Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 22 (2022)

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Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 22 (2022)

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Research Articles

Article
Polypharmacology of some medicinal plant metabolites against SARS-CoV-2 and host targets: Molecular dynamics evaluation of NSP9 RNA binding protein
Suritra Bandyopadhyay, Omobolanle Abimbola Abiodun, Blessing Chinweotito Ogboo, Adeola Tawakalitu Kola-Mustapha, Emmanuel Ifeanyi Attah, Lawrence Edemhanria, Ankita Kumari, Ravindran Jaganathan & Niyi S. Adelakun
Pages: 11467-11483
Published online: 09 Aug 2021
AbstractforPolypharmacology of some medicinal plant metabolites against SARS-CoV-2 and host targets: Molecular dynamics evaluation of NSP9 RNA binding protein | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 600 Views
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Article
In vitro DNA binding, pBR322 cleavage and molecular docking studies of 1,2-diaminobenzene, dichloro glycyl glycinate tin(IV) and zirconium(IV) complexes
Waddhaah M. Alasbahy & Manal Shamsi
Pages: 11484-11494
Published online: 05 Aug 2021
AbstractforIn vitro DNA binding, pBR322 cleavage and molecular docking studies of 1,2-diaminobenzene, dichloro glycyl glycinate tin(IV) and zirconium(IV) complexes | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 94 Views
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Article
Exploring the antileishmanial activity of N1,N2-disubstituted-benzoylguanidines: synthesis and molecular modeling studies
Kaio Maciel de Santiago-Silva, Bruna Taciane da Silva Bortoleti, Tiago de Oliveira Brito, Ivete Conchon Costa, Camilo Henrique da Silva Lima, Fernando Macedo Jr., Milena Menegazzo Miranda-Sapla, Wander Rogério Pavanelli & Marcelle de Lima Ferreira Bispo
Pages: 11495-11510
Published online: 06 Aug 2021
AbstractforExploring the antileishmanial activity of N1,N2-disubstituted-benzoylguanidines: synthesis and molecular modeling studies | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 220 Views
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Article
In silico and in vitro investigation of anticancer effect of newly synthesized nonivamide-s-allyl cysteine ester
Sudha Vijayan, Chitra Loganathan, Penislusshiyan Sakayanathan & Palvannan Thayumanavan
Pages: 11511-11525
Published online: 03 Aug 2021
AbstractforIn silico and in vitro investigation of anticancer effect of newly synthesized nonivamide-s-allyl cysteine ester | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 306 Views
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Article
In silico analysis of marine natural product from sponge (Clathria Sp.) for their activity as inhibitor of SARS-CoV-2 Main Protease
Dwi Syah Fitra Ramadhan, Fatmasari Siharis, Syawal Abdurrahman, Muhammad Isrul & Taufik Muhammad Fakih
Pages: 11526-11532
Published online: 02 Aug 2021
AbstractforIn silico analysis of marine natural product from sponge (Clathria Sp.) for their activity as inhibitor of SARS-CoV-2 Main Protease | Full Text | References | PDF (1.5 MB) | EPUB
  • 233 Views
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Article
A detailed understanding of the COL10A1 and SOX9 genes interaction based on potentially damaging mutations in gastric cancer using computational techniques
Sedef Hande Aktas, Tugba Taskin-Tok, Khattab Al-Khafaji & Dilara Fatma Akın-Balı
Pages: 11533-11544
Published online: 12 Aug 2021
AbstractforA detailed understanding of the COL10A1 and SOX9 genes interaction based on potentially damaging mutations in gastric cancer using computational techniques | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 307 Views
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Article
Flavan-based phytoconstituents inhibit Mpro, a SARS-COV-2 molecular target, in silico
Soham Mukherjee, Deepika Sharma, Ajay Kumar Sharma, Shreya Jaiswal, Nancy Sharma, Sangkha Borah & Gurjot Kaur
Pages: 11545-11559
Published online: 04 Aug 2021
AbstractforFlavan-based phytoconstituents inhibit Mpro, a SARS-COV-2 molecular target, in silico | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 237 Views
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Article
In silico identification of natural antiviral compounds as a potential inhibitor of chikungunya virus non-structural protein 3 macrodomain
Meenakshi Chaudhary & Deepak Sehgal
Pages: 11560-11570
Published online: 06 Aug 2021
AbstractforIn silico identification of natural antiviral compounds as a potential inhibitor of chikungunya virus non-structural protein 3 macrodomain | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 248 Views
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Article
In silico investigations of some Cyperus rotundus compounds as potential anti-inflammatory inhibitors of 5-LO and LTA4H enzymes
Fares Fenanir, Abderrahmane Semmeq, Yacine Benguerba, Michael Badawi, Marie-Antoinette Dziurla, Smain Amira & Hocine Laouer
Pages: 11571-11586
Published online: 06 Aug 2021
AbstractforIn silico investigations of some Cyperus rotundus compounds as potential anti-inflammatory inhibitors of 5-LO and LTA4H enzymes | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 234 Views
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Article
In vitro and in silico enzyme inhibition effects of some metal ions and compounds on glutathione S-transferase enzyme purified from Vaccinium arctostapylous L.
Neslihan Balcı, Halis Şakiroğlu, Fikret Türkan & Ercan Bursal
Pages: 11587-11593
Published online: 05 Aug 2021
AbstractforIn vitro and in silico enzyme inhibition effects of some metal ions and compounds on glutathione S-transferase enzyme purified from Vaccinium arctostapylous L. | Full Text | References | PDF (1.4 MB) | EPUB
  • 270 Views
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Article
Vitamin D3 and its hydroxyderivatives as promising drugs against COVID-19: a computational study
Yuwei Song, Shariq Qayyum, Rory A. Greer, Radomir M. Slominski, Chander Raman, Andrzej T. Slominski & Yuhua Song
Pages: 11594-11610
Published online: 20 Aug 2021
AbstractforVitamin D3 and its hydroxyderivatives as promising drugs against COVID-19: a computational study | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 276 Views
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Article
In silico screening of Pueraria tuberosa (PTY-2) for targeting COVID-19 by countering dual targets Mpro and TMPRSS2
Priya Shree, Priyanka Mishra, Prateek Kumar, Harsh Pandey, Rajanish Giri, Radha Chaube, Neha Garg & Yamini Bhusan Tripathi
Pages: 11611-11624
Published online: 23 Aug 2021
AbstractforIn silico screening of Pueraria tuberosa (PTY-2) for targeting COVID-19 by countering dual targets Mpro and TMPRSS2 | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 208 Views
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Article
Insights of ligand binding in modeled h5-HT1A receptor: homology modeling, docking, MM-GBSA, screening and molecular dynamics
Preeti Jha, Shubhra Chaturvedi, Ruchika Bhat, Nidhi Jain & Anil K. Mishra
Pages: 11625-11637
Published online: 13 Aug 2021
AbstractforInsights of ligand binding in modeled h5-HT1A receptor: homology modeling, docking, MM-GBSA, screening and molecular dynamics | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 275 Views
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Article
Machine learning modeling to identify affinity improved biobetter anticancer drug trastuzumab and the insight of molecular recognition of trastuzumab towards its antigen HER2
Nataraj Balakrishnan, Gurunathan Baskar, Sathyanarayan Balaji, Malathi Kullappan & Surapaneni Krishna Mohan
Pages: 11638-11652
Published online: 14 Aug 2021
AbstractforMachine learning modeling to identify affinity improved biobetter anticancer drug trastuzumab and the insight of molecular recognition of trastuzumab towards its antigen HER2 | Full Text | References | PDF (3.8 MB) | EPUB
  • 339 Views
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Article
Molecular dynamics simulation, synthesis and topoisomerase inhibitory actions of vanillin derivatives: a systematic computational structural integument
Chita Ranjan Sahoo, Sudhir Kumar Paidesetty, Subbarayan Sarathbabu, Budheswar Dehury, Nachimuthu Senthil Kumar & Rabindra Nath Padhy
Pages: 11653-11663
Published online: 06 Aug 2021
AbstractforMolecular dynamics simulation, synthesis and topoisomerase inhibitory actions of vanillin derivatives: a systematic computational structural integument | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 314 Views
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Article
In silico study to predict potential precursors of human dipeptidyl peptidase-IV inhibitors from hazelnut
Congcong Li, Renrui Qi, Jiawei Yuan, Lu Han, Song Wang, Wannan Li & Weiwei Han
Pages: 11664-11675
Published online: 05 Aug 2021
AbstractforIn silico study to predict potential precursors of human dipeptidyl peptidase-IV inhibitors from hazelnut | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 216 Views
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Article
Identification of miRNAs and related hub genes associated with the triple negative breast cancer using integrated bioinformatics analysis and in vitro approach
Mohd Shuaib, Kumari Sunita Prajapati, Atul Kumar Singh, Prem Prakash Kushwaha, Mohammad Waseem & Shashank Kumar
Pages: 11676-11690
Published online: 13 Aug 2021
AbstractforIdentification of miRNAs and related hub genes associated with the triple negative breast cancer using integrated bioinformatics analysis and in vitro approach | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 304 Views
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Article
iGluK-Deep: computational identification of lysine glutarylation sites using deep neural networks with general pseudo amino acid compositions
Sheraz Naseer, Rao Faizan Ali, Yaser Daanial Khan & P. D. D. Dominic
Pages: 11691-11704
Published online: 16 Aug 2021
AbstractforiGluK-Deep: computational identification of lysine glutarylation sites using deep neural networks with general pseudo amino acid compositions | Full Text | References | PDF (3.1 MB) | EPUB
  • 280 Views
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Article
A combinatorial approach to screen structurally diverse acetylcholinesterase inhibitory plant secondary metabolites targeting Alzheimer’s disease
Gourav Choudhir, Satyawati Sharma & P. Hariprasad
Pages: 11705-11718
Published online: 05 Aug 2021
AbstractforA combinatorial approach to screen structurally diverse acetylcholinesterase inhibitory plant secondary metabolites targeting Alzheimer’s disease | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 617 Views
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Article
Featuring ACE2 binding SARS-CoV and SARS-CoV-2 through a conserved evolutionary pattern of amino acid residues
Patrícia P. D. Carvalho & Nelson A. Alves
Pages: 11719-11728
Published online: 06 Sep 2021
AbstractforFeaturing ACE2 binding SARS-CoV and SARS-CoV-2 through a conserved evolutionary pattern of amino acid residues | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 2085 Views
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Article
The role of Colchicine on actin polymerization dynamics: as a potent anti-angiogenic factor
Samridhi Pathak, Rahul Gupta, Haifa Parkar, Neha Joshi, Shirisha Nagotu & Avinash Kale
Pages: 11729-11743
Published online: 23 Aug 2021
AbstractforThe role of Colchicine on actin polymerization dynamics: as a potent anti-angiogenic factor | Full Text | References | PDF (3.8 MB) | EPUB
  • 288 Views
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Article
Targeting the EGFR in cancer cells by fusion protein consisting of arazyme and third loop of TGF-alpha: an in silico study
Abdolamir Ghadaksaz, Abbas Ali Imani Fooladi, Hamideh Mahmoodzadeh Hosseini, Taher Nejad Satari & Mohsen Amin
Pages: 11744-11757
Published online: 11 Aug 2021
AbstractforTargeting the EGFR in cancer cells by fusion protein consisting of arazyme and third loop of TGF-alpha: an in silico study | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 248 Views
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Article
Deciphering the structural and functional impact of missense mutations in Egr1-DNA interacting interface: an integrative computational approach
Hemavathy Nagarajan & Umashankar Vetrivel
Pages: 11758-11770
Published online: 17 Aug 2021
AbstractforDeciphering the structural and functional impact of missense mutations in Egr1-DNA interacting interface: an integrative computational approach | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 181 Views
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Article
In-silico evidence of ADAM metalloproteinase pathology in cancer signaling networks
Plaboni Sen, Thirukumaran Kandasamy & Siddhartha Sankar Ghosh
Pages: 11771-11786
Published online: 17 Aug 2021
AbstractforIn-silico evidence of ADAM metalloproteinase pathology in cancer signaling networks | Full Text | References | PDF (4.6 MB) | EPUB | Supplemental
  • 608 Views
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Article
Molecular dynamics simulation, 3D-pharmacophore and scaffold hopping analysis in the design of multi-target drugs to inhibit potential targets of COVID-19
Neda Fayyazi, Tahereh Mostashari-Rad, Jahan B. Ghasemi, Mehran Mirabzadeh Ardakani & Farzad Kobarfard
Pages: 11787-11808
Published online: 18 Aug 2021
AbstractforMolecular dynamics simulation, 3D-pharmacophore and scaffold hopping analysis in the design of multi-target drugs to inhibit potential targets of COVID-19 | Full Text | References | PDF (7.1 MB) | EPUB | Supplemental
  • 341 Views
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Article
Immunoinformatic approach employing modeling and simulation to design a novel vaccine construct targeting MDR efflux pumps to confer wide protection against typhoidal Salmonella serovars
Soumya Ranjan Mahapatra, Jyotirmayee Dey, Gajraj Singh Kushwaha, Puspasree Puhan, Nirmal Kumar Mohakud, Santosh Kumar Panda, S Lata, Namrata Misra & Mrutyunjay Suar
Pages: 11809-11821
Published online: 31 Aug 2021
AbstractforImmunoinformatic approach employing modeling and simulation to design a novel vaccine construct targeting MDR efflux pumps to confer wide protection against typhoidal Salmonella serovars | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 346 Views
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Article
Computational study for identifying promising therapeutic agents of hydroxychloroquine analogues against SARS‐CoV‐2
D. S. N. B. K. Prasanth, Manikanta Murahari, Vivek Chandramohan, Chakravarthi Guntupalli & Lakshmana Rao Atmakuri
Pages: 11822-11836
Published online: 16 Aug 2021
AbstractforComputational study for identifying promising therapeutic agents of hydroxychloroquine analogues against SARS‐CoV‐2 | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 142 Views
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Article
Design, synthesis, DFT calculations, molecular docking and antimicrobial activities of novel cobalt, chromium metal complexes of heterocyclic moiety-based 1,3,4-oxadiazole derivatives
Taoufik Rohand, Hicham Ben EL Ayouchia, Hafid Achtak, Adib Ghaleb, Yavuz Derin, Ahmet Tutar & Kiyoshi Tanemura
Pages: 11837-11850
Published online: 17 Aug 2021
AbstractforDesign, synthesis, DFT calculations, molecular docking and antimicrobial activities of novel cobalt, chromium metal complexes of heterocyclic moiety-based 1,3,4-oxadiazole derivatives | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 450 Views
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Article
In silico trials to design potent inhibitors against matrilysin (MMP-7)
Sudheer Kumar Katari, Chiranjeevi Pasala, Ravina Madhulitha Nalamolu, Aparna R. Bitla & Amineni Umamaheswari
Pages: 11851-11862
Published online: 18 Aug 2021
AbstractforIn silico trials to design potent inhibitors against matrilysin (MMP-7) | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 192 Views
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Article
Insights into the interaction of azinphos-methyl with bovine serum albumin: experimental and molecular docking studies
Bahareh Farasati Far, Soada Asadi, Mohammad Reza Naimi-Jamal, Walid Kamal Abdelbasset & Ali Aghajani Shahrivar
Pages: 11863-11873
Published online: 24 Aug 2021
AbstractforInsights into the interaction of azinphos-methyl with bovine serum albumin: experimental and molecular docking studies | Full Text | References | PDF (2.2 MB) | EPUB
  • 183 Views
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Article
In silico study on spice-derived antiviral phytochemicals against SARS-CoV-2 TMPRSS2 target
Pradeep Kumar Yadav, Amit Jaiswal & Rajiv Kumar Singh
Pages: 11874-11884
Published online: 24 Aug 2021
AbstractforIn silico study on spice-derived antiviral phytochemicals against SARS-CoV-2 TMPRSS2 target | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 294 Views
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Article
Flavanones: A potential natural inhibitor of the ATP binding site of PknG of Mycobacterium tuberculosis
Supriya P. Swain, Subhi Gupta, Nidhi Das, Tanos Celmar Costa Franca, Arlan da Silva Goncalves, Teodorico Castro Ramalho, Shreya Subrahmanya, Utkarsh Narsaria, Debashrito Deb & Neelam Mishra
Pages: 11885-11899
Published online: 19 Aug 2021
AbstractforFlavanones: A potential natural inhibitor of the ATP binding site of PknG of Mycobacterium tuberculosis | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 435 Views
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Article
Heat-induced transitions of an empty minute virus of mice capsid in explicit water: all-atom MD simulation
Arup Kumar Pathak & Tusar Bandyopadhyay
Pages: 11900-11913
Published online: 30 Aug 2021
AbstractforHeat-induced transitions of an empty minute virus of mice capsid in explicit water: all-atom MD simulation | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 128 Views
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Article
Strategic analyses to identify key structural features of antiviral/antimalarial compounds for their binding interactions with 3CLpro, PLpro and RdRp of SARS-CoV-2: in silico molecular docking and dynamic simulation studies
Ashish M. Dhote, Vikas R. Patil, Deepak K. Lokwani, Nikhil D. Amnerkar, Vinod G. Ugale, Nitin B. Charbe, Bhoomendra A. Bhongade & Saurabh C. Khadse
Pages: 11914-11931
Published online: 25 Aug 2021
AbstractforStrategic analyses to identify key structural features of antiviral/antimalarial compounds for their binding interactions with 3CLpro, PLpro and RdRp of SARS-CoV-2: in silico molecular docking and dynamic simulation studies | Full Text | References | PDF (6.1 MB) | EPUB | Supplemental
  • 340 Views
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Article
Phytochemical constituents of Inula britannica as potential inhibitors of dihydrofolate reductase: A strategic approach against shigellosis
Sandra Jose, Sreevidya S. Devi, Shakthi P.Khattab Al-Khafaji
Pages: 11932-11947
Published online: 23 Aug 2021
AbstractforPhytochemical constituents of Inula britannica as potential inhibitors of dihydrofolate reductase: A strategic approach against shigellosis | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 212 Views
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Article
Covid-19 rapid test by combining a Random Forest-based web system and blood tests
Valter Augusto de Freitas Barbosa, Juliana Carneiro Gomes, Maíra Araújo de Santana, Clarisse Lins de Lima, Raquel Bezerra Calado, Cláudio Roberto Bertoldo Júnior, Jeniffer Emidio de Almeida Albuquerque, Rodrigo Gomes de Souza, Ricardo Juarez Escorel de Araújo, Luiz Alberto Reis Mattos Júnior, Ricardo Emmanuel de Souza & Wellington Pinheiro dos Santos
Pages: 11948-11967
Published online: 31 Aug 2021
AbstractforCovid-19 rapid test by combining a Random Forest-based web system and blood tests | Full Text | References | PDF (4.1 MB) | EPUB
  • 1346 Views
  • 7 CrossRef citations
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Article
Thermal shift assays of marine-derived fungal metabolites from Aspergillus fischeri MMERU 23 against Leishmania major pteridine reductase 1 and molecular dynamics studies
Harol R. Arias Cardona, Thamires Q. Froes, Bruno C. De Souza, Franco H. A. Leite, Hugo Neves Brandão, Jamrearn Buaruang, Anake Kijjoa & Clayton Q. Alves
Pages: 11968-11976
Published online: 20 Aug 2021
AbstractforThermal shift assays of marine-derived fungal metabolites from Aspergillus fischeri MMERU 23 against Leishmania major pteridine reductase 1 and molecular dynamics studies | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 213 Views
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Article
Determining structure and action mechanism of LBF14 by molecular simulation
Florian Solbach, Austen Bernardi, Shivani Bansal, Madhu S. Budamagunta, Lukas Krep, Kai Leonhard, John C. Voss, Kit S. Lam & Roland Faller
Pages: 11977-11988
Published online: 23 Aug 2021
AbstractforDetermining structure and action mechanism of LBF14 by molecular simulation | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 300 Views
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Article
Comprehensive sequence and structure analysis of algal lipid catabolic enzyme Triacylglycerol lipase: an in silico study to vitalize the development of optimum engineered strains with high lipid productivity
Susrita Sahoo, Budheswar Dehury, Parminder Kaur Narang, Vishakha Raina, Namrata Misra & Mrutyunjay Suar
Pages: 11989-12007
Published online: 20 Aug 2021
AbstractforComprehensive sequence and structure analysis of algal lipid catabolic enzyme Triacylglycerol lipase: an in silico study to vitalize the development of optimum engineered strains with high lipid productivity | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 292 Views
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Article
Molecular docking and inhibition studies of vulpinic, carnosic and usnic acids on polyol pathway enzymes
Yeliz Demir, Hamid Ceylan, Cüneyt Türkeş & Şükrü Beydemir
Pages: 12008-12021
Published online: 23 Aug 2021
AbstractforMolecular docking and inhibition studies of vulpinic, carnosic and usnic acids on polyol pathway enzymes | Full Text | References | PDF (3.1 MB) | EPUB
  • 741 Views
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Article
Molecular modeling and dynamics simulation of alcohol dehydrogenase enzyme from high efficacy cellulosic ethanol-producing yeast mutant strain Pichia kudriavzevii BGY1-γm
Neha Bisht, Vikram Dalal & Lakshmi Tewari
Pages: 12022-12036
Published online: 23 Aug 2021
AbstractforMolecular modeling and dynamics simulation of alcohol dehydrogenase enzyme from high efficacy cellulosic ethanol-producing yeast mutant strain Pichia kudriavzevii BGY1-γm | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 342 Views
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Article
Exploring novel and potent molecules for disrupting DEPTOR-mTOR interaction through structure-steered screening, extra-exactitude molecular docking, prime binding free energy estimation and voguish molecular dynamics
Basit Amin Shah, Shabir Ahmad Ganai, Aabid M. Koul, Suma Mohan, Asif Amin, Zubair Wani, Umer Majeed, Sundaraj Rajamanikandan, Faizah Farooq, Firdose Ahmad Malik, Naveed Nazir Shah & Raies A. Qadri
Pages: 12037-12047
Published online: 25 Aug 2021
AbstractforExploring novel and potent molecules for disrupting DEPTOR-mTOR interaction through structure-steered screening, extra-exactitude molecular docking, prime binding free energy estimation and voguish molecular dynamics | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 243 Views
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Article
MD simulation and MM/PBSA identifies phytochemicals as bifunctional inhibitors of SARS-CoV-2
Monica Sharma, Jai Krishna Mahto, Preeti Dhaka, Neetu Neetu, Shailly Tomar & Pravindra Kumar
Pages: 12048-12061
Published online: 27 Aug 2021
AbstractforMD simulation and MM/PBSA identifies phytochemicals as bifunctional inhibitors of SARS-CoV-2 | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 483 Views
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Article
Discovering potential inhibitors against SARS-CoV-2 by targeting Nsp13 Helicase
Rajat Nandi, Deep Bhowmik, Rakesh Srivastava, Amresh Prakash & Diwakar Kumar
Pages: 12062-12074
Published online: 28 Aug 2021
AbstractforDiscovering potential inhibitors against SARS-CoV-2 by targeting Nsp13 Helicase | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 619 Views
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Article
The antioxidant and antidiabetic potentials of polyphenolic-rich extracts of Cyperus rotundus (Linn.)
Almahi I. Mohamed, Brian K. Beseni, Nontokozo Z. Msomi, Veronica F. Salau, Ochuko L. Erukainure, Aimen Aljoundi & Md. Shahidul Islam
Pages: 12075-12087
Published online: 28 Aug 2021
AbstractforThe antioxidant and antidiabetic potentials of polyphenolic-rich extracts of Cyperus rotundus (Linn.) | Full Text | References | PDF (3.8 MB) | EPUB
  • 464 Views
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Article
Venetoclax: a promising repurposed drug against SARS-CoV-2 main protease
Suvankar Ghosh, Debojit Bhattacherjee, Priyadarshi Satpati & Krishna Pada Bhabak
Pages: 12088-12099
Published online: 23 Aug 2021
AbstractforVenetoclax: a promising repurposed drug against SARS-CoV-2 main protease | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 448 Views
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Article
Computational analysis of protein conformational heterogeneity
Kristen Rhinehardt & Ming Dong
Pages: 12100-12105
Published online: 23 Aug 2021
AbstractforComputational analysis of protein conformational heterogeneity | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 153 Views
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Article
Design, synthesis of pyridine coupled pyrimidinone/pyrimidinthione as anti-MRSA agent: Validation by molecular docking and dynamics simulation
S. Nanjundaswamy, S. Bindhu, R. R. Arun Renganathan, S. Nagashree, C. S. Karthik, P. Mallu & V. Ravishankar Rai
Pages: 12106-12117
Published online: 23 Aug 2021
AbstractforDesign, synthesis of pyridine coupled pyrimidinone/pyrimidinthione as anti-MRSA agent: Validation by molecular docking and dynamics simulation | Full Text | References | PDF (2.6 MB) | EPUB
  • 397 Views
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Article
In silico prediction of natural compounds as potential multi-target inhibitors of structural proteins of SARS-CoV-2
Jyoti Rani, Anasuya Bhargav, Faez Iqbal Khan, Srinivasan Ramachandran, Dakun Lai & Urmi Bajpai
Pages: 12118-12134
Published online: 06 Sep 2021
AbstractforIn silico prediction of natural compounds as potential multi-target inhibitors of structural proteins of SARS-CoV-2 | Full Text | References | PDF (6 MB) | EPUB | Supplemental
  • 1119 Views
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Article
Elucidation of binding mechanism of stigmasterol with human serum albumin: a biophysical and molecular dynamics simulation approach
Daniel Pushparaju Yeggoni, Shreya Dubey, Yusuf Zamal Mohammad, Aparna Rachamallu & Rajagopal Subramanyam
Pages: 12135-12147
Published online: 31 Aug 2021
AbstractforElucidation of binding mechanism of stigmasterol with human serum albumin: a biophysical and molecular dynamics simulation approach | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 151 Views
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Article
Structural, spectroscopic, in silico, in vitro and DNA binding evaluations of tyrosyl-lysyl-threonine
Bilge Bicak, Serda Kecel Gunduz, Yasemin Budama Kilinc, Petra Imhof, Bahar Gok, Gizem Akman & Ayşen E. Ozel
Pages: 12148-12164
Published online: 31 Aug 2021
AbstractforStructural, spectroscopic, in silico, in vitro and DNA binding evaluations of tyrosyl-lysyl-threonine | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 496 Views
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Article
Computational investigation of phytoalexins as potential antiviral RAP-1 and RAP-2 (Replication Associated Proteins) inhibitor for the management of cucumber mosaic virus (CMV): a molecular modeling, in silico docking and MM-GBSA study
Roshni Mohan Kumar, Ramachandra Anantapur, Anitha Peter & Chaitra H. V.
Pages: 12165-12183
Published online: 31 Aug 2021
AbstractforComputational investigation of phytoalexins as potential antiviral RAP-1 and RAP-2 (Replication Associated Proteins) inhibitor for the management of cucumber mosaic virus (CMV): a molecular modeling, in silico docking and MM-GBSA study | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
  • 264 Views
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Synthesis, in silico, and in vivo anti-inflammatory evaluation of 3β-cinnamoyloxy substituted pregna-4,16-diene-6,20-diones derivatives
Elkin Sanabria-Chanaga, Dulce María Meneses-Ruiz, Erick Francisco Puertas-Santamaría, Fernando Manuel Mancha-Meléndez, Eugene Bratoeff, Marco A. Loza-Mejía & Juan Rodrigo Salazar
Pages: 12184-12193
Published online: 01 Sep 2021
AbstractforSynthesis, in silico, and in vivo anti-inflammatory evaluation of 3β-cinnamoyloxy substituted pregna-4,16-diene-6,20-diones derivatives | Full Text | References | PDF (1.4 MB) | EPUB
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Article
Synthesis, spectroscopic characterization, antimicrobial activity, molecular docking and DFT studies of proton transfer (H-bonded) complex of 8-aminoquinoline (donor) with chloranilic acid (acceptor)
Ishaat M. Khan, Maidul Islam, Sonam Shakya, Nisat Alam, Shah Imtiaz & Md. Rabiul Islam
Pages: 12194-12208
Published online: 02 Sep 2021
AbstractforSynthesis, spectroscopic characterization, antimicrobial activity, molecular docking and DFT studies of proton transfer (H-bonded) complex of 8-aminoquinoline (donor) with chloranilic acid (acceptor) | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 332 Views
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Article
Myxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein
Rey Arturo Fernandez, Mark Tristan Quimque, Kin Israel Notarte, Joe Anthony Manzano, Delfin Yñigo Pilapil IV, Von Novi de Leon, John Jeric San Jose, Omar Villalobos, Nisha Harur Muralidharan, M. Michael Gromiha, Simone Brogi & Allan Patrick G. Macabeo
Pages: 12209-12220
Published online: 31 Aug 2021
AbstractforMyxobacterial depsipeptide chondramides interrupt SARS-CoV-2 entry by targeting its broad, cell tropic spike protein | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 1319 Views
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In-silico screening and identification of phytochemicals from Centella asiatica as potential inhibitors of sodium-glucose co-transporter 2 for treating diabetes
Mark Andrian B. Macalalad & Arthur A. Gonzales III
Pages: 12221-12238
Published online: 28 Aug 2021
AbstractforIn-silico screening and identification of phytochemicals from Centella asiatica as potential inhibitors of sodium-glucose co-transporter 2 for treating diabetes | Full Text | References | PDF (7 MB) | EPUB | Supplemental
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Open Access
Article
Insights into the mutations leading to capreomycin resistance in S-adenosyl-L-methionine binding motif in TlyA from Mycobacterium tuberculosis
Waseem Ali, Salma Jamal, Abhinav Grover & Sonam Grover
Pages: 12239-12247
Published online: 31 Aug 2021
AbstractforInsights into the mutations leading to capreomycin resistance in S-adenosyl-L-methionine binding motif in TlyA from Mycobacterium tuberculosis | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 178 Views
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FMS-like tyrosine kinase-3 (FLT3) inhibitors with better binding affinity and ADMET properties than sorafenib and gilteritinib against acute myeloid leukemia: in silico studies
Chukwuebuka Egbuna, Kingsley C. Patrick-Iwuanyanwu, Eugene N. Onyeike, Johra Khan & Bader Alshehri
Pages: 12248-12259
Published online: 06 Sep 2021
AbstractforFMS-like tyrosine kinase-3 (FLT3) inhibitors with better binding affinity and ADMET properties than sorafenib and gilteritinib against acute myeloid leukemia: in silico studies | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
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Open Access
Article
New chalcone derivative, ethyl 2-(4-(3-(benzo[b]thiophen-2-yl)acryloyl)phenoxy)acetate: synthesis, characterization, DFT study, enzyme inhibition activities and docking study
Fatih Çelik, Nevin Süleymanoğlu, Reşat Ustabaş, Fikret Türkan, Halil İbrahim Güler, Yasemin Ünver & Nuran Kahriman
Pages: 12260-12267
Published online: 26 Aug 2021
AbstractforNew chalcone derivative, ethyl 2-(4-(3-(benzo[b]thiophen-2-yl)acryloyl)phenoxy)acetate: synthesis, characterization, DFT study, enzyme inhibition activities and docking study | Full Text | References | PDF (1.2 MB) | EPUB | Supplemental
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Novel bioengineered MBenes for the treatment of Alzheimer's disease: An in-Sillico study
Mohammad Dahri, Ahmad Miri Jahromi, Arash Nikzad, Maryam Mohammadgholian, Mohammad Rahmanian, Samira Sadat Abolmaali & Reza Maleki
Pages: 12268-12276
Published online: 24 Aug 2021
AbstractforNovel bioengineered MBenes for the treatment of Alzheimer's disease: An in-Sillico study | Full Text | References | PDF (2.5 MB) | EPUB
  • 405 Views
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Article
Insights into small molecule inhibitor bindings to PD-L1 with residue-specific binding free energy calculation
Wei Xia, Liping He, Jingxiao Bao, Yifei Qi & John Z.H. Zhang
Pages: 12277-12285
Published online: 06 Sep 2021
AbstractforInsights into small molecule inhibitor bindings to PD-L1 with residue-specific binding free energy calculation | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 418 Views
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Ebselen suitably interacts with the potential SARS-CoV-2 targets: an in-silico approach
Chandan Sarkar, Mohnad Abdalla, Milon Mondal, Abul Bashar Ripon Khalipha & Nasir Ali
Pages: 12286-12301
Published online: 30 Aug 2021
AbstractforEbselen suitably interacts with the potential SARS-CoV-2 targets: an in-silico approach | Full Text | References | PDF (4.6 MB) | EPUB
  • 324 Views
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Antiproliferative activity on Trypanosoma cruzi (Y strain) of the triterpene 3β,6β,16β-trihidroxilup-20 (29)-ene isolated from Combretum leprosum
José Ismael F. de Araújo, Natália L. Aires, Francisco W. Q. Almeida-Neto, Márcia M. Marinho, Emanuelle M. Marinho, Emanuel Paula Magalhães, Ramon R. P. P. B. de Menezes, Tiago L. Sampaio, Alice Maria Costa Martins, Edson H. Teixeira, Ana Rafaela Freitas Dotto, Wanderlei do Amaral, Alexandre Magno R. Teixeira, Pedro de Lima-Neto, Emmanuel S. Marinho & Hélcio S. dos Santos
Pages: 12302-12315
Published online: 26 Aug 2021
AbstractforAntiproliferative activity on Trypanosoma cruzi (Y strain) of the triterpene 3β,6β,16β-trihidroxilup-20 (29)-ene isolated from Combretum leprosum | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 194 Views
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Article
Promoter sequence interaction and structure based multi-targeted (redox regulatory genes) molecular docking analysis of vitamin E and curcumin in T4 induced oxidative stress model using H9C2 cardiac cell line
Pallavi Mishra, Gitanjali Tandon, Manoj Kumar, Biswaranjan Paital, Shasanka Sekhar Swain, Sunil Kumar & Luna Samanta
Pages: 12316-12335
Published online: 31 Aug 2021
AbstractforPromoter sequence interaction and structure based multi-targeted (redox regulatory genes) molecular docking analysis of vitamin E and curcumin in T4 induced oxidative stress model using H9C2 cardiac cell line | Full Text | References | PDF (7.1 MB) | EPUB | Supplemental
  • 274 Views
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Article
Organotin (IV) complexes with sulphonyl hydrazide moiety. Design, synthesis, characterization, docking studies, cytotoxic and anti-leishmanial activity
Rehman Zafar, Khadija Shahid, Lee D. Wilson, Muhammad Fahid, Majid Sartaj, Wajeeha Waseem, Muhammad Saeed Jan, Muhammad Zubair, Ali Irfan, Sami Ullah & Abdul Sadiq
Pages: 12336-12346
Published online: 30 Aug 2021
AbstractforOrganotin (IV) complexes with sulphonyl hydrazide moiety. Design, synthesis, characterization, docking studies, cytotoxic and anti-leishmanial activity | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 263 Views
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SARS-COV-2 Mpro conformational changes induced by covalently bound ligands
Glaucio Monteiro Ferreira, Thales Kronenberger, Arun Kumar Tonduru, Rosario Dominguez Crespo Hirata, Mario Hiroyuki Hirata & Antti Poso
Pages: 12347-12357
Published online: 13 Sep 2021
AbstractforSARS-COV-2 Mpro conformational changes induced by covalently bound ligands | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 2336 Views
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Arjunetin as a promising drug candidate against SARS-CoV-2: molecular dynamics simulation studies
Gandarvakottai Senthilkumar Arumugam, Asmita Sen, Swati S. Dash, Kartik Mitra, Mukesh Doble, Gopalan Rajaraman & Sathyanarayana N. Gummadi
Pages: 12358-12379
Published online: 17 Sep 2021
AbstractforArjunetin as a promising drug candidate against SARS-CoV-2: molecular dynamics simulation studies | Full Text | References | PDF (8.4 MB) | EPUB | Supplemental
  • 1726 Views
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M6A-GSMS: Computational identification of N6-methyladenosine sites with GBDT and stacking learning in multiple species
Shengli Zhang, Jinyue Wang, Xinjie Li & Yunyun Liang
Pages: 12380-12391
Published online: 30 Aug 2021
AbstractforM6A-GSMS: Computational identification of N6-methyladenosine sites with GBDT and stacking learning in multiple species | Full Text | References | PDF (3.5 MB) | EPUB
  • 346 Views
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Drug repurposing combined with MM/PBSA based validation strategies towards MEK inhibitors screening
Muthu Kumar Thirunavukkarasu & Ramanathan Karuppasamy
Pages: 12392-12403
Published online: 30 Aug 2021
AbstractforDrug repurposing combined with MM/PBSA based validation strategies towards MEK inhibitors screening | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 244 Views
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Article
Exploration of the binding between cuminol and bovine serum albumin through spectroscopic, molecular docking and molecular dynamics methods
Mohd Sajid Ali, Md Tabish Rehman, Hamad A. Al-Lohedan & Mohamed Fahad AlAjmi
Pages: 12404-12412
Published online: 06 Sep 2021
AbstractforExploration of the binding between cuminol and bovine serum albumin through spectroscopic, molecular docking and molecular dynamics methods | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 194 Views
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