Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 7 (2023)

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Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 7 (2023)

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Research Articles

Article
Simulation analysis of selective alanine mutation effect on stability of human prion protein
Kyung-Hoon Lee & Krzysztof Kuczera
Pages: 2619-2629
Published online: 18 Feb 2022
AbstractforSimulation analysis of selective alanine mutation effect on stability of human prion protein | Full Text | References | PDF (1.4 MB) | EPUB
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Article
Molecular interactions of esculin with bovine serum albumin and recognition of binding sites with spectroscopy and molecular docking
Mohd Aamir Qureshi, Mahmood Akbar, Mohd Amir & Saleem Javed
Pages: 2630-2644
Published online: 09 Feb 2022
AbstractforMolecular interactions of esculin with bovine serum albumin and recognition of binding sites with spectroscopy and molecular docking | Full Text | References | PDF (3.4 MB) | EPUB
  • 322 Views
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Article
Natural phytocompounds physalin D, withaferin a and withanone target L-asparaginase of Mycobacterium tuberculosis: a molecular dynamics study
Deepankar Sharma, Ravi Saini & Abha Mishra
Pages: 2645-2659
Published online: 08 Feb 2022
AbstractforNatural phytocompounds physalin D, withaferin a and withanone target L-asparaginase of Mycobacterium tuberculosis: a molecular dynamics study | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 217 Views
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Article
In silico evaluation of binding of phytochemicals from bayati (Anamirta cocculus Linn) to the glutathione-s-transferase of Asian Corn Borer (Ostrinia furnacalis Guenée)
Melvin A. Castrosanto, Annabelle T. Abrera, Marlon N. Manalo & Arabinda Ghosh
Pages: 2660-2666
Published online: 09 Feb 2022
AbstractforIn silico evaluation of binding of phytochemicals from bayati (Anamirta cocculus Linn) to the glutathione-s-transferase of Asian Corn Borer (Ostrinia furnacalis Guenée) | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 364 Views
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Article
Design, synthesis, and computational studies of benzimidazole derivatives as new antitubercular agents
Gozde Yalcin-Ozkat, Ronak H. Ersan, Mahmut Ulger, Seda T. Ulger, Serdar Burmaoglu, Ilkay Yildiz & Oztekin Algul
Pages: 2667-2686
Published online: 08 Feb 2022
AbstractforDesign, synthesis, and computational studies of benzimidazole derivatives as new antitubercular agents | Full Text | References | PDF (4.6 MB) | EPUB | Supplemental
  • 832 Views
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Article
In silico molecular docking study of Andrographis paniculata phytochemicals against TNF-α as a potent anti-rheumatoid drug
Sharma Pooja Tarachand, Gopishankar Thirumoorthy, Vasantha Veerappa Lakshmaiah & Praveen Nagella
Pages: 2687-2697
Published online: 11 Feb 2022
AbstractforIn silico molecular docking study of Andrographis paniculata phytochemicals against TNF-α as a potent anti-rheumatoid drug | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 676 Views
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Article
High throughput virtual screening and molecular dynamics simulation analysis of phytomolecules against BfmR of Acinetobacter baumannii: anti-virulent drug development campaign
Kiran Bharat Lokhande, Sarika Vishnu Pawar, Smriti Madkaiker, Neelu Nawani, Swamy K. Venkateswara & Payel Ghosh
Pages: 2698-2712
Published online: 14 Feb 2022
AbstractforHigh throughput virtual screening and molecular dynamics simulation analysis of phytomolecules against BfmR of Acinetobacter baumannii: anti-virulent drug development campaign | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 725 Views
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Article
Deciphering the immunogenic T-cell epitopes from spike protein of SARS-CoV-2 concerning the diverse population of India
Sreevidya S. Devi, Vandana Kardam, Kshatresh D. Dubey & Manish Dwivedi
Pages: 2713-2732
Published online: 08 Feb 2022
AbstractforDeciphering the immunogenic T-cell epitopes from spike protein of SARS-CoV-2 concerning the diverse population of India | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 265 Views
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Article
In silico analysis of comparative affinity of phytosiderophore and bacillibactin for iron uptake by YSL15 and YSL18 receptors of Oryza sativa
Pratika Singh, Azmi Khan, Rakesh Kumar, Krishna Kumar Ojha, Vijay Kumar Singh & Amrita Srivastava
Pages: 2733-2746
Published online: 09 Feb 2022
AbstractforIn silico analysis of comparative affinity of phytosiderophore and bacillibactin for iron uptake by YSL15 and YSL18 receptors of Oryza sativa | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 323 Views
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Article
Development of nanostructured lipid carriers as a promising tool for methotrexate delivery: physicochemical and in vitro evaluation
Jyoti Rathee, Rohini Kanwar, Laxmi Kumari, Sandip V. Pawar, Shikha Sharma, Md. Ehesan Ali, Deepak B. Salunke & Surinder Kumar Mehta
Pages: 2747-2758
Published online: 03 Mar 2022
AbstractforDevelopment of nanostructured lipid carriers as a promising tool for methotrexate delivery: physicochemical and in vitro evaluation | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 347 Views
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Article
Chemical profiling, cytotoxic activities through apoptosis induction in human fibrosarcoma and carcinoma cells, and molecular docking of some 1,2,3-triazole-isoxazoline hybrids using the eugenol as a precursors
Ali Oubella, Abdelmaoujoud Taia, Said Byadi, Marouane Ait Lahcen, Abdoullah Bimoussa, Mohamed Essaber, Crtomir Podlipnik, Hamid Morjani, My Youssef Ait Itto & Abdeljalil Aatif
Pages: 2759-2771
Published online: 17 Feb 2022
AbstractforChemical profiling, cytotoxic activities through apoptosis induction in human fibrosarcoma and carcinoma cells, and molecular docking of some 1,2,3-triazole-isoxazoline hybrids using the eugenol as a precursors | Full Text | References | PDF (4.4 MB) | EPUB
  • 281 Views
  • 9 CrossRef citations
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Article
Whole genome analysis and homology modeling of SARS-CoV-2 Indian isolate reveals potent FDA approved drug choice for treating COVID-19
Periyannan Velu, Thirumalaisamy Rathinavel, Suresh Kumarasamy, Muhammad Nasir Iqbal, Hasnat Noor, Ayesha Ikram, Karthika Rajamanickam & Gnanendra Shanmugam
Pages: 2772-2788
Published online: 09 Feb 2022
AbstractforWhole genome analysis and homology modeling of SARS-CoV-2 Indian isolate reveals potent FDA approved drug choice for treating COVID-19 | Full Text | References | PDF (5.3 MB) | EPUB
  • 225 Views
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Article
Identification of dual binding mode of Orthodiffenes towards human topoisomerase-I and α-tubulin: exploring the potential role in anti-cancer activity via in silico study
Doddabasappa Talimarada, Akanksha Sharma & Harish Holla
Pages: 2789-2803
Published online: 17 Feb 2022
AbstractforIdentification of dual binding mode of Orthodiffenes towards human topoisomerase-I and α-tubulin: exploring the potential role in anti-cancer activity via in silico study | Full Text | References | PDF (3.8 MB) | EPUB
  • 225 Views
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Article
A new bio-active asymmetric-Schiff base: synthesis and evaluation of calf thymus DNA interaction, topoisomerase IIα inhibition, in vitro antiproliferative activity, SEM analysis and molecular docking studies
Zehra Kübra Yılmaz, Özlem Özdemir, Belma Aslim, Zekiye Suludere & Egemen Şahin
Pages: 2804-2822
Published online: 18 Feb 2022
AbstractforA new bio-active asymmetric-Schiff base: synthesis and evaluation of calf thymus DNA interaction, topoisomerase IIα inhibition, in vitro antiproliferative activity, SEM analysis and molecular docking studies | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 442 Views
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Article
Unraveling the possible inhibitors for Chorismate synthase to combat tuberculosis using in silico approach
Muhammad Hanif, Sara Khan, Umar Farooq, Faisal Nouroz & Rizwana Sarwar
Pages: 2823-2830
Published online: 15 Feb 2022
AbstractforUnraveling the possible inhibitors for Chorismate synthase to combat tuberculosis using in silico approach | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 253 Views
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Article
Molecular interactions of trichoderma β-1,4-glucosidase (ThBglT12) with mycelial cell wall components of phytopathogenic Macrophomina phaseolina
Mohammad Hakim Mohammad Hood, Tengku Haziyamin Tengku Abdul Hamid, Roswanira Abdul Abdul Wahab, Fahrul Zaman Huyop, Yilmaz Kaya & Azzmer Azzar Abdul Abdul Hamid
Pages: 2831-2847
Published online: 17 Feb 2022
AbstractforMolecular interactions of trichoderma β-1,4-glucosidase (ThBglT12) with mycelial cell wall components of phytopathogenic Macrophomina phaseolina | Full Text | References | PDF (6 MB) | EPUB
  • 317 Views
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Article
Isolation and biological evaluation 7-hydroxy flavone from Avicennia officinalis L: insights from extensive in vitro, DFT, molecular docking and molecular dynamics simulation studies
A. Parthiban, V. Sachithanandam, P. Lalitha, Dhanasekar Elumalai, Radhakrishnan Nandini Asha, Thayalaraj Christopher Jeyakumar, J. Muthukumaran, Monika Jain, Kamalraja Jayabal, T. Mageswaran, R. Sridhar, R. Purvaja & R. Ramesh
Pages: 2848-2860
Published online: 22 Feb 2022
AbstractforIsolation and biological evaluation 7-hydroxy flavone from Avicennia officinalis L: insights from extensive in vitro, DFT, molecular docking and molecular dynamics simulation studies | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 353 Views
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Article
New styrylquinoxaline: synthesis, structural, biological evaluation, ADMET prediction and molecular docking investigations
Salma Mortada, Mohcine Missioui, Walid Guerrab, Güneş Demirtaş, Joel T. Mague, My El Abbes Faouzi & Youssef Ramli
Pages: 2861-2877
Published online: 17 Feb 2022
AbstractforNew styrylquinoxaline: synthesis, structural, biological evaluation, ADMET prediction and molecular docking investigations | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 336 Views
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Article
Discovery of multi-target mur enzymes inhibitors with anti-mycobacterial activity through a Scaffold approach
Madhulata Kumari, Mohd Waseem & Naidu Subbarao
Pages: 2878-2899
Published online: 17 Feb 2022
AbstractforDiscovery of multi-target mur enzymes inhibitors with anti-mycobacterial activity through a Scaffold approach | Full Text | References | PDF (8.1 MB) | EPUB | Supplemental
  • 275 Views
  • 2 CrossRef citations
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Article
In silico discovery of novel inhibitors from Northern African natural products database against main protease (Mpro) of SARS-CoV-2
Said Byadi, Domen Oblak, Yassine Kassmi, Karima Sadik, Mouhi Eddine Hachim, Črtomir Podlipnik & Aziz Aboulmouhajir
Pages: 2900-2910
Published online: 15 Feb 2022
AbstractforIn silico discovery of novel inhibitors from Northern African natural products database against main protease (Mpro) of SARS-CoV-2 | Full Text | References | PDF (3.9 MB) | EPUB
  • 257 Views
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Article
Efficacy of defensins as neutralizing agents against the deadly SARS-CoV-2
Varughese Deepthi, Kochupurackal P Mohanakumar & Usha Rajamma
Pages: 2911-2925
Published online: 22 Feb 2022
AbstractforEfficacy of defensins as neutralizing agents against the deadly SARS-CoV-2 | Full Text | References | PDF (3.3 MB) | EPUB
  • 227 Views
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Article
In vitro and in silico screening of novel typhoid drugs from endangered herb (Enicostema axillare)
Sasidharan Perumal, MadhanaVigneshwari Gopal Samy & Dharaneedharan Subramanian
Pages: 2926-2936
Published online: 17 Feb 2022
AbstractforIn vitro and in silico screening of novel typhoid drugs from endangered herb (Enicostema axillare) | Full Text | References | PDF (2.6 MB) | EPUB
  • 140 Views
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Article
A sequence space search engine for computational protein design to modulate molecular functionality
Ayush Malik, Anupam Banerjee, Abantika Pal & Pralay Mitra
Pages: 2937-2946
Published online: 26 Feb 2022
AbstractforA sequence space search engine for computational protein design to modulate molecular functionality | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 261 Views
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Article
Human variation in the protein receptor ACE2 affects its binding affinity to SARS-CoV-2 in a variant-dependent manner
Thiago M. Santos, Ayrton B. P. Lisboa, Wenderson Rodrigues, Helena Gomes, Jônatas Abrahão & Luiz-Eduardo Del-Bem
Pages: 2947-2955
Published online: 23 Feb 2022
AbstractforHuman variation in the protein receptor ACE2 affects its binding affinity to SARS-CoV-2 in a variant-dependent manner | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 796 Views
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Article
Structure-based pharmacophore mapping and virtual screening of natural products to identify polypharmacological inhibitor against c-MET/EGFR/VEGFR-2
Diksha A. Varma, Mrityunjay Singh, Sharad Wakode, N. E. Dinesh, Simran Vinaik, Shailendra Asthana & Manisha Tiwari
Pages: 2956-2970
Published online: 23 Feb 2022
AbstractforStructure-based pharmacophore mapping and virtual screening of natural products to identify polypharmacological inhibitor against c-MET/EGFR/VEGFR-2 | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 377 Views
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Article
Identification of new putative inhibitors of Mycobacterium tuberculosis 3-dehydroshikimate dehydratase from a combination of ligand- and structure-based and deep learning in silico approaches
João Vítor Perez de Souza, Erika Seki Kioshima, Letícia Sayuri Murase, Diego de Souza Lima, Flavio Augusto Vicente Seixas, Bernard Maigret & Rosilene Fressatti Cardoso
Pages: 2971-2980
Published online: 23 Feb 2022
AbstractforIdentification of new putative inhibitors of Mycobacterium tuberculosis 3-dehydroshikimate dehydratase from a combination of ligand- and structure-based and deep learning in silico approaches | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 401 Views
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Article
Virtual screening of small natural compounds against NS1 protein of DENV, YFV and ZIKV
Gabriela de Lima Menezes, Marielena Vogel Saivish, Maurício Lacerda Nogueira & Roosevelt Alves da Silva
Pages: 2981-2991
Published online: 20 Feb 2022
AbstractforVirtual screening of small natural compounds against NS1 protein of DENV, YFV and ZIKV | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 357 Views
  • 3 CrossRef citations
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Article
Inhibitory mechanism of clioquinol and its derivatives at the exopeptidase site of human angiotensin-converting enzyme-2 and receptor binding domain of SARS-CoV-2 viral spike
Idowu A. Kehinde, Anu Egbeyemi, Manvir Kaur, Collins Onyenaka, Tolulope Adebusuyi & Omonike A. Olaleye
Pages: 2992-3001
Published online: 26 Feb 2022
AbstractforInhibitory mechanism of clioquinol and its derivatives at the exopeptidase site of human angiotensin-converting enzyme-2 and receptor binding domain of SARS-CoV-2 viral spike | Full Text | References | PDF (2.6 MB) | EPUB
  • 152 Views
  • 1 CrossRef citations
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Article
Luminescence studies of binding affinity of vildagliptin with bovine serum albumin
Piyush Verma, Lajpreet Kaur, Priyanka Aswal, Anju Singh, Himanshu Ojha, Afreen Jahan Rahman, Rahul Singhal, Anjani K. Tiwari & Mallika Pathak
Pages: 3002-3013
Published online: 26 Feb 2022
AbstractforLuminescence studies of binding affinity of vildagliptin with bovine serum albumin | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 202 Views
  • 1 CrossRef citations
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Article
Targeting two potential sites of SARS-CoV-2 main protease through computational drug repurposing
Archisha Prakash, Subhomoi Borkotoky & Vikash Kumar Dubey
Pages: 3014-3024
Published online: 10 Mar 2022
AbstractforTargeting two potential sites of SARS-CoV-2 main protease through computational drug repurposing | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 271 Views
  • 4 CrossRef citations
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Article
An integrated computational approach to screening of alkaloids inhibitors of TBX3 in breast cancer cell lines
Anjasu Paul, Md. Belayet Hasan Limon, Md. Mobarok Hossain & Md. Thosif Raza
Pages: 3025-3041
Published online: 05 Mar 2022
AbstractforAn integrated computational approach to screening of alkaloids inhibitors of TBX3 in breast cancer cell lines | Full Text | References | PDF (4.2 MB) | EPUB
  • 347 Views
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Article
Single-walled silicon nanotube as an exceptional candidate to eliminate SARS-CoV-2: a theoretical study
Pedro Simão Sousa Mendonça, Jeziel Rodrigues dos Santos, Osmair Vital de Oliveira, José Divino dos Santos & Elson Longo
Pages: 3042-3051
Published online: 26 Feb 2022
AbstractforSingle-walled silicon nanotube as an exceptional candidate to eliminate SARS-CoV-2: a theoretical study | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 208 Views
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Article
In silico and in vitro evaluation of imatinib as an inhibitor for SARS-CoV-2
Nirmitee Mulgaonkar, Haoqi Wang, Samavath Mallawarachchi, Daniel Růžek, Byron Martina & Sandun Fernando
Pages: 3052-3061
Published online: 26 Feb 2022
AbstractforIn silico and in vitro evaluation of imatinib as an inhibitor for SARS-CoV-2 | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 381 Views
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Article
Rad5 HIRAN domain: Structural insights into its interaction with ssDNA through molecular modeling approaches
Bruno M. Silva, Lucianna H. Santos, João Paulo P. de Almeida & Mariana T. Q. de Magalhães
Pages: 3062-3075
Published online: 07 Mar 2022
AbstractforRad5 HIRAN domain: Structural insights into its interaction with ssDNA through molecular modeling approaches | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 235 Views
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Article
Structures and dynamics of peptide and peptidomimetic inhibitors bound to the NS2B-NS3 protease of the ZIKA virus
S. Pant, G. Bhattacharya & N.R Jena
Pages: 3076-3088
Published online: 03 Mar 2022
AbstractforStructures and dynamics of peptide and peptidomimetic inhibitors bound to the NS2B-NS3 protease of the ZIKA virus | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 263 Views
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Article
Molecular modelling studies and identification of novel phytochemical inhibitor of DLL3
Bhrugesh Pravinchandra Joshi, Vishwambhar Vishnu Bhandare, Prittesh Patel, Abhishek Sharma, Rajesh Patel & Ramar Krishnamurthy
Pages: 3089-3109
Published online: 27 Feb 2022
AbstractforMolecular modelling studies and identification of novel phytochemical inhibitor of DLL3 | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 280 Views
  • 1 CrossRef citations
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Article
Molecular evolution and structural analyses of the spike glycoprotein from Brazilian SARS-CoV-2 genomes: the impact of selected mutations
Patrícia Aline Gröhs Ferrareze, Ricardo Ariel Zimerman, Vinícius Bonetti Franceschi, Gabriel Dickin Caldana, Paulo Augusto Netz & Claudia Elizabeth Thompson
Pages: 3110-3128
Published online: 20 May 2022
AbstractforMolecular evolution and structural analyses of the spike glycoprotein from Brazilian SARS-CoV-2 genomes: the impact of selected mutations | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 177 Views
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Article
In silico screening of the effectiveness of natural compounds from algae as SARS-CoV-2 inhibitors: molecular docking, ADMT profile and molecular dynamic studies
Hani S. H. Mohammed Ali, Hisham N. Altayb, Ahmed Atef Mohamed Bayoumi, Abdelfatteh El Omri, Ahmad Firoz & Kamel Chaieb
Pages: 3129-3144
Published online: 07 Mar 2022
AbstractforIn silico screening of the effectiveness of natural compounds from algae as SARS-CoV-2 inhibitors: molecular docking, ADMT profile and molecular dynamic studies | Full Text | References | PDF (2.7 MB) | EPUB
  • 350 Views
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Rapid Communications

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An in silico study on pulmonary fibrosis inhibitors from Tinospora cordifolia and Curcuma longa targeting TGF-β RI
Nagalakshmi Annam, Abraham Peele Karlapudi, Mukesh Doble, Krupanidhi Srirama & Venkateswarulu T.C.
Pages: 3145-3161
Published online: 24 Jan 2022
AbstractforAn in silico study on pulmonary fibrosis inhibitors from Tinospora cordifolia and Curcuma longa targeting TGF-β RI | Full Text | References | PDF (5.3 MB) | EPUB
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Published online: 11 Feb 2022
AbstractforAnosmia (smell failure) and dysgeusia (taste distortion) in COVID-19: it is genetic | Full Text | References | PDF (503.8 KB) | EPUB
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