Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 18 (2023)

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Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 18 (2023)

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Research Articles

Article
3D QSAR pharmacophore based lead identification of G9a lysine methyltransferase towards epigenetic therapeutics
Abhisek Jana, Rahul Naga, Sougata Saha & Deb Ranjan Banerjee
Pages: 8635-8653
Published online: 20 Oct 2022
Abstractfor3D QSAR pharmacophore based lead identification of G9a lysine methyltransferase towards epigenetic therapeutics | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
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Article
Identification of defactinib derivatives targeting focal adhesion kinase using ensemble docking, molecular dynamics simulations and binding free energy calculations
Chuan Guo, Qinxuan Li, Jiujia Xiao, Feng Ma, Xun Xia & Mingsong Shi
Pages: 8654-8670
Published online: 25 Oct 2022
AbstractforIdentification of defactinib derivatives targeting focal adhesion kinase using ensemble docking, molecular dynamics simulations and binding free energy calculations | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 386 Views
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Article
Binding of piperine to mycobacterial RNA polymerase improves the efficacy of rifampicin activity against Mycobacterium leprae and nontuberculous mycobacteria
Letícia Sayuri Murase, Diego de Souza Lima, João Vítor Perez de Souza, Carolina Trevisolli Palomo, Katiany Rizzieri Caleffi-Ferracioli, Regiane Bertin de Lima Scodro, Vera Lúcia Dias Siqueira, Flavio Augusto Vicente Seixas & Rosilene Fressatti Cardoso
Pages: 8671-8681
Published online: 18 Oct 2022
AbstractforBinding of piperine to mycobacterial RNA polymerase improves the efficacy of rifampicin activity against Mycobacterium leprae and nontuberculous mycobacteria | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 154 Views
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Article
Pharmacological inhibition of cathepsin C (CatC) as a potential approach for cancer therapeutics
Syed Ainul Abideen, Murad Khan, Alhanouf I. Al-Harbi & Sajjad Ahmad
Pages: 8682-8689
Published online: 20 Oct 2022
AbstractforPharmacological inhibition of cathepsin C (CatC) as a potential approach for cancer therapeutics | Full Text | References | PDF (1.2 MB) | EPUB | Supplemental
  • 181 Views
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Article
Virtually selected phytochemicals from edible seeds as possible potential medicaments for hypercholesterolemia: an in silico approach
Shubhi Singh & Smriti Gaur
Pages: 8690-8700
Published online: 19 Oct 2022
AbstractforVirtually selected phytochemicals from edible seeds as possible potential medicaments for hypercholesterolemia: an in silico approach | Full Text | References | PDF (1.3 MB) | EPUB | Supplemental
  • 199 Views
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Article
Synthesis and characterization of a novel Mannich base benzimidazole derivative to explore interaction with human serum albumin and antimicrobial property: experimental and theoretical approach
F. M. Mashood Ahamed, Barkha Shakya & Sonam Shakya
Pages: 8701-8714
Published online: 25 Oct 2022
AbstractforSynthesis and characterization of a novel Mannich base benzimidazole derivative to explore interaction with human serum albumin and antimicrobial property: experimental and theoretical approach | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 251 Views
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Article
Computational identification and experimental validation of anti-filarial lead molecules targeting metal binding/substrate channel residues of Cu/Zn SOD1 from Wuchereria bancrofti
Muthusamy Sureshan, Dhamodharan Prabhu & Saraboji Kadhirvel
Pages: 8715-8728
Published online: 28 Oct 2022
AbstractforComputational identification and experimental validation of anti-filarial lead molecules targeting metal binding/substrate channel residues of Cu/Zn SOD1 from Wuchereria bancrofti | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 162 Views
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Article
New hybrids based on benzimidazole and diazepine moieties: design, synthesis, characterization, molecular docking studies and their in vitro interactions with benzodiazepine receptors
Samaneh Takhti, Mehdi Pordel, Mohammad Reza Bozorgmehr & Abolghasem Davoodnia
Pages: 8729-8737
Published online: 21 Oct 2022
AbstractforNew hybrids based on benzimidazole and diazepine moieties: design, synthesis, characterization, molecular docking studies and their in vitro interactions with benzodiazepine receptors | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 133 Views
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Article
Computational approaches for innovative anti-viral drug discovery using Orthosiphon aristatus blume miq against dengue virus
Sumera Zaib, Fatima Akram, Wania Waris, Syed Talha Liaqat, Zainab Zaib, Imtiaz Khan, Ayed A. Dera, Rami Adel Pashameah, Eman Alzahrani & Abd-ElAziem Farouk
Pages: 8738-8750
Published online: 27 Oct 2022
AbstractforComputational approaches for innovative anti-viral drug discovery using Orthosiphon aristatus blume miq against dengue virus | Full Text | References | PDF (2 MB) | EPUB
  • 258 Views
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Article
Intercalative binding of two new five-coordinated anticancer Pt(II) complexes to DNA: experimental and computational approaches
Fayezeh Samari, Bahram Hemmateenejad, Santiago Aparicio, Mehdi Rashidi, Mojtaba Shamsipur & Sayed Mostafa Hosseini
Pages: 8751-8761
Published online: 01 Nov 2022
AbstractforIntercalative binding of two new five-coordinated anticancer Pt(II) complexes to DNA: experimental and computational approaches | Full Text | References | PDF (2.3 MB) | EPUB
  • 168 Views
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Article
Insights into molecular docking and dynamics to reveal therapeutic potential of natural compounds against P53 protein
Bashir Ahmad Malla, Aarif Ali, Irfan Maqbool, Nazir Ahmad Dar, Sheikh Bilal Ahmad, Rana M. Alsaffar & Muneeb U. Rehman
Pages: 8762-8781
Published online: 25 Oct 2022
AbstractforInsights into molecular docking and dynamics to reveal therapeutic potential of natural compounds against P53 protein | Full Text | References | PDF (4.8 MB) | EPUB
  • 575 Views
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Article
Structural and spectroscopic details of polysaccharide–bile acid composites from molecular dynamics simulations
Sruthi Peesapati & Durba Roy
Pages: 8782-8794
Published online: 30 Oct 2022
AbstractforStructural and spectroscopic details of polysaccharide–bile acid composites from molecular dynamics simulations | Full Text | References | PDF (2.4 MB) | EPUB
  • 110 Views
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Article
In vitro and in silico binding studies of phytochemical isochroman with calf thymus DNA using multi-spectroscopic and computational modelling techniques
Sana Fatima, Irfan Hussain, Shahbaz Ahmed & Mohammad Tabish
Pages: 8795-8809
Published online: 25 Oct 2022
AbstractforIn vitro and in silico binding studies of phytochemical isochroman with calf thymus DNA using multi-spectroscopic and computational modelling techniques | Full Text | References | PDF (2 MB) | EPUB
  • 135 Views
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Article
Interaction of heavy metals in Drosophila melanogaster larvae: Fourier transform infrared spectroscopy and single-cell electrophoresis study
B. Saroha, A. Kumar, V. Bhan, S. Singh, K. Tumba, P. Singh & I. Bahadur
Pages: 8810-8823
Published online: 21 Nov 2022
AbstractforInteraction of heavy metals in Drosophila melanogaster larvae: Fourier transform infrared spectroscopy and single-cell electrophoresis study | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 148 Views
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Article
Role of lisinopril in the therapeutic management of cardiovascular disease by targeting microtubule affinity regulating kinase 4: molecular docking and molecular dynamics simulation approaches
Akhtar Atiya, Abdulrhman Alsayari, Abdullatif Bin Muhsinah, Dalia Almaghaslah, Anwar L. Bilgrami, Waleed Al Abdulmonem, Nasser M. Alorfi, Debarati DasGupta, Ghulam Md. Ashraf, Anas Shamsi & Moyad Shahwan
Pages: 8824-8830
Published online: 14 Nov 2022
AbstractforRole of lisinopril in the therapeutic management of cardiovascular disease by targeting microtubule affinity regulating kinase 4: molecular docking and molecular dynamics simulation approaches | Full Text | References | PDF (1.1 MB) | EPUB
  • 194 Views
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Article
Identification of potential mutational hotspots in serratiopeptidase to address its poor pH tolerance issue
Ankita Dhiman & Rituraj Purohit
Pages: 8831-8843
Published online: 28 Oct 2022
AbstractforIdentification of potential mutational hotspots in serratiopeptidase to address its poor pH tolerance issue | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 387 Views
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Article
DFT analysis on the adsorption of melamine in Ga12-N12/P12 nanocages: solvent effects, SERS analysis, reactivity properties
Jamelah S. Al-Otaibi, Y. Sheena Mary, Shyma Mary, Asmita Mondal & Nivedita Acharjee
Pages: 8844-8855
Published online: 27 Oct 2022
AbstractforDFT analysis on the adsorption of melamine in Ga12-N12/P12 nanocages: solvent effects, SERS analysis, reactivity properties | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 106 Views
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Article
Exploring the mechanism of action of podophyllotoxin derivatives through molecular docking, molecular dynamics simulation and MM/PBSA studies
Anamika Mishra, Viswajit Mulpuru & Nidhi Mishra
Pages: 8856-8865
Published online: 28 Oct 2022
AbstractforExploring the mechanism of action of podophyllotoxin derivatives through molecular docking, molecular dynamics simulation and MM/PBSA studies | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 185 Views
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Article
Identification of novel peptide inhibitors for the KRas-G12C variant to prevent oncogenic signaling
Amar Ajmal, Yasir Ali, Ajmal Khan, Abdul Wadood & Ashfaq Ur Rehman
Pages: 8866-8875
Published online: 27 Oct 2022
AbstractforIdentification of novel peptide inhibitors for the KRas-G12C variant to prevent oncogenic signaling | Full Text | References | PDF (1.6 MB) | EPUB
  • 504 Views
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Article
Synthesis, crystallographic, DNA binding, and molecular docking/dynamic studies of a privileged chalcone-sulfonamide hybrid scaffold as a promising anticancer agent
Moataz Shaldam, Haytham Tawfik, Heba Elmansi, Fathalla Belal, Koki Yamaguchi, Masaharu Sugiura & Galal Magdy
Pages: 8876-8890
Published online: 30 Oct 2022
AbstractforSynthesis, crystallographic, DNA binding, and molecular docking/dynamic studies of a privileged chalcone-sulfonamide hybrid scaffold as a promising anticancer agent | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 237 Views
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Article
Disordered regions endow structural flexibility to shell proteins and function towards shell–enzyme interactions in 1,2-propanediol utilization microcompartment
Gaurav Kumar, Jagadish Prasad Hazra & Sharmistha Sinha
Pages: 8891-8901
Published online: 01 Nov 2022
AbstractforDisordered regions endow structural flexibility to shell proteins and function towards shell–enzyme interactions in 1,2-propanediol utilization microcompartment | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 228 Views
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Article
Comprehensive analysis and validation reveal potential MYCN regulatory biomarkers associated with neuroblastoma prognosis
Xiuni Qin & Bo Chen
Pages: 8902-8917
Published online: 27 Oct 2022
AbstractforComprehensive analysis and validation reveal potential MYCN regulatory biomarkers associated with neuroblastoma prognosis | Full Text | References | PDF (3.4 MB) | EPUB
  • 246 Views
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Article
An in-silico insight into the predictive interaction of Apolipoprotein-E with Epstein-Barr virus proteins and their probable role in mediating Alzheimer’s disease
Deeksha Tiwari, Gaurava Srivastava, Omkar Indari, Vijay Tripathi, Mohammad Imran Siddiqi & Hem Chandra Jha
Pages: 8918-8926
Published online: 28 Oct 2022
AbstractforAn in-silico insight into the predictive interaction of Apolipoprotein-E with Epstein-Barr virus proteins and their probable role in mediating Alzheimer’s disease | Full Text | References | PDF (1.4 MB) | EPUB | Supplemental
  • 444 Views
  • 3 CrossRef citations
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Article
Comparative homology of Pleurotus ostreatus laccase enzyme: Swiss model or Modeller?
Marco Antonio Silva, José Cordeiro do Nascimento Júnior, Douglas Vieira Thomaz, Rafael Trindade Maia, Vinícius Costa Amador, Giovana Tommaso & Glauciane Danusa Coelho
Pages: 8927-8940
Published online: 30 Oct 2022
AbstractforComparative homology of Pleurotus ostreatus laccase enzyme: Swiss model or Modeller? | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 393 Views
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Article
Developing human olfactory network and exploring olfactory receptor-odorant interaction
Anju Sharma, Rajnish Kumar & Pritish Varadwaj
Pages: 8941-8960
Published online: 30 Oct 2022
AbstractforDeveloping human olfactory network and exploring olfactory receptor-odorant interaction | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 311 Views
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Article
Virtual screening and molecular dynamics simulation study of abyssomicins as potential inhibitors of COVID‐19 virus main protease and spike protein
Lamya H. Al-Wahaibi, Md Tabish Rehman, Muneera S. M. Al-Saleem, Omer A. Basudan, Ali A. El-Gamal, Mohamed S. A. Abdelkader, Mohamed F. AlAjmi & Wael M. Abdel-Mageed
Pages: 8961-8977
Published online: 27 Oct 2022
AbstractforVirtual screening and molecular dynamics simulation study of abyssomicins as potential inhibitors of COVID‐19 virus main protease and spike protein | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 285 Views
  • 1 CrossRef citations
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Article
In silico approaches and in vitro assays identify a coumarin derivative as antiviral potential against SARS-CoV-2
Gabriel Felix da Silva Gomes, Priscila Goes Camargo, Kaio Maciel de Santiago-Silva, Helena Tiemi Suzukawa, Ana Paula Sotero da Silva Ribeiro, Alexandre Orsato, Gerson Nakazato, Sueli Fumie Yamada-Ogatta, Ligia Carla Faccin-Galhardi, Camilo Henrique da Silva Lima, Marcelle de Lima Ferreira Bispo & Carla Cristina Perez
Pages: 8978-8991
Published online: 03 Nov 2022
AbstractforIn silico approaches and in vitro assays identify a coumarin derivative as antiviral potential against SARS-CoV-2 | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 322 Views
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Article
In silico designed microtubule-stabilizer drugs against tauopathy in Alzheimer’s disease
Edita Sarukhanyan & Thomas Dandekar
Pages: 8992-9012
Published online: 04 Nov 2022
AbstractforIn silico designed microtubule-stabilizer drugs against tauopathy in Alzheimer’s disease | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 196 Views
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Article
Elucidation of the anti-plasmodial activity of novel imidazole and oxazole compounds through computational and in vivo experimental approaches
Titilayo Omolara Johnson, Olugbenga Eyitayo Adeyemi, Abayomi Emmanuel Adegboyega, Segun Afolabi Olomu, Festus Enokela, Sherifat Ibrahim, Bernard Gwantu, Bukola Afolayan, Kamo Stephen, Abiodun Omokehinde Eseola, Winfried Plass & Oluyomi Stephen Adeyemi
Pages: 9013-9021
Published online: 30 Oct 2022
AbstractforElucidation of the anti-plasmodial activity of novel imidazole and oxazole compounds through computational and in vivo experimental approaches | Full Text | References | PDF (1.4 MB) | EPUB
  • 205 Views
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Article
Design, synthesis and molecular docking and ADME studies of novel hydrazone derivatives for AChE inhibitory, BBB permeability and antioxidant effects
Derya Osmaniye, Iqrar Ahmad, Begüm Nurpelin Sağlık, Serkan Levent, Harun M. Patel, Yusuf Ozkay & Zafer Asım Kaplancıklı
Pages: 9022-9038
Published online: 03 Nov 2022
AbstractforDesign, synthesis and molecular docking and ADME studies of novel hydrazone derivatives for AChE inhibitory, BBB permeability and antioxidant effects | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 520 Views
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Article
In silico characterization, molecular docking, and dynamic simulation of a novel fungal cell-death suppressing effector, MoRlpA as potential cathepsin B-like cysteine protease inhibitor during rice blast infection
Debrup Sarkar, Satyabrata Majumder, Kalyan Giri & Nazmiara Sabnam
Pages: 9039-9056
Published online: 08 Nov 2022
AbstractforIn silico characterization, molecular docking, and dynamic simulation of a novel fungal cell-death suppressing effector, MoRlpA as potential cathepsin B-like cysteine protease inhibitor during rice blast infection | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 361 Views
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Article
An immunoinformatic approach employing molecular docking and molecular dynamics simulation for evaluation of l-asparaginase produced by Bacillus velezensis
Fereshteh Hozoorbakhsh, Mozhgan Ghiasian, Fereshte Ghandehari, Zarrindokht Emami-Karvani & Maryam Khademi Dehkordi
Pages: 9057-9071
Published online: 15 Nov 2022
AbstractforAn immunoinformatic approach employing molecular docking and molecular dynamics simulation for evaluation of l-asparaginase produced by Bacillus velezensis | Full Text | References | PDF (2 MB) | EPUB
  • 188 Views
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Article
In Silico molecular docking and dynamic analysis of natural compounds against major non-structural proteins of SARS-COV-2
Muneeb U. Rehman, Aarif Ali, Ruhban Ansar, Azher Arafah, Zuha Imtiyaz, Tanveer A. Wani, Seema Zargar & Showkat A. Ganie
Pages: 9072-9088
Published online: 03 Nov 2022
AbstractforIn Silico molecular docking and dynamic analysis of natural compounds against major non-structural proteins of SARS-COV-2 | Full Text | References | PDF (3.2 MB) | EPUB
  • 328 Views
  • 7 CrossRef citations
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Article
Unravelling hub genes as potential therapeutic targets in lung cancer using integrated transcriptomic meta-analysis and in silico approach
Aiman Mushtaq, Prithvi Singh, Gulnaz Tabassum, Taj Mohammad, Md Imtaiyaz Hassan, Mansoor Ali Syed & Ravins Dohare
Pages: 9089-9102
Published online: 01 Nov 2022
AbstractforUnravelling hub genes as potential therapeutic targets in lung cancer using integrated transcriptomic meta-analysis and in silico approach | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 323 Views
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Article
Inhibition of the predicted allosteric site of the SARS-CoV-2 main protease through flavonoids
Bibi Kubra, Syed Lal Badshah, Shah Faisal, Mohamed Sharaf, Abdul-Hamid Emwas, Mariusz Jaremko & Mohnad Abdalla
Pages: 9103-9120
Published online: 20 Nov 2022
AbstractforInhibition of the predicted allosteric site of the SARS-CoV-2 main protease through flavonoids | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 337 Views
  • 3 CrossRef citations
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Article
PheroxyPyrabenz and Carbopyrropyridin against major proteins of SARS CoV-2: a comprehensive in-silico molecular docking and dynamics simulation studies
Misbahuddin M. Rafeeq, Alaa F. Nahhas, Najat Binothman, Alaa Hamed Habib, Majidah Aljadani, Ziaullah M. Sain, Abeer Al Tuwaijri, Mohammed Ali Alshehri & Othman R. Alzahrani
Pages: 9121-9133
Published online: 01 Nov 2022
AbstractforPheroxyPyrabenz and Carbopyrropyridin against major proteins of SARS CoV-2: a comprehensive in-silico molecular docking and dynamics simulation studies | Full Text | References | PDF (2.3 MB) | EPUB
  • 62 Views
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Article
An insight into the binding and inhibition of eye ζ-crystallin by the environmental toxin arsenic: implications in eye diseases
Md Amiruddin Hashmi, Ajamaluddin Malik, Faizan Abul Qais, Masood Alam Khan, Fahad Abdulrahman Alhumaydhi & Hina Younus
Pages: 9134-9142
Published online: 03 Nov 2022
AbstractforAn insight into the binding and inhibition of eye ζ-crystallin by the environmental toxin arsenic: implications in eye diseases | Full Text | References | PDF (1.8 MB) | EPUB
  • 105 Views
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Article
Structure and dynamic simulation-based interactions of benzenoids, pyrroles and organooxygen compounds for effective targeting of GPX4 in ischemic stroke
Namrata Sangwan, Jitender Singh, Arushi Chauhan, Ajay Prakash, Krishan L. Khanduja, Bikash Medhi & Pramod K Avti
Pages: 9143-9156
Published online: 03 Nov 2022
AbstractforStructure and dynamic simulation-based interactions of benzenoids, pyrroles and organooxygen compounds for effective targeting of GPX4 in ischemic stroke | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 164 Views
  • 3 CrossRef citations
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Article
Computational prediction of B and T-cell epitopes of Kyasanur Forest Disease virus marker proteins towards the development of precise diagnosis and potent subunit vaccine
Sayad Hafeez, Rajeshwara Achur, S. K. Kiran & N. B. Thippeswamy
Pages: 9157-9176
Published online: 06 Nov 2022
AbstractforComputational prediction of B and T-cell epitopes of Kyasanur Forest Disease virus marker proteins towards the development of precise diagnosis and potent subunit vaccine | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 321 Views
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Review Article

Review Article
Deep learning in drug discovery: a futuristic modality to materialize the large datasets for cheminformatics
Ali Raza, Talha Ali Chohan, Manal Buabeid, El-Shaima A. Arafa, Tahir Ali Chohan, Batool Fatima, Kishwar Sultana, Malik Saad Ullah & Ghulam Murtaza
Pages: 9177-9192
Published online: 28 Oct 2022
AbstractforDeep learning in drug discovery: a futuristic modality to materialize the large datasets for cheminformatics | Full Text | References | PDF (1.5 MB) | EPUB
  • 646 Views
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