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Article
Phenolic compounds as α-glucosidase inhibitors: a docking and molecular dynamics simulation study
Ananta Swargiary, Mritunjoy Kumar Roy & Shafi Mahmud
Pages: 3862-3871
Published online: 01 Apr 2022
AbstractforPhenolic compounds as α-glucosidase inhibitors: a docking and molecular dynamics simulation study | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 576 Views
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Article
Molecular modelling and in vitro studies of Daruharidra as a potent alpha-amylase inhibitor
Aditi Bhatnagar, Ravi Saini, Priya Dagar & Abha Mishra
Pages: 3872-3883
Published online: 12 Apr 2022
AbstractforMolecular modelling and in vitro studies of Daruharidra as a potent alpha-amylase inhibitor | Full Text | References | PDF (2.3 MB) | EPUB
  • 176 Views
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Article
3β-Acetoxy-21α-H-hop-22(29)ene, a novel multitargeted phytocompound against SARS-CoV-2: in silico screening
Simna Siddique & R. Pradeep Kumar
Pages: 3884-3891
Published online: 04 Apr 2022
Abstractfor3β-Acetoxy-21α-H-hop-22(29)ene, a novel multitargeted phytocompound against SARS-CoV-2: in silico screening | Full Text | References | PDF (1.1 MB) | EPUB | Supplemental
  • 111 Views
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Article
Molecular properties of Ca2+ transport through TRPV2 channel: a molecular dynamics simulations study
Mozhgan Alipour, Behnam Hajipour-Verdom, Parviz Abdolmaleki & Mohammad Javan
Pages: 3892-3899
Published online: 06 Apr 2022
AbstractforMolecular properties of Ca2+ transport through TRPV2 channel: a molecular dynamics simulations study | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 222 Views
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Article
Molecular insights to the binding interactions of APNS containing HIV-protease inhibitors against SARS-CoV-2 Mpro: an in silico approach towards drug repurposing
Priyanka Purohit, Jiban Jyoti Dash, Jules Tshishimbi Muya & Biswa Ranjan Meher
Pages: 3900-3913
Published online: 07 Apr 2022
AbstractforMolecular insights to the binding interactions of APNS containing HIV-protease inhibitors against SARS-CoV-2 Mpro: an in silico approach towards drug repurposing | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 198 Views
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Article
Elucidating novel antibacterial compounds from the NPASS database against the FimH lectin domain for the treatment of urinary tract infections: an in-silico study
Mrtatha K. Al-Zrkani, Rafid A. Abdulkareem, Dhurgham Al-Fahad, Marwah Al Shouber, Amaal Mohammed Salih Nasr & Ahmad Al-Khdhairawi
Pages: 3914-3925
Published online: 09 Apr 2022
AbstractforElucidating novel antibacterial compounds from the NPASS database against the FimH lectin domain for the treatment of urinary tract infections: an in-silico study | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 277 Views
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Article
Target prediction, computational identification, and network-based pharmacology of most potential phytoconstituent in medicinal leaves of Justicia adhatoda against SARS-CoV-2
Pankaj Dagur, Gourav Rakshit, Murtuja Sheikh, Abanish Biswas, Parineeta Jha, Khattab Al-Khafaji & Manik Ghosh
Pages: 3926-3942
Published online: 12 Apr 2022
AbstractforTarget prediction, computational identification, and network-based pharmacology of most potential phytoconstituent in medicinal leaves of Justicia adhatoda against SARS-CoV-2 | Full Text | References | PDF (5.7 MB) | EPUB | Supplemental
  • 369 Views
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Article
Investigating the novel acetonitrile derivatives as potential SARS-CoV-2 main protease inhibitor using molecular modeling approach
Anandsing Fattesing Patil, Vijay Shivaji Patil, Dipak Premchand Jaiswal, Sandip Sumant Palakhe, Sandip Pandurang Patil & Bajarang Vasant Kumbhar
Pages: 3943-3955
Published online: 06 Apr 2022
AbstractforInvestigating the novel acetonitrile derivatives as potential SARS-CoV-2 main protease inhibitor using molecular modeling approach | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 184 Views
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Article
In silico analysis of the predicted protein-protein interaction of syntaxin-18, a putative receptor of Peregrinus maidis Ashmead (Hemiptera: Delphacidae) with Maize mosaic virus glycoprotein
Melvin A. Castrosanto, Apel Jae N. Clemente, Anna E. Whitfield & Karen B. Alviar
Pages: 3956-3963
Published online: 04 Apr 2022
AbstractforIn silico analysis of the predicted protein-protein interaction of syntaxin-18, a putative receptor of Peregrinus maidis Ashmead (Hemiptera: Delphacidae) with Maize mosaic virus glycoprotein | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 488 Views
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Article
Computational screening and analysis of deleterious nsSNPs in human p14ARF (CDKN2A gene) protein using molecular dynamic simulation approach
Syed Umair Ahmad, Yasir Ali, Zainab Jan, Salman Rasheed, Noor ul Ain Nazir, Asif Khan, Shah Rukh Abbas, Abdul Wadood & Ashfaq Ur Rehman
Pages: 3964-3975
Published online: 21 Apr 2022
AbstractforComputational screening and analysis of deleterious nsSNPs in human p14ARF (CDKN2A gene) protein using molecular dynamic simulation approach | Full Text | References | PDF (2.6 MB) | EPUB
  • 427 Views
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Article
Anticancer, antioxidant activities and molecular docking study of thiazolidine-4-one and thiadiazol derivatives
Noor M. Nasir, Tahseen A. Alsalim, Amr Ahmed El-Arabey & Mohnad Abdalla
Pages: 3976-3992
Published online: 25 Apr 2022
AbstractforAnticancer, antioxidant activities and molecular docking study of thiazolidine-4-one and thiadiazol derivatives | Full Text | References | PDF (4.6 MB) | EPUB
  • 223 Views
  • 1 CrossRef citations
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Article
The physiological role of complex V in ATP synthesis: Murzyme functioning is viable whereas rotary conformation change model is untenable
Kelath Murali Manoj, Nikolai Mikhailovich Bazhin, Hirohisa Tamagawa, Laurent Jaeken & Abhinav Parashar
Pages: 3993-4012
Published online: 08 Apr 2022
AbstractforThe physiological role of complex V in ATP synthesis: Murzyme functioning is viable whereas rotary conformation change model is untenable | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 198 Views
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Article
Reporting dinaciclib and theodrenaline as a multitargeted inhibitor against SARS-CoV-2: an in-silico study
Shaban Ahmad, Mussuvir Pasha KM, Khalid Raza, Misbahuddin M. Rafeeq, Alaa Hamed Habib, Murugesh Eswaran & Manoj Kumar Yadav
Pages: 4013-4023
Published online: 22 Apr 2022
AbstractforReporting dinaciclib and theodrenaline as a multitargeted inhibitor against SARS-CoV-2: an in-silico study | Full Text | References | PDF (2.8 MB) | EPUB
  • 273 Views
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Article
Chebulinic and chebulagic acid binding with serum proteins: biophysical and molecular docking approach
Daniel Pushparaju Yeggoni, Manjunath Meti & Rajagopal Subramanyam
Pages: 4024-4039
Published online: 09 Apr 2022
AbstractforChebulinic and chebulagic acid binding with serum proteins: biophysical and molecular docking approach | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 191 Views
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Article
Bicyclo-DNA mimics with enhanced protein binding affinities: insights from molecular dynamics simulations
Pradeep Pant, Amita Pathak & B. Jayaram
Pages: 4040-4047
Published online: 09 Apr 2022
AbstractforBicyclo-DNA mimics with enhanced protein binding affinities: insights from molecular dynamics simulations | Full Text | References | PDF (1.9 MB) | EPUB
  • 258 Views
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Article
Identification of a 3-(5-methyl-2-thiazolylamino)phthalide as a new minor groove agent
Zeynep Tanrıkulu Yılmaz, Hakkı Yasin Odabaşoğlu, Pelin Şenel, Elif Çepni Yüzbaşıoğlu, Taner Erdoğan, Ayşe Daut Özdemir, Ayşegül Gölcü, Mustafa Odabaşoğlu & Orhan Büyükgüngör
Pages: 4048-4064
Published online: 13 Apr 2022
AbstractforIdentification of a 3-(5-methyl-2-thiazolylamino)phthalide as a new minor groove agent | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 400 Views
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Article
In silico design and computational evaluation of novel 2-arylaminopyrimidine-based compounds as potential multi-targeted protein kinase inhibitors: application for the native and mutant (T315I) Bcr-Abl tyrosine kinase
Elena V. Koroleva, Yuri V. Kornoushenko, Anna D. Karpenko, Ivan P. Bosko, Julia V. Siniutsich, Zhanna V. Ignatovich & Alexander M. Andrianov
Pages: 4065-4080
Published online: 26 Apr 2022
AbstractforIn silico design and computational evaluation of novel 2-arylaminopyrimidine-based compounds as potential multi-targeted protein kinase inhibitors: application for the native and mutant (T315I) Bcr-Abl tyrosine kinase | Full Text | References | PDF (3.3 MB) | EPUB
  • 309 Views
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Article
Mining of molecular insights of CYP2A6 and its variants complex with coumarin (CYP2A6*-coumarin) using molecular dynamics simulation
Anamika Yadav, Akanksha Kesharwani, Dheeraj Kumar Chaurasia & Pramod Katara
Pages: 4081-4092
Published online: 15 Apr 2022
AbstractforMining of molecular insights of CYP2A6 and its variants complex with coumarin (CYP2A6*-coumarin) using molecular dynamics simulation | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 243 Views
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Article
A molecular dynamics perspective into estrogen receptor inhibition by selective flavonoids as alternative therapeutic options
Angela Sinyani, Kehinde Idowu, Letitia Shunmugam, Hezekiel Mathambo Kumalo & Rene Khan
Pages: 4093-4105
Published online: 27 Apr 2022
AbstractforA molecular dynamics perspective into estrogen receptor inhibition by selective flavonoids as alternative therapeutic options | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 2873 Views
  • 3 CrossRef citations
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Open Access
Article
Evaluation of phytoconstituents of Tinospora cordifolia against K417N and N501Y mutant spike glycoprotein and main protease of SARS-CoV-2- an in silico study
Princy Choudhary, Tanu Singh, Ayush Amod & Sangeeta Singh
Pages: 4106-4123
Published online: 25 Apr 2022
AbstractforEvaluation of phytoconstituents of Tinospora cordifolia against K417N and N501Y mutant spike glycoprotein and main protease of SARS-CoV-2- an in silico study | Full Text | References | PDF (5.3 MB) | EPUB | Supplemental
  • 206 Views
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Article
Combined machine learning and pharmacophore based virtual screening approaches to screen for antibiofilm inhibitors targeting LasR of Pseudomonas aeruginosa
Aishwarya Vetrivel, Janani Ramasamy, Santhi Natchimuthu, Kalaiselvi Senthil, Monica Ramasamy & Rajeswari Murugesan
Pages: 4124-4142
Published online: 22 Apr 2022
AbstractforCombined machine learning and pharmacophore based virtual screening approaches to screen for antibiofilm inhibitors targeting LasR of Pseudomonas aeruginosa | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 392 Views
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Article
Pharmacological assessment of Ru(II) complex with GidA protein- A novel topoisomerase II inhibitor towards cancer therapeutics
Antony K Teresa Infanta. S, Nisshanthini Durairaju, Senthil Raja, Thandeeswaran Murugesan, Anand Raj Dhanapal, Karupannan Natarajan, Ajithkumar Balakrishnan, Hemamalini Vedagiri, Palaniswamy Muthusamy & Angayarkanni Jayaraman
Pages: 4143-4153
Published online: 05 May 2022
AbstractforPharmacological assessment of Ru(II) complex with GidA protein- A novel topoisomerase II inhibitor towards cancer therapeutics | Full Text | References | PDF (1.8 MB) | EPUB
  • 135 Views
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Article
Assessing the effect of a series of mutations on the dynamic behavior of phosphite dehydrogenase using molecular docking, molecular dynamics and quantum mechanics/molecular mechanics simulations
Soukayna Baammi, Rachid Daoud & Achraf El Allali
Pages: 4154-4166
Published online: 20 Apr 2022
AbstractforAssessing the effect of a series of mutations on the dynamic behavior of phosphite dehydrogenase using molecular docking, molecular dynamics and quantum mechanics/molecular mechanics simulations | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 317 Views
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Article
Synthesis, structural characterization, antioxidant and antidiabetic activities, DFT calculation, and molecular docking of novel substituted phenolic and heterocyclic compounds
Sanae Lahmidi, El Hassane Anouar, Salma Mortada, Mohamed El Hafi, Faouzi My El Abbes, El Mokhtar Essassi & Joel T. Mague
Pages: 4167-4179
Published online: 20 Apr 2022
AbstractforSynthesis, structural characterization, antioxidant and antidiabetic activities, DFT calculation, and molecular docking of novel substituted phenolic and heterocyclic compounds | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 155 Views
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Article
Understanding the binding behavior of Malathion with calf thymus DNA by spectroscopic, cell viability and molecular dynamics simulation techniques: binary and ternary systems comparison
Sara Ezazi-Toroghi, Shadi Salarinejad, Melika Kamkar-Vatanparast, Parisa Mokaberi, Zeinab Amiri-Tehranizadeh, Mohammad Reza Saberi & Jamshidkhan Chamani
Pages: 4180-4193
Published online: 18 Apr 2022
AbstractforUnderstanding the binding behavior of Malathion with calf thymus DNA by spectroscopic, cell viability and molecular dynamics simulation techniques: binary and ternary systems comparison | Full Text | References | PDF (2.6 MB) | EPUB
  • 130 Views
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Article
Targeting EGFR, RSK1, RAF1, PARP2 and LIN28B for several cancer type therapies with newly synthesized pyrazole derivatives via a computational study
Fatima Ezzahra Bennani, Latifa Doudach, Khalid Karrouchi, Abdelilah Tarib, Christopher E Rudd, M’hammed Ansar & My El Abbes Faouzi
Pages: 4194-4218
Published online: 20 Apr 2022
AbstractforTargeting EGFR, RSK1, RAF1, PARP2 and LIN28B for several cancer type therapies with newly synthesized pyrazole derivatives via a computational study | Full Text | References | PDF (5.9 MB) | EPUB | Supplemental
  • 274 Views
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Review Article

Review Article
Recent progression of cyanobacteria and their pharmaceutical utility: an update
Ajit Kumar Bishoyi, Chita Ranjan Sahoo & Rabindra Nath Padhy
Pages: 4219-4252
Published online: 12 Apr 2022
AbstractforRecent progression of cyanobacteria and their pharmaceutical utility: an update | Full Text | References | PDF (8.2 MB) | EPUB
  • 368 Views
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