Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 14 (2023)

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Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 14 (2023)

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Research Articles

Article
Molecular dynamics and docking studies on potentially active natural phytochemicals for targeting SARS-CoV-2 main protease
Sandhya Karakkadparambil Sankaran & Achuthsankar S. Nair
Pages: 6459-6475
Published online: 05 Aug 2022
AbstractforMolecular dynamics and docking studies on potentially active natural phytochemicals for targeting SARS-CoV-2 main protease | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 265 Views
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Article
High-resolution liquid chromatography and mass spectrometry (HR-LCMS) assisted phytochemical profiling and an assessment of anticancer activities of Gracilaria foliifera and Turbinaria conoides using in vitro and molecular docking analysis
Mohini Anandrao Salunke, Balaji Sopanrao Wakure & Pravin Shridhar Wakte
Pages: 6476-6491
Published online: 17 Aug 2022
AbstractforHigh-resolution liquid chromatography and mass spectrometry (HR-LCMS) assisted phytochemical profiling and an assessment of anticancer activities of Gracilaria foliifera and Turbinaria conoides using in vitro and molecular docking analysis | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 217 Views
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Article
Mechanistic insight toward EGFR activation induced by ATP: role of mutations and water in ATP binding patterns
Emiliano Laudadio, Giovanna Mobbili, Leonardo Sorci, Roberta Galeazzi & Cristina Minnelli
Pages: 6492-6501
Published online: 13 Aug 2022
AbstractforMechanistic insight toward EGFR activation induced by ATP: role of mutations and water in ATP binding patterns | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 196 Views
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Article
A computational study to target necroptosis via RIPK1 inhibition
Asim Kumar Bepari, Hirohide Takebayashi, Jannatun Nayem Namme, Ghazi Muhammad Sayedur Rahman & Hasan Mahmud Reza
Pages: 6502-6517
Published online: 08 Aug 2022
AbstractforA computational study to target necroptosis via RIPK1 inhibition | Full Text | References | PDF (5.4 MB) | EPUB | Supplemental
  • 381 Views
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Article
Structural aspects of SARS-CoV-2 mutations: Implications to plausible infectivity with ACE-2 using computational modeling approach
Priyanka Gopi, Manisha Gurnani, Shweta Singh, Palak Sharma & Prateek Pandya
Pages: 6518-6533
Published online: 08 Aug 2022
AbstractforStructural aspects of SARS-CoV-2 mutations: Implications to plausible infectivity with ACE-2 using computational modeling approach | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 276 Views
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Article
Spectrin: an alternate target for cytoskeletal drugs
Sansa Dutta, Dipayan Bose, Semanti Ghosh & Abhijit Chakrabarti
Pages: 6534-6545
Published online: 22 Aug 2022
AbstractforSpectrin: an alternate target for cytoskeletal drugs | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 192 Views
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Article
Association study of leptin receptor polymorphisms in women with obesity and their impact on protein domains: a case-control study and in silico analyses
Meriem El Fessikh, Zouhair Elkarhat, Delphine Flatters, Anne-Claude Camproux, Hakim Belghiti, Hassania Guerinech, Youssef Bakri, Nadia Dakka & Jamila El Baghdadi
Pages: 6546-6558
Published online: 13 Aug 2022
AbstractforAssociation study of leptin receptor polymorphisms in women with obesity and their impact on protein domains: a case-control study and in silico analyses | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 114 Views
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Article
Molecular insights into the structural and dynamical changes of calcium channel TRPV6 induced by its interaction with phosphatidylinositol 4,5-bisphosphate
Lingyun Wang, Ruiqi Cai, Xing-Zhen Chen & Ji-Bin Peng
Pages: 6559-6568
Published online: 11 Aug 2022
AbstractforMolecular insights into the structural and dynamical changes of calcium channel TRPV6 induced by its interaction with phosphatidylinositol 4,5-bisphosphate | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 192 Views
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Article
Development of QSAR model using machine learning and molecular docking study of polyphenol derivatives against obesity as pancreatic lipase inhibitor
Shristi Modanwal, Akhilesh Kumar Maurya, Saurav Kumar Mishra & Nidhi Mishra
Pages: 6569-6580
Published online: 10 Aug 2022
AbstractforDevelopment of QSAR model using machine learning and molecular docking study of polyphenol derivatives against obesity as pancreatic lipase inhibitor | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 482 Views
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Article
Ab initio modelling of an essential mammalian protein: Transcription Termination Factor 1 (TTF1)
Kumud Tiwari, Aditi Gangopadhyay, Gajender Singh, Vinay Kumar Singh & Samarendra Kumar Singh
Pages: 6581-6590
Published online: 10 Aug 2022
AbstractforAb initio modelling of an essential mammalian protein: Transcription Termination Factor 1 (TTF1) | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 172 Views
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Article
Interaction of the insecticide bioallethrin with human hemoglobin: biophysical, in silico and enzymatic studies
Amin Arif, Md. Amiruddin Hashmi, Samreen Salam, Hina Younus & Riaz Mahmood
Pages: 6591-6602
Published online: 11 Aug 2022
AbstractforInteraction of the insecticide bioallethrin with human hemoglobin: biophysical, in silico and enzymatic studies | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 149 Views
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Article
Chemoprofiling and insilico prioritization of bioactive compounds from Laetiporus versisporus (Lloyd) Imazeki reveals potential Bcl-2 inhibitor
Shoba G, Samdani A, Umashankar Vetrivel & Usha Raja Nanthini Ayyakannu
Pages: 6603-6615
Published online: 16 Aug 2022
AbstractforChemoprofiling and insilico prioritization of bioactive compounds from Laetiporus versisporus (Lloyd) Imazeki reveals potential Bcl-2 inhibitor | Full Text | References | PDF (3.1 MB) | EPUB
  • 94 Views
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Article
Anti-lung cancer drug discovery approaches by polysaccharides: an in silico study, quantum calculation and molecular dynamics study
Md. Eleas Kobir, Asif Ahmed, Md. Abul Hasan Roni, Unesco Chakma, Md. Ruhul Amin, Akhel Chandro & Ajoy Kumer
Pages: 6616-6632
Published online: 13 Aug 2022
AbstractforAnti-lung cancer drug discovery approaches by polysaccharides: an in silico study, quantum calculation and molecular dynamics study | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 431 Views
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Article
Unveiling the multitargeted potential of N-(4-Aminobutanoyl)-S-(4-methoxybenzyl)-L-cysteinylglycine (NSL-CG) against SARS CoV-2: a virtual screening and molecular dynamics simulation study
Youssef Saeed Alghamdi, Mutaib M. Mashraqi, Ahmad Alzamami, Norah A. Alturki, Shaban Ahmad, Afaf Awwadh Alharthi, Saleh Alshamrani & Saeed A. Asiri
Pages: 6633-6642
Published online: 16 Aug 2022
AbstractforUnveiling the multitargeted potential of N-(4-Aminobutanoyl)-S-(4-methoxybenzyl)-L-cysteinylglycine (NSL-CG) against SARS CoV-2: a virtual screening and molecular dynamics simulation study | Full Text | References | PDF (2 MB) | EPUB
  • 162 Views
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Article
Phytochemical drug discovery for COVID-19 using high-resolution computational docking and machine learning assisted binder prediction
Zirui Wang, Theodore Belecciu, Joelle Eaves, Mark Reimers, Michael H. Bachmann & Daniel Woldring
Pages: 6643-6663
Published online: 22 Aug 2022
AbstractforPhytochemical drug discovery for COVID-19 using high-resolution computational docking and machine learning assisted binder prediction | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 364 Views
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Article
Novel drug design framework as a response to neglected and emerging diseases
Stanisław Kulczyk & Mariola Koszytkowska-Stawińska
Pages: 6664-6675
Published online: 13 Aug 2022
AbstractforNovel drug design framework as a response to neglected and emerging diseases | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 190 Views
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Article
Immunoinformatics design of multi-epitope peptide for the diagnosis of Schistosoma haematobium infection
Elijah Kolawole Oladipo, Esther Moradeyo Jimah, Boluwatife Abayomi Irewolede, Elizabeth Oluwatoyin Folakanmi, Odunola Abimbola Olubodun, Daniel Adewole Adediran, Samuel Adebowale Akintibubo, Foluso Daniel Odunlami, Seun Elijah Olufemi, Taiwo Ooreoluwa Ojo, Omodamola Paulina Akinro, Oluwaseun Samuel Hezekiah, Adenike Titilayo Olayinka, Grace Asegunloluwa Abiala, Akindele Felix Idowu, James Akinwunmi Ogunniran, Mary Omotoyinbo Ikuomola, Hadijat Motunrayo Adegoke, Usman Abiodun Idowu, Olawumi Elizabeth Akindiya, Glory Jesudara Oluwasanya, Gideon Mayowa Akanbi, Favour Oluwadara Bamigboye, Rasidat Oyindamola Aremu, Hezekiah Oluwajoba Awobiyi, Kehinde Temitope Kolapo, Jerry Ayobami Oluwasegun, Simeon Kayowa Olatunde & Temitope Isaac Adelusi
Pages: 6676-6683
Published online: 13 Aug 2022
AbstractforImmunoinformatics design of multi-epitope peptide for the diagnosis of Schistosoma haematobium infection | Full Text | References | PDF (1.4 MB) | EPUB
  • 411 Views
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Article
New sulphonamide-peptide hybrid molecules as potential PBP 2a ligands and methicillin resistant Staphylococcus aureus actives
Akachukwu Ibezim, Raphael Onuku, Chidalu Ottih, Ifeoma Ezeonu, Efeturi Onoabedje, Karuppasamy Ramanathan & Ngozi Nwodo
Pages: 6684-6694
Published online: 17 Aug 2022
AbstractforNew sulphonamide-peptide hybrid molecules as potential PBP 2a ligands and methicillin resistant Staphylococcus aureus actives | Full Text | References | PDF (3.6 MB) | EPUB
  • 140 Views
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Article
Drug design of new therapeutic agents: molecular docking, molecular dynamics simulation, DFT and POM analyses of new Schiff base ligands and impact of substituents on bioactivity of their potential antifungal pharmacophore site
Senem Akkoc, Halis Karatas, Muhammed Tilahun Muhammed, Zülbiye Kökbudak, Ahmet Ceylan, Faisal Almalki, Hamid Laaroussi & Taibi Ben Hadda
Pages: 6695-6708
Published online: 13 Aug 2022
AbstractforDrug design of new therapeutic agents: molecular docking, molecular dynamics simulation, DFT and POM analyses of new Schiff base ligands and impact of substituents on bioactivity of their potential antifungal pharmacophore site | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 735 Views
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Article
Virtual screening reveals liquiritigenin as a broad-spectrum inhibitor of SARS-CoV-2 variants of concern: an in silico study
Sheikh Sunzid Ahmed, Abdullah Al-Mamun, Shah Imran Hossain, Farzana Akter, Ishtiaque Ahammad, Zeshan Mahmud Chowdhury & Md. Salimullah
Pages: 6709-6727
Published online: 16 Aug 2022
AbstractforVirtual screening reveals liquiritigenin as a broad-spectrum inhibitor of SARS-CoV-2 variants of concern: an in silico study | Full Text | References | PDF (3.5 MB) | EPUB
  • 268 Views
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Article
Virtual screening and molecular dynamics study of natural products against Rab10 for the treatment of Alzheimer’s disease
Levy Bueno Alves, Willian Orlando Castillo-Ordoñez & Silvana Giuliatti
Pages: 6728-6748
Published online: 22 Aug 2022
AbstractforVirtual screening and molecular dynamics study of natural products against Rab10 for the treatment of Alzheimer’s disease | Full Text | References | PDF (6.1 MB) | EPUB | Supplemental
  • 321 Views
  • 1 CrossRef citations
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Article
Identifying Isoononin and Candidissiol as Rho-associated protein kinase 1 (ROCK1) inhibitors: a combined virtual screening and MD simulation approach
Bader Saud Alotaibi, Jatin Joshi, Mohammad Raghibul Hasan, Mohd Shahnawaz Khan, Salem Hussain Alharethi, Taj Mohammad, Fahad A. Alhumaydhi, Abdelbaset Mohamed Elasbali & Md. Imtaiyaz Hassan
Pages: 6749-6758
Published online: 13 Aug 2022
AbstractforIdentifying Isoononin and Candidissiol as Rho-associated protein kinase 1 (ROCK1) inhibitors: a combined virtual screening and MD simulation approach | Full Text | References | PDF (2.5 MB) | EPUB
  • 256 Views
  • 7 CrossRef citations
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Article
Atom-based 3D-QSAR and DFT analysis of 5‐substituted 2‐acylaminothiazole derivatives as HIV-1 latency-reversing agents
Mohammad Aqueel Khan & Sanjeev Kumar Singh
Pages: 6759-6774
Published online: 16 Aug 2022
AbstractforAtom-based 3D-QSAR and DFT analysis of 5‐substituted 2‐acylaminothiazole derivatives as HIV-1 latency-reversing agents | Full Text | References | PDF (3.2 MB) | EPUB
  • 154 Views
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Article
Discovery of novel potential inhibitors of TMPRSS2 and Mpro of SARS‐CoV‐2 using E-pharmacophore and docking-based virtual screening combined with molecular dynamic and quantum mechanics
Mohanad A. Mahgoub, Ahmed Alnaem, Mohammed Fadlelmola, Mazin Abo-idris, Alaa A. Makki, Abdelgadir A. Abdelgadir & Abdulrahim A. Alzain
Pages: 6775-6788
Published online: 23 Aug 2022
AbstractforDiscovery of novel potential inhibitors of TMPRSS2 and Mpro of SARS‐CoV‐2 using E-pharmacophore and docking-based virtual screening combined with molecular dynamic and quantum mechanics | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 237 Views
  • 3 CrossRef citations
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Article
Identification of new small molecule monoamine oxidase-B inhibitors through pharmacophore-based virtual screening, molecular docking and molecular dynamics simulation studies
Sandeep Kumar & Senthil Raja Ayyannan
Pages: 6789-6810
Published online: 18 Aug 2022
AbstractforIdentification of new small molecule monoamine oxidase-B inhibitors through pharmacophore-based virtual screening, molecular docking and molecular dynamics simulation studies | Full Text | References | PDF (6.8 MB) | EPUB | Supplemental
  • 554 Views
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Article
Crystal structure analysis and molecular dynamics simulations of arginase from Thermus thermophilus
Dhanalakshmi K, Seiki Kuramitsu, Shigeyuki Yokoyama, Kumarevel Thirumananseri & Karthe Ponnuraj
Pages: 6811-6821
Published online: 22 Aug 2022
AbstractforCrystal structure analysis and molecular dynamics simulations of arginase from Thermus thermophilus | Full Text | References | PDF (3.4 MB) | EPUB
  • 165 Views
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Article
Repurposing small molecules of Tephrosia purpurea against SARS-CoV-2 main protease
Rosaleen Sahoo, Parameswar Sahu, Sandeep Swargam, Indu Kumari & Banshidhar Behera
Pages: 6822-6833
Published online: 18 Aug 2022
AbstractforRepurposing small molecules of Tephrosia purpurea against SARS-CoV-2 main protease | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 204 Views
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Article
Interaction of panduratin A and derivatives with the SARS-CoV-2 main protease (mpro): a molecular docking study
Gérard Vergoten & Christian Bailly
Pages: 6834-6844
Published online: 17 Aug 2022
AbstractforInteraction of panduratin A and derivatives with the SARS-CoV-2 main protease (mpro): a molecular docking study | Full Text | References | PDF (2.3 MB) | EPUB
  • 219 Views
  • 2 CrossRef citations
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Article
HIF1 inhibition of the biflavonoids against pancreas cancer: drug-likeness, bioavailability, ADMET, PASS, molecular docking, molecular dynamics, and MM/GBSA calculations
Lucas Soares Frota, Matheus Nunes da Rocha, Lucas Lima Bezerra, Aluísio Marques da Fonseca, Emmanuel Silva Marinho & Selene Maia de Morais
Pages: 6845-6856
Published online: 24 Aug 2022
AbstractforHIF1 inhibition of the biflavonoids against pancreas cancer: drug-likeness, bioavailability, ADMET, PASS, molecular docking, molecular dynamics, and MM/GBSA calculations | Full Text | References | PDF (3.1 MB) | EPUB
  • 277 Views
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Article
Rational design of 1,2,3-triazole hybrid structures as novel anticancer agents: synthesis, biological evaluation and molecular docking studies
Aynur Çot, Mustafa Çeşme, Sultan Onur, Elif Aksakal, İrfan Şahin & Ferhan Tümer
Pages: 6857-6865
Published online: 18 Aug 2022
AbstractforRational design of 1,2,3-triazole hybrid structures as novel anticancer agents: synthesis, biological evaluation and molecular docking studies | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 521 Views
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Article
Identification of a promising inhibitor from Illicium verum (star anise) against the main protease of SARS-CoV-2: insights from the computational study
Manish Kumar Tripathi, Pushpendra Singh, Mukesh Kumar, Kuldeep Sharma, T. P. Singh, A. S. Ethayathulla & Punit Kaur
Pages: 6866-6882
Published online: 18 Aug 2022
AbstractforIdentification of a promising inhibitor from Illicium verum (star anise) against the main protease of SARS-CoV-2: insights from the computational study | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 173 Views
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Article
Analysis of medicinal and therapeutic potential of Withania somnifera derivatives against COVID-19
Saman Zare Gheshlaghi, Ebrahim Nakhaei, Ali Ebrahimi, Majid Jafari, Asiyeh Shahraki, Shiva Rezazadeh, Erfan Saberinasab, Alireza Nowroozi & Seyede Samira Hosseini
Pages: 6883-6893
Published online: 22 Aug 2022
AbstractforAnalysis of medicinal and therapeutic potential of Withania somnifera derivatives against COVID-19 | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 118 Views
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Article
Identification of NEK7 inhibitors: structure based virtual screening, molecular docking, density functional theory calculations and molecular dynamics simulations
Mubashir Aziz, Syeda Abida Ejaz, Hafiz Muzzammel Rehman, A. SA. Alsubaie, K. H. Mahmoud, Farhan Siddique, M. S. Al-Buriahi & Z. A. Alrowaili
Pages: 6894-6908
Published online: 18 Aug 2022
AbstractforIdentification of NEK7 inhibitors: structure based virtual screening, molecular docking, density functional theory calculations and molecular dynamics simulations | Full Text | References | PDF (3.9 MB) | EPUB
  • 572 Views
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Article
Drug repurposing against galectin-3 using simulation-based studies
Ghulam Md Ashraf, Mohd Rehan, Alhuseen O. Alsayed, Pallavi Somvanshi & Shafiul Haque
Pages: 6909-6916
Published online: 02 Oct 2022
AbstractforDrug repurposing against galectin-3 using simulation-based studies | Full Text | References | PDF (1.9 MB) | EPUB
  • 167 Views
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Article
Assessment of tools for RNA secondary structure prediction and extraction: a final-user perspective
Margherita A. G. Matarrese, Alessandro Loppini, Martina Nicoletti, Simonetta Filippi & Letizia Chiodo
Pages: 6917-6936
Published online: 15 Sep 2022
AbstractforAssessment of tools for RNA secondary structure prediction and extraction: a final-user perspective | Full Text | References | PDF (4.6 MB) | EPUB | Supplemental
  • 373 Views
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Article
Interdisciplinary in silico studies to understand in-depth molecular level mechanism of drug resistance involving NS3-4A protease of HCV
Mousumi Hazra & Ramesh Chandra Dubey
Pages: 6937-6956
Published online: 22 Aug 2022
AbstractforInterdisciplinary in silico studies to understand in-depth molecular level mechanism of drug resistance involving NS3-4A protease of HCV | Full Text | References | PDF (4.7 MB) | EPUB | Supplemental
  • 159 Views
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Article
Absolute binding free energies of mucroporin and its analog mucroporin-M1 with the heptad repeat 1 domain and RNA-dependent RNA polymerase of SARS-CoV-2
Felipe Rodrigues Souza, Paloma Guimarães Moura, Rayla Kelly Magalhães Costa, Rudielson Santos Silva & André Silva Pimentel
Pages: 6957-6968
Published online: 22 Aug 2022
AbstractforAbsolute binding free energies of mucroporin and its analog mucroporin-M1 with the heptad repeat 1 domain and RNA-dependent RNA polymerase of SARS-CoV-2 | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 161 Views
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Article
Systems biology approach delineates critical pathways associated with disease progression in rheumatoid arthritis
Sai Krishna Srimadh Bhagavatham, Sujith Kumar Pulukool, Sai Sanwid Pradhan, Saiswaroop R.Ashwin Ashok Naik, Datta Darshan V. M.Venketesh Sivaramakrishnan
Pages: 6969-6990
Published online: 01 Sep 2022
AbstractforSystems biology approach delineates critical pathways associated with disease progression in rheumatoid arthritis | Full Text | References | PDF (5.1 MB) | EPUB | Supplemental
  • 420 Views
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Review Articles

Review Article
2D-QSAR, docking, molecular dynamics, studies of PF-07321332 analogues to identify alternative inhibitors against 3CLpro enzyme in SARS-CoV disease
Said Bitam, Mabrouk Hamadache & Salah Hanini
Pages: 6991-7000
Published online: 18 Aug 2022
Abstractfor2D-QSAR, docking, molecular dynamics, studies of PF-07321332 analogues to identify alternative inhibitors against 3CLpro enzyme in SARS-CoV disease | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 210 Views
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Opinion Piece

Article
Giloy: a potential anti-COVID-19 herb with propitious pharmacological attributes: a short review
Shefali Arora, Anjali Goyal, Devendra Singh Rawat & Krishna Samantha
Pages: 7001-7008
Published online: 11 Aug 2022
AbstractforGiloy: a potential anti-COVID-19 herb with propitious pharmacological attributes: a short review | Full Text | References | PDF (1.9 MB) | EPUB
  • 128 Views
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