Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 10 (2023)

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Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 10 (2023)

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Research Articles

Article
Metronidazole, acyclovir and tetrahydrobiopterin may be promising to treat COVID-19 patients, through interaction with interleukin-12
Bahareh Farasati Far, Dmitry Bokov, Gunawan Widjaja, Hendrik Setia Budi, Walid Kamal Abdelbasset, Shahrzad Javanshir, Farhad Seif, Hamidreza Pazoki-Toroudi & Sanjay Kumar Dey
Pages: 4253-4271
Published online: 21 Apr 2022
AbstractforMetronidazole, acyclovir and tetrahydrobiopterin may be promising to treat COVID-19 patients, through interaction with interleukin-12 | Full Text | References | PDF (4.5 MB) | EPUB
  • 322 Views
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Article
Nanovectorization of Ivermectin to avoid overdose of drugs
Eric Duverger, Guillaume Herlem & Fabien Picaud
Pages: 4272-4285
Published online: 26 Apr 2022
AbstractforNanovectorization of Ivermectin to avoid overdose of drugs | Full Text | References | PDF (4 MB) | EPUB
  • 82 Views
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Article
Synthesis and acetylcholinesterase enzyme inhibitory effects of some novel 4,5-Dihydro-1H-1,2,4-triazol-5-one derivatives; an in vitro and in silico study
Hilal Medetalibeyoğlu, Fikret Türkan, Sevda Manap, Ercan Bursal, Murat Beytur, Abdülmelik Aras, Onur Akyıldırım, Gül Kotan, Özlem Gürsoy-Kol & Haydar Yüksek
Pages: 4286-4294
Published online: 20 Apr 2022
AbstractforSynthesis and acetylcholinesterase enzyme inhibitory effects of some novel 4,5-Dihydro-1H-1,2,4-triazol-5-one derivatives; an in vitro and in silico study | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 896 Views
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Article
Insights into structure and activity relationship of clinically mutated PER1 and PER2 class A β-lactamase enzymes
Vidhu Agarwal, Tara Chand Yadav, Akhilesh Tiwari & Pritish Kumar Varadwaj
Pages: 4295-4312
Published online: 27 Apr 2022
AbstractforInsights into structure and activity relationship of clinically mutated PER1 and PER2 class A β-lactamase enzymes | Full Text | References | PDF (5.8 MB) | EPUB | Supplemental
  • 264 Views
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Article
Theoretical insights of the drug-drug interaction between favipiravir and ibuprofen: a DFT, QTAIM and drug-likeness investigation
Cemal Parlak, Özgür Alver, Özge Bağlayan & Ponnadurai Ramasami
Pages: 4313-4320
Published online: 01 May 2022
AbstractforTheoretical insights of the drug-drug interaction between favipiravir and ibuprofen: a DFT, QTAIM and drug-likeness investigation | Full Text | References | PDF (1.2 MB) | EPUB
  • 360 Views
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Article
Molecular docking of the pentapeptide derived from rice bran protein as anticancer agent inhibiting both receptor and non-receptor tyrosine kinases
Oktay K. Gasymov, Serda Kecel-Gunduz, Sefa Celik, Sevim Akyuz, Ayşen E. Ozel, Gulshen Agaeva, Leman M. Suleymanova, Ulker Agaeva, Matanat Bakhishova & J.A Aliyev
Pages: 4321-4343
Published online: 27 Apr 2022
AbstractforMolecular docking of the pentapeptide derived from rice bran protein as anticancer agent inhibiting both receptor and non-receptor tyrosine kinases | Full Text | References | PDF (4.6 MB) | EPUB | Supplemental
  • 320 Views
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Article
Computational identification and characterization of vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici) CAZymes in tomato xylem sap
Abhijeet Roy, Barsha Kalita, Aiswarya Jayaprakash, Amrendra Kumar & P. T. V. Lakshmi
Pages: 4344-4360
Published online: 26 Apr 2022
AbstractforComputational identification and characterization of vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici) CAZymes in tomato xylem sap | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 405 Views
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Article
Synthesis, structural characterizations and in vitro cytotoxic activities of new sulfonamide-based Schiff base derivatives
Hakan Şahal, Samet Öz, Suat Tekin & Erdal Canpolat
Pages: 4361-4367
Published online: 27 Apr 2022
AbstractforSynthesis, structural characterizations and in vitro cytotoxic activities of new sulfonamide-based Schiff base derivatives | Full Text | References | PDF (1.1 MB) | EPUB
  • 365 Views
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Article
Study of the dynamic behavior of the cruzain enzyme in free and complexed forms with competitive and noncovalent benzimidazole inhibitors
Caroline Rodrigues Chaves dos Reis, Hellen Valério Chaves Moura de Souza, Rennan Papaleo Paes Leme, Frederico Silva Castelo-Branco, Tácio Vinício Amorim Fernandes, Núbia Boechat, Luiza Rosaria Sousa Dias & Lucas Villas Bôas Hoelz
Pages: 4368-4382
Published online: 27 Apr 2022
AbstractforStudy of the dynamic behavior of the cruzain enzyme in free and complexed forms with competitive and noncovalent benzimidazole inhibitors | Full Text | References | PDF (5.3 MB) | EPUB | Supplemental
  • 283 Views
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Article
Application of amino acid ionic liquids for increasing the stability of DNA in long term storage
Mohammad Khavani, Aliyeh Mehranfar & Hossein Vahid
Pages: 4383-4397
Published online: 25 Apr 2022
AbstractforApplication of amino acid ionic liquids for increasing the stability of DNA in long term storage | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 415 Views
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Article
Effect of pH on structural dynamics of HMG-CoA reductase and binding affinity to β-sitosterol
Toluwase Hezekiah Fatoki
Pages: 4398-4404
Published online: 26 Apr 2022
AbstractforEffect of pH on structural dynamics of HMG-CoA reductase and binding affinity to β-sitosterol | Full Text | References | PDF (1.9 MB) | EPUB
  • 138 Views
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Article
Data mining and structural analysis for multi-tissue regeneration potential of BMP-4 and activator drugs
Nishant Tyagi, Kirtida Gambhir, Deepak Sharma, Gurudutta Gangenahalli & Yogesh Kumar Verma
Pages: 4405-4420
Published online: 01 May 2022
AbstractforData mining and structural analysis for multi-tissue regeneration potential of BMP-4 and activator drugs | Full Text | References | PDF (4.6 MB) | EPUB | Supplemental
  • 163 Views
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Article
Molecular dynamic assisted investigation on impact of mutations in deazaflavin dependent nitroreductase against pretomanid: a computational study
Ravi Singh, Muhammed Shaheer & M. Elizabeth Sobhia
Pages: 4421-4443
Published online: 14 May 2022
AbstractforMolecular dynamic assisted investigation on impact of mutations in deazaflavin dependent nitroreductase against pretomanid: a computational study | Full Text | References | PDF (7.8 MB) | EPUB | Supplemental
  • 199 Views
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Article
Base pairs with 4-amino-3-nitrobenzonitrile: comparison with the natural WC pairs. Dimer and tetramer forms, Infrared and Raman spectra, and several proposed antiviral modified nucleosides
M. Alcolea Palafox, D. Kattan, M. L. de Pedraza Velasco, J. Isasi, P. Posada-Moreno, Kaushal Rani, S.P. Singh & V.K. Rastogi
Pages: 4444-4466
Published online: 18 May 2022
AbstractforBase pairs with 4-amino-3-nitrobenzonitrile: comparison with the natural WC pairs. Dimer and tetramer forms, Infrared and Raman spectra, and several proposed antiviral modified nucleosides | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 225 Views
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Article
Identification of potential bioactive natural compounds from Indonesian medicinal plants against 3-chymotrypsin-like protease (3CLpro) of SARS-CoV-2: molecular docking, ADME/T, molecular dynamic simulations, and DFT analysis
Wahyu Eko Prasetyo, Heri Purnomo, Miracle Sadrini, Fajar Rakhman Wibowo, Maulidan Firdaus & Triana Kusumaningsih
Pages: 4467-4484
Published online: 26 Apr 2022
AbstractforIdentification of potential bioactive natural compounds from Indonesian medicinal plants against 3-chymotrypsin-like protease (3CLpro) of SARS-CoV-2: molecular docking, ADME/T, molecular dynamic simulations, and DFT analysis | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 358 Views
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Article
Modulation of GPCR receptors common to gut inflammatory diseases and neuronal disorders, Alzheimer’s and Parkinson’s diseases as druggable targets through Withania somnifera bioactives: an in silico study
Richa Shukla, Sonu Pahal, Ayushi Gupta, Princy Choudhary, Krishna Misra & Sangeeta Singh
Pages: 4485-4503
Published online: 01 May 2022
AbstractforModulation of GPCR receptors common to gut inflammatory diseases and neuronal disorders, Alzheimer’s and Parkinson’s diseases as druggable targets through Withania somnifera bioactives: an in silico study | Full Text | References | PDF (5.1 MB) | EPUB | Supplemental
  • 498 Views
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Article
Identification of neo-andrographolide compound targeting NS1 Lys14: an important residue in NS1 activity driving dengue pathogenesis
Elakkiya Elumalai & M. Suresh Kumar
Pages: 4504-4514
Published online: 01 May 2022
AbstractforIdentification of neo-andrographolide compound targeting NS1 Lys14: an important residue in NS1 activity driving dengue pathogenesis | Full Text | References | PDF (3.7 MB) | EPUB
  • 212 Views
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Article
Alpha-mangostin as an inhibitor of GSK3β in triple-negative breast cancer
Citra Dewi, Adryan Fristiohady, Riezki Amalia, Edwin J. Bunggulawa & Muchtaridi Muchtaridi
Pages: 4515-4521
Published online: 23 Apr 2022
AbstractforAlpha-mangostin as an inhibitor of GSK3β in triple-negative breast cancer | Full Text | References | PDF (1.2 MB) | EPUB
  • 216 Views
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Article
DFT and MD investigations of the biomolecules of phenothiazine derivatives: interactions with gold and water molecules and investigations in search of effective drug for SARS-CoV-2
Jamelah S. Al-Otaibi, Y. Sheena Mary, Shyma Mary, Ravi Trivedi, Brahmananda Chakraborty, Rohitash Yadav, Ismail Celik & Sreejit Soman
Pages: 4522-4533
Published online: 26 Apr 2022
AbstractforDFT and MD investigations of the biomolecules of phenothiazine derivatives: interactions with gold and water molecules and investigations in search of effective drug for SARS-CoV-2 | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 227 Views
  • 1 CrossRef citations
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Article
Investigation of molecular mechanism leading to gefitinib and osimertinib resistance against EGFR tyrosine kinase: molecular dynamics and binding free energy calculation
Amit Singh & Abha Mishra
Pages: 4534-4548
Published online: 04 May 2022
AbstractforInvestigation of molecular mechanism leading to gefitinib and osimertinib resistance against EGFR tyrosine kinase: molecular dynamics and binding free energy calculation | Full Text | References | PDF (4 MB) | EPUB
  • 178 Views
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Article
Combined study of docking and molecular dynamics against DNV-3 SN1 protein by bixinoids
Aluísio Marques da Fonseca, Neidelênio Baltazar Soares, Maria Imaculada Lourenço Meirú, Regilany Paulo Colares, Moises Maia Neto, Antonio Carlos Nogueira Sobrinho, Hélcio Silva dos Santos & Emmanuel Silva Marinho
Pages: 4549-4559
Published online: 05 May 2022
AbstractforCombined study of docking and molecular dynamics against DNV-3 SN1 protein by bixinoids | Full Text | References | PDF (3.1 MB) | EPUB
  • 148 Views
  • 1 CrossRef citations
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Article
Identification of potential human beta-secretase 1 inhibitors by hierarchical virtual screening and molecular dynamics
Mayra Ramos do Bomfim, Deyse Brito Barbosa, Paulo Batista de Carvalho, Alisson Marques da Silva, Tiago Alves de Oliveira, Alex Gutterres Taranto & Franco Henrique Andrade Leite
Pages: 4560-4574
Published online: 01 May 2022
AbstractforIdentification of potential human beta-secretase 1 inhibitors by hierarchical virtual screening and molecular dynamics | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 198 Views
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Article
Computational assessment of pigment epithelium-derived factor as an anti-cancer protein during its interaction with the receptors
Behzad Shahbazi, Seyed Shahriar Arab, Ladan Mafakher, Kayhan Azadmansh & Ladan Teimoori-Toolabi
Pages: 4575-4591
Published online: 05 May 2022
AbstractforComputational assessment of pigment epithelium-derived factor as an anti-cancer protein during its interaction with the receptors | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 259 Views
  • 3 CrossRef citations
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Article
Synthesis, molecular docking, ADMET evaluation and in vitro cytotoxic activity evaluation on RD and L20B cell lines of 3-substituted 5,5-diphenylimidazolidine-2,4-dione derivatives
Walid Guerrab, Jihane Akachar, Meryem El Jemli, Abdul-Malik Abudunia, Rachida Ouaabou, Katim Alaoui, Azeddine Ibrahimi & Youssef Ramli
Pages: 4592-4600
Published online: 01 May 2022
AbstractforSynthesis, molecular docking, ADMET evaluation and in vitro cytotoxic activity evaluation on RD and L20B cell lines of 3-substituted 5,5-diphenylimidazolidine-2,4-dione derivatives | Full Text | References | PDF (2.2 MB) | EPUB
  • 155 Views
  • 4 CrossRef citations
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Article
GBP5 and ACSS3: two potential biomarkers of high-grade ovarian cancer identified through downstream analysis of microarray data
Ayooshi Mitra, Shrayana Ghosh, Sayam Porey & Chittabrata Mal
Pages: 4601-4613
Published online: 03 May 2022
AbstractforGBP5 and ACSS3: two potential biomarkers of high-grade ovarian cancer identified through downstream analysis of microarray data | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 219 Views
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Article
A multi-epitope vaccine candidate developed from unique immunogenic epitopes against Cryptosporidium hominis by utilizing an immunoinformatics-driven approach
Nirali Pandya & Amit Kumar
Pages: 4614-4631
Published online: 05 May 2022
AbstractforA multi-epitope vaccine candidate developed from unique immunogenic epitopes against Cryptosporidium hominis by utilizing an immunoinformatics-driven approach | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 284 Views
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Article
Chemical complementarity between immune receptor CDR3s and candidate cancer antigens correlating with reduced survival: evidence for outcome mitigation with corticosteroid treatments
Anishaa R. Patel, Dhruv N. Patel, Yaping N. Tu, Michelle Yeagley, Andrea Chobrutskiy, Boris I. Chobrutskiy & George Blanck
Pages: 4632-4640
Published online: 10 May 2022
AbstractforChemical complementarity between immune receptor CDR3s and candidate cancer antigens correlating with reduced survival: evidence for outcome mitigation with corticosteroid treatments | Full Text | References | PDF (1.2 MB) | EPUB | Supplemental
  • 113 Views
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Article
TULP3 NLS inhibition: an in silico study to hamper cargo transport to nucleus
Rana Muhammad Mateen, Asma Tariq, Muhammad Sohail Afzal, Muhammad Ali, Imran Tipu, Mureed Hussain, Mahjabeen Saleem & Muhammad Naveed
Pages: 4641-4649
Published online: 05 May 2022
AbstractforTULP3 NLS inhibition: an in silico study to hamper cargo transport to nucleus | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 402 Views
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Article
Promising antivirals for PLpro of SARS-CoV-2 using virtual screening, molecular docking, dynamics, and MMPBSA
Reena Kumari, Viney Kumar, Poonam Dhankhar & Vikram Dalal
Pages: 4650-4666
Published online: 05 May 2022
AbstractforPromising antivirals for PLpro of SARS-CoV-2 using virtual screening, molecular docking, dynamics, and MMPBSA | Full Text | References | PDF (4.9 MB) | EPUB | Supplemental
  • 530 Views
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Article
Development of novel monoamine oxidase B (MAO-B) inhibitors by combined application of docking-based alignment, 3D-QSAR, ADMET prediction, molecular dynamics simulation, and MM_GBSA binding free energy
Abdellah El Aissouq, Oussama Chedadi, Mohammed Bouachrine, Abdelkrim Ouammou & Fouad Khalil
Pages: 4667-4680
Published online: 05 May 2022
AbstractforDevelopment of novel monoamine oxidase B (MAO-B) inhibitors by combined application of docking-based alignment, 3D-QSAR, ADMET prediction, molecular dynamics simulation, and MM_GBSA binding free energy | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 351 Views
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Article
“In silico identification of ethoxy phthalimide pyrazole derivatives as IL-17A and IL-18 targeted gouty arthritis agents”
Abhishek Kumar Verma, Md. Shahadat Hossain, SK. Faisal Ahmed, Nasir Hussain, Mohammad Ashid, Sudhir K. Upadhyay, Naveen Kumar Vishvakarma, Ali Asger Bhojiya & Sandeep Kumar Srivastava
Pages: 4681-4695
Published online: 09 May 2022
Abstractfor“In silico identification of ethoxy phthalimide pyrazole derivatives as IL-17A and IL-18 targeted gouty arthritis agents” | Full Text | References | PDF (5.2 MB) | EPUB | Supplemental
  • 297 Views
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Article
Molecular dynamic simulations based discovery and development of thiazolidin-4-one derivatives as EGFR inhibitors targeting resistance in non-small cell lung cancer (NSCLC)
Kshipra S. Karnik, Aniket P. Sarkate, Deepak K. Lokwani, Shailee V. Tiwari, Rajaram Azad & Pravin S. Wakte
Pages: 4696-4710
Published online: 09 May 2022
AbstractforMolecular dynamic simulations based discovery and development of thiazolidin-4-one derivatives as EGFR inhibitors targeting resistance in non-small cell lung cancer (NSCLC) | Full Text | References | PDF (2.8 MB) | EPUB
  • 237 Views
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Article
Efficient synthesis and antitumor activity of novel oxazaphosphinane derivatives: X-ray crystallography, DFT study and molecular docking
Rania Bahadi, Malika Berredjem, Billel Belhani, Seif-Eddine Djouad, Sofiane Bouacida, Tan Sothea Ouk, Yacine Laichi, Khaldoun Bachari & Rayenne Redjemia
Pages: 4711-4722
Published online: 09 May 2022
AbstractforEfficient synthesis and antitumor activity of novel oxazaphosphinane derivatives: X-ray crystallography, DFT study and molecular docking | Full Text | References | PDF (3.1 MB) | EPUB
  • 95 Views
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Article
Investigation of the tight binding mechanism of a new anticoagulant DD217 to factor Xa by means of molecular docking and molecular dynamics
Dmitry A. Shulga, Natalia A. Tserkovnikova, Dmitry N. Tarasov & Dmitry G. Tovbin
Pages: 4723-4734
Published online: 09 May 2022
AbstractforInvestigation of the tight binding mechanism of a new anticoagulant DD217 to factor Xa by means of molecular docking and molecular dynamics | Full Text | References | PDF (2.9 MB) | EPUB
  • 153 Views
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Article
Impact of compound mutations I1171N + F1174I and I1171N + L1198H on the structure of ALK in NSCLC pathogenesis: atomistic insights
Elliasu Y. Salifu, Issahaku A. Rashid & Mahmoud E. S. Soliman
Pages: 4735-4743
Published online: 05 May 2022
AbstractforImpact of compound mutations I1171N + F1174I and I1171N + L1198H on the structure of ALK in NSCLC pathogenesis: atomistic insights | Full Text | References | PDF (2.2 MB) | EPUB
  • 135 Views
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Article
25 (S)-Hydroxycholesterol acts as a possible dual enzymatic inhibitor of SARS-CoV-2 Mpro and RdRp–: an insight from molecular docking and dynamics simulation approaches
Faisal A. Alzahrani, Saleh A. Alkarim, Yousef M. Hawsawi, Wesam H. Abdulaal, Raed Albiheyri, Bassem Kurdi, Hassan Alguridi & Mohammed A. El-Magd
Pages: 4744-4755
Published online: 05 May 2022
Abstractfor25 (S)-Hydroxycholesterol acts as a possible dual enzymatic inhibitor of SARS-CoV-2 Mpro and RdRp–: an insight from molecular docking and dynamics simulation approaches | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 283 Views
  • 1 CrossRef citations
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Article
Structural aspects of triazole derivatives as HSP90 inhibitors for the treatment of cancer: in silico studies
Shubham Dhiman, Moumita Saha, Amena Ali, Abuzer Ali, G. D Gupta & Vivek Asati
Pages: 4756-4769
Published online: 06 Jun 2022
AbstractforStructural aspects of triazole derivatives as HSP90 inhibitors for the treatment of cancer: in silico studies | Full Text | References | PDF (2.5 MB) | EPUB
  • 156 Views
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Article
Plant-derived active compounds as a potential nucleocapsid protein inhibitor of SARS-CoV-2: an in-silico study
Dharmendra Kashyap, Rajarshi Roy, Parimal Kar & Hem Chandra Jha
Pages: 4770-4785
Published online: 09 May 2022
AbstractforPlant-derived active compounds as a potential nucleocapsid protein inhibitor of SARS-CoV-2: an in-silico study | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 487 Views
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Article
Design, synthesis, in vitro and in silico bioactivity profiles of new urea/thiourea derivatives of 2-pyridyl piperazine as potent antioxidant and antimicrobial agents: chemo-bio-computational approach
S. Sumalatha, Ch. Venkataramaiah & C. Naga Raju
Pages: 4786-4797
Published online: 09 May 2022
AbstractforDesign, synthesis, in vitro and in silico bioactivity profiles of new urea/thiourea derivatives of 2-pyridyl piperazine as potent antioxidant and antimicrobial agents: chemo-bio-computational approach | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 152 Views
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Review Article

Review Article
Structure and inhibition mechanism of some synthetic compounds and phenolic derivatives as tyrosinase inhibitors: review and new insight
Morteza Vaezi
Pages: 4798-4810
Published online: 05 May 2022
AbstractforStructure and inhibition mechanism of some synthetic compounds and phenolic derivatives as tyrosinase inhibitors: review and new insight | Full Text | References | PDF (1.8 MB) | EPUB
  • 567 Views
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Brief Report

Brief Report
Computational studies reveal potential dolichyl-phosphate N-acetylglucosaminephosphotransferase inhibitors amidst existing drugs
Akachukwu Ibezim, Sochi Osigwe, Philip Uzor, Nadja Engel, Karuppasamy Ramanathan & Ngozi Nwodo
Pages: 4811-4818
Published online: 25 Apr 2022
AbstractforComputational studies reveal potential dolichyl-phosphate N-acetylglucosaminephosphotransferase inhibitors amidst existing drugs | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 80 Views
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