Works in Journal of Biomolecular Structure & Dynamics, 2023, Vol 41, Issue 8

Results: 39

Screening of novel and selective inhibitors for neuronal nitric oxide synthase (nNOS) via structure-based drug design techniques.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3607, doi. 10.1080/07391102.2022.2054471

By:

Boumezber, Sarah;
Yelekçi, Kemal

Publication type:

Article

Exploring binding stability of hydroxy-3-(4-hydroxyphenyl)-5-(4-nitrophenyl)-5,5a,7,8,9,9a-hexahydrothiazolo[2,3-b] quinazolin-6-one with T790M/L858R EGFR-TKD.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3702, doi. 10.1080/07391102.2022.2053748

By:

Mir, Showkat Ahmad;
Nayak, Binata

Publication type:

Article

Elucidating the binding mechanism of an antimigraine agent with a model protein: insights from molecular spectroscopic, calorimetric and computational approaches.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3686, doi. 10.1080/07391102.2022.2053747

By:

Naik, Roopa;
Seetharamappa, J.

Publication type:

Article

De novo designed EBAI as a potential inhibitor of the viral protein BHRF1. Research in silico.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3680, doi. 10.1080/07391102.2022.2053746

By:

Zaremba, Andrii A.;
Zaremba, Polina Y.;
Platonov, Maxim O.

Publication type:

Article

Screening of indole derivatives as the potent anticancer agents on dihydrofolate reductase: pharmaco-informatics and molecular dynamics simulation.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3667, doi. 10.1080/07391102.2022.2053745

By:

Abdolmaleki, Behnaz;
Maddah, Mina

Publication type:

Article

Urea ameliorates trimethylamine N-oxide-Induced aggregation of intrinsically disordered α-casein protein: the other side of the urea-methylamine counteraction.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3659, doi. 10.1080/07391102.2022.2053744

By:

Bhat, Mohd Younus;
Mir, Irfan Ahmad;
Ul Hussain, Mahboob;
Singh, Laishram Rajendrakumar;
Dar, Tanveer Ali

Publication type:

Article

Computational investigation of aphid odorant receptor structure and binding function.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3647, doi. 10.1080/07391102.2022.2053743

By:

Sims, Cassie;
Withall, David M.;
Oldham, Neil;
Stockman, Robert;
Birkett, Michael

Publication type:

Article

A foundational theoreticalAl12E12(E = N, P) adsorption and quinolone docking study: cage–quinolone pairs, optics and possible therapeutic and diagnostic applications.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3630, doi. 10.1080/07391102.2022.2053742

By:

Ullah, Zakir;
Sonawane, Prasad M.;
Mary, Y. Sheena;
Mary, Y. Shyma;
Yohannan Panicker, C.;
Churchill, David G.

Publication type:

Article

Fibroblast growth factor receptor (FGFR) inhibitors as anticancer agents: 3D-QSAR, molecular docking and dynamics simulation studies of 1, 6-naphthyridines and pyridopyrimidines.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3591, doi. 10.1080/07391102.2022.2053206

By:

Modh, Dharti H.;
Modi, Siddharth J.;
Deokar, Hemant;
Yadav, Savita;
Kulkarni, Vithal M.

Publication type:

Article

Molecular structure determination, spectroscopic, quantum computational studies and molecular docking of 4-(E)-[2-(benzylamino)phenylimino) methyl-2]ethoxy phenol.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3574, doi. 10.1080/07391102.2022.2052354

By:

Towseef Ahmad, Hajam;
Mohammed Ameen, K. K.;
Saleem, H.;
Syed Ali Padusha, M.;
Mashood Ahamed, F. M.

Publication type:

Article

Molecular insights of hyaluronic acid – ethambutol and hyaluronic acid – isoniazid drug conjugates act as promising novel drugs for the treatment of tuberculosis.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3562, doi. 10.1080/07391102.2022.2051748

By:

Thirumalaisamy, R.;
Aroulmoji, V.;
Iqbal, Muhammad Nasir;
Saride, Shreyas;
Bhuvaneswari, M.;
Deepa, M.;
Sivasankar, C.;
Khan, Riaz

Publication type:

Article

A closer look at the mode of binding of drug pemetrexed with CT-DNA.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3553, doi. 10.1080/07391102.2022.2051747

By:

Ponkarpagam, S.;
Vennila, K. N.;
Elango, Kuppanagounder P.

Publication type:

Article

Immune escape facilitation by mutations of epitope residues in RdRp of SARS-CoV-2.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3542, doi. 10.1080/07391102.2022.2051746

By:

Mallick Gupta, Aayatti;
Mandal, SasthiCharan;
Mandal, Sukhendu;
Chakrabarti, Jaydeb

Publication type:

Article

Molecular dynamics and 3D-QSAR studies on indazole derivatives as HIF-1α inhibitors.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3524, doi. 10.1080/07391102.2022.2051745

By:

Singh, Yogesh;
Sanjay, Kulkarni Swanand;
Kumar, Pradeep;
Singh, Satwinder;
Thareja, Suresh

Publication type:

Article

In-silico studies on wild orange (Citrus macroptera Mont.) compounds against COVID-19 pro-inflammation targets.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3511, doi. 10.1080/07391102.2022.2051744

By:

Lala, Mousikha;
Bhattacharjee, Soumita;
Ghosh, Chandra;
Sen, Arnab;
Sarkar, Indrani

Publication type:

Article

Exploring species-specific inhibitors with multiple target sites on S. aureus pyruvate kinase using a computational workflow.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3496, doi. 10.1080/07391102.2022.2051743

By:

Yuce, Merve;
Sarica, Zehra;
Ates, Beril;
Kurkcuoglu, Ozge

Publication type:

Article

Discovery of a novel inhibitor against urokinase-type plasminogen activator, a potential enzyme with a role in atherosclerotic plaque instability.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3485, doi. 10.1080/07391102.2022.2051742

By:

Ganguly, Rik;
Mylliemngap, Baphilinia Jones;
Bhattacharjee, Atanu

Publication type:

Article

Investigating binding of insecticide buprofezin to DNA by experimental and metadynamics simulation studies.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3476, doi. 10.1080/07391102.2022.2050949

By:

Ponkarpagam, S.;
Vennila, K. N.;
Elango, Kuppanagounder P.

Publication type:

Article

Molecular docking and dynamics approach to in silico drug repurposing for inflammatory bowels disease by targeting TNF alpha.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3462, doi. 10.1080/07391102.2022.2050948

By:

Halder, Debojyoti;
Das, Subham;
Joseph, Alex;
Jeyaprakash, R. S.

Publication type:

Article

Parallel actin monomers in the 8S complex of actin–INF2.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3295, doi. 10.1080/07391102.2022.2050947

By:

Das, Sanchaita;
Zhang, Zixin;
Kalvakota, Saichandra;
Soto Jr., Raul;
Phillips, Martin L.;
Terman, Jonathan R.;
Reisler, Emil

Publication type:

Article

Atomic level and structural understanding of natural ligands inhibiting Helicobacter pylori peptide deformylase through ligand and receptor based screening, SIFT, molecular dynamics and DFT – a structural computational approach.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3440, doi. 10.1080/07391102.2022.2050946

By:

Sunder Raj, Divya;
Kesavan, Dinesh Kumar;
Kottaisamy, Chidhambara Priya Dharshini;
Kumar, V. Prasanth;
Hopper, Waheetha;
Sankaran, Umamaheshwari

Publication type:

Article

Computational vaccinology guided design of multi-epitope subunit vaccine against a neglected arbovirus of the Americas.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3321, doi. 10.1080/07391102.2022.2050301

By:

da Silva, Maria Karolaynne;
Azevedo, Arthur Antunes Coimbra;
Campos, Daniel Melo de Oliveira;
de Souto, Janeusa Trindade;
Fulco, Umberto Laino;
Oliveira, Jonas Ivan Nobre

Publication type:

Article

Three-dimensional modeling of streptomycin binding single-stranded DNA for aptamer-based biosensors, a molecular dynamics simulation approach.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3430, doi. 10.1080/07391102.2022.2050945

By:

Nosrati, Masoumeh;
Roushani, Mahmoud

Publication type:

Article

Interaction of Anagrelide drug molecule on pristine and doped boron nitride nanocages: a DFT, RDG, PCM and QTAIM investigation.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3413, doi. 10.1080/07391102.2022.2049369

By:

Nishat, Maliha;
Hossain, Md. Rakib;
Hasan, Md. Mehade;
Hossain, Md. Kamal;
Hossain, Md. Abul;
Ahmed, Farid

Publication type:

Article

Identification of tumor homing peptides by utilizing hybrid feature representation.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3405, doi. 10.1080/07391102.2022.2049368

By:

Zou, Hongliang;
Yang, Fan;
Yin, Zhijian

Publication type:

Article

Computational studies suggest compounds restoring function of p53 cancer mutants can bind SARS-CoV-2 spike protein.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3368, doi. 10.1080/07391102.2022.2048081

By:

Das, Tanushree;
Mukhopadhyay, Chaitali

Publication type:

Article

In silico identification of small molecule protein-protein interaction inhibitors: targeting hotspot regions at the interface of MXRA8 and CHIKV envelope protein.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3349, doi. 10.1080/07391102.2022.2048080

By:

Verma, Jyoti;
Subbarao, Naidu

Publication type:

Article

Development of peptide vaccine candidate using highly antigenic PE-PGRS family proteins to stimulate the host immune response against Mycobacterium tuberculosis H37Rv: an immuno-informatics approach.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3382, doi. 10.1080/07391102.2022.2048079

By:

Kumar, Ajit;
Sharma, Priyanka;
Arun, Akanksha;
Meena, Laxman S.

Publication type:

Article

Dealkenylation of neoandrographolide, a phytochemical from Andrographis paniculata stimulates FXR (Farnesoid X Receptor) and enhances gallstone dissolution.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3339, doi. 10.1080/07391102.2022.2048078

By:

Sharma, Rajani;
Kumar, Kunal;
Tanvi, Kumari

Publication type:

Article

Neem and Turmeric in the management of Covid Associated Mucormycosis (CAM) derived through network pharmacology.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3281, doi. 10.1080/07391102.2022.2048077

By:

Datta, Sutapa;
Sarkar, Indrani;
Sen, Gargi;
Sen, Arnab

Publication type:

Article

Monosaccharide induced temporal delay in cholesterol self-aggregation.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3205, doi. 10.1080/07391102.2022.2048076

By:

Hazra, Rituparna;
Roy, Durba

Publication type:

Article

In the footsteps of an inhibitor unbinding from the active site of human carbonic anhydrase II.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3187, doi. 10.1080/07391102.2022.2048075

By:

Khatua, Satyajit;
Taraphder, Srabani

Publication type:

Article

Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3305, doi. 10.1080/07391102.2022.2047109

By:

Roy, Rajarshi;
Poddar, Sayan;
Sk, Md Fulbabu;
Kar, Parimal

Publication type:

Article

An in silico discovery of potential 3CL protease inhibitors of SARS-CoV-2 based upon inactivation of the cysteine 145-Histidine 41 catalytic dyad.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3167, doi. 10.1080/07391102.2022.2047108

By:

Mishra, Bibhudutta;
Ballaney, Pranav;
Saha, Gourav;
Shinde, Akshay;
Banerjee, Subhadeep;
Thimmakondu, Venkatesan S.;
Aduri, Raviprasad

Publication type:

Article

In silico and in vitro studies on inhibitors for SARS-CoV-2 non-structural proteins with dual herbal combination of Withania somnifera with five rasayana herbs.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3265, doi. 10.1080/07391102.2022.2046642

By:

Bhargavi, Srinivasan;
Madhan Shankar, S. R.;
Jemmy, Christy H.

Publication type:

Article

Unbinding of hACE2 and inhibitors from the receptor binding domain of SARS-CoV-2 spike protein.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3245, doi. 10.1080/07391102.2022.2046641

By:

Mishra, Lokpati;
Bandyopadhyay, Tusar

Publication type:

Article

Exploring electronic, structural and dynamics parameters of phenylbenzothiazole complexes with Mn2+, Cu2+ and Zn2+ for designing new magnetic resonance imaging (MRI) probes: congruence between computation and spectroscopic data

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3234, doi. 10.1080/07391102.2022.2046639

By:

Rosa, Isael Aparecido;
Gonçalves, Mateus A.;
Krambrock, Klaus Wilhelm Heinrich;
dos Santos, Marcelo Henrique;
Braga, Letícia S.;
da Cunha, Elaine F. F.;
Ramalho, Teodorico C.

Publication type:

Article

Vitamin B12 binding to mutated human transcobalamin, in-silico study of TCN2 alanine scanning and ClinVar missense mutations/SNPs.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3222, doi. 10.1080/07391102.2022.2046638

By:

Abuyaman, Omar;
Hatmal, Ma'mon M.;
Hijjawi, Nawal;
Deeb, Ahmad A.;
Abuothman, Mohammad;
Taha, Mutasem

Publication type:

Article

Thermodynamics of globular protein native structure.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 8, p. 3218, doi. 10.1080/07391102.2022.2046637

By:

Khechinashvili, Nikolay N.;
Kondratyev, Maxim S.;
Polozov, Robert V.

Publication type:

Article

Works in Journal of Biomolecular Structure & Dynamics, 2023, Vol 41, Issue 8

Screening of novel and selective inhibitors for neuronal nitric oxide synthase (nNOS) via structure-based drug design techniques.

Exploring binding stability of hydroxy-3-(4-hydroxyphenyl)-5-(4-nitrophenyl)-5,5a,7,8,9,9a-hexahydrothiazolo[2,3-b] quinazolin-6-one with T790M/L858R EGFR-TKD.

Elucidating the binding mechanism of an antimigraine agent with a model protein: insights from molecular spectroscopic, calorimetric and computational approaches.

De novo designed EBAI as a potential inhibitor of the viral protein BHRF1. Research in silico.

Screening of indole derivatives as the potent anticancer agents on dihydrofolate reductase: pharmaco-informatics and molecular dynamics simulation.

Urea ameliorates trimethylamine N-oxide-Induced aggregation of intrinsically disordered α-casein protein: the other side of the urea-methylamine counteraction.

Computational investigation of aphid odorant receptor structure and binding function.

A foundational theoreticalAl<sub>12</sub>E<sub>12</sub>(E = N, P) adsorption and quinolone docking study: cage–quinolone pairs, optics and possible therapeutic and diagnostic applications.

Fibroblast growth factor receptor (FGFR) inhibitors as anticancer agents: 3D-QSAR, molecular docking and dynamics simulation studies of 1, 6-naphthyridines and pyridopyrimidines.

Molecular structure determination, spectroscopic, quantum computational studies and molecular docking of 4-(E)-[2-(benzylamino)phenylimino) methyl-2]ethoxy phenol.

Molecular insights of hyaluronic acid – ethambutol and hyaluronic acid – isoniazid drug conjugates act as promising novel drugs for the treatment of tuberculosis.

A closer look at the mode of binding of drug pemetrexed with CT-DNA.

Immune escape facilitation by mutations of epitope residues in RdRp of SARS-CoV-2.

Molecular dynamics and 3D-QSAR studies on indazole derivatives as HIF-1α inhibitors.

In-silico studies on wild orange (Citrus macroptera Mont.) compounds against COVID-19 pro-inflammation targets.

Exploring species-specific inhibitors with multiple target sites on S. aureus pyruvate kinase using a computational workflow.

Discovery of a novel inhibitor against urokinase-type plasminogen activator, a potential enzyme with a role in atherosclerotic plaque instability.

Investigating binding of insecticide buprofezin to DNA by experimental and metadynamics simulation studies.

Molecular docking and dynamics approach to in silico drug repurposing for inflammatory bowels disease by targeting TNF alpha.

Parallel actin monomers in the 8S complex of actin–INF2.

Atomic level and structural understanding of natural ligands inhibiting Helicobacter pylori peptide deformylase through ligand and receptor based screening, SIFT, molecular dynamics and DFT – a structural computational approach.

Computational vaccinology guided design of multi-epitope subunit vaccine against a neglected arbovirus of the Americas.

Three-dimensional modeling of streptomycin binding single-stranded DNA for aptamer-based biosensors, a molecular dynamics simulation approach.

Interaction of Anagrelide drug molecule on pristine and doped boron nitride nanocages: a DFT, RDG, PCM and QTAIM investigation.

Identification of tumor homing peptides by utilizing hybrid feature representation.

Computational studies suggest compounds restoring function of p53 cancer mutants can bind SARS-CoV-2 spike protein.

In silico identification of small molecule protein-protein interaction inhibitors: targeting hotspot regions at the interface of MXRA8 and CHIKV envelope protein.

Development of peptide vaccine candidate using highly antigenic PE-PGRS family proteins to stimulate the host immune response against Mycobacterium tuberculosis H<sub>37</sub>Rv: an immuno-informatics approach.

Dealkenylation of neoandrographolide, a phytochemical from Andrographis paniculata stimulates FXR (Farnesoid X Receptor) and enhances gallstone dissolution.

Neem and Turmeric in the management of Covid Associated Mucormycosis (CAM) derived through network pharmacology.

Monosaccharide induced temporal delay in cholesterol self-aggregation.

In the footsteps of an inhibitor unbinding from the active site of human carbonic anhydrase II.

Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations.

An in silico discovery of potential 3CL protease inhibitors of SARS-CoV-2 based upon inactivation of the cysteine 145-Histidine 41 catalytic dyad.

In silico and in vitro studies on inhibitors for SARS-CoV-2 non-structural proteins with dual herbal combination of Withania somnifera with five rasayana herbs.

Unbinding of hACE2 and inhibitors from the receptor binding domain of SARS-CoV-2 spike protein.

Exploring electronic, structural and dynamics parameters of phenylbenzothiazole complexes with Mn<sup>2+</sup>, Cu<sup>2+</sup> and Zn<sup>2+</sup> for designing new magnetic resonance imaging (MRI) probes: congruence between computation and spectroscopic data

Vitamin B12 binding to mutated human transcobalamin, in-silico study of TCN2 alanine scanning and ClinVar missense mutations/SNPs.

Thermodynamics of globular protein native structure.