Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 23 (2023)

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Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 23 (2023)

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Research Articles

Article
Structural modeling and analyses of genetic variations in the human XPC nucleotide excision repair protein
Jennifer Le & Jung-Hyun Min
Pages: 13535-13562
Published online: 08 Mar 2023
AbstractforStructural modeling and analyses of genetic variations in the human XPC nucleotide excision repair protein | Full Text | References | PDF (7.8 MB) | EPUB | Supplemental
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Article
An immunoinformatics analysis: design of a multi-epitope vaccine against Cryptosporidium hominis by employing heat shock protein triggers the innate and adaptive immune responses
Nirali Pandya & Amit Kumar
Pages: 13563-13579
Published online: 10 Feb 2023
AbstractforAn immunoinformatics analysis: design of a multi-epitope vaccine against Cryptosporidium hominis by employing heat shock protein triggers the innate and adaptive immune responses | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
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Article
Arginine transportation mechanism through cationic amino acid transporter 1: insights from molecular dynamics studies
Maral Afshinpour & Hamid Mahdiuni
Pages: 13580-13594
Published online: 10 Feb 2023
AbstractforArginine transportation mechanism through cationic amino acid transporter 1: insights from molecular dynamics studies | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 197 Views
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Article
Virtual screening, molecular docking, molecular dynamics and quantum chemical studies on (2-methoxy-4-prop-2-enylphenyl) N-(2-methoxy-4-nitrophenyl) carbamate: a novel inhibitor of hepatocellular carcinoma
T. Rajesh Kumar, R. Premkumar, K. Langeswaran, K. Ramavenkateswari, S. Anitha, P. Sangavi & R. Sangeetha
Pages: 13595-13604
Published online: 03 Apr 2023
AbstractforVirtual screening, molecular docking, molecular dynamics and quantum chemical studies on (2-methoxy-4-prop-2-enylphenyl) N-(2-methoxy-4-nitrophenyl) carbamate: a novel inhibitor of hepatocellular carcinoma | Full Text | References | PDF (1.4 MB) | EPUB | Supplemental
  • 161 Views
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Article
Bioactive plantaricins as potent anti-cancer drug candidates: double docking, molecular dynamics simulation and in vitro cytotoxicity analysis
Soumyadip Chakrobarty, Swarnava Garai, Arabinda Ghosh, Nobendu Mukerjee & Deeplina Das
Pages: 13605-13615
Published online: 12 Feb 2023
AbstractforBioactive plantaricins as potent anti-cancer drug candidates: double docking, molecular dynamics simulation and in vitro cytotoxicity analysis | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 309 Views
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Article
Quantitative structure activity relationship studies of androgen receptor binding affinity of endocrine disruptor chemicals with index of ideality of correlation, their molecular docking, molecular dynamics and ADME studies
Surbhi Goyal, Payal Rani, Monika Chahar, Khalid Hussain, Parvin Kumar & Jayant Sindhu
Pages: 13616-13631
Published online: 03 Apr 2023
AbstractforQuantitative structure activity relationship studies of androgen receptor binding affinity of endocrine disruptor chemicals with index of ideality of correlation, their molecular docking, molecular dynamics and ADME studies | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 182 Views
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Article
Usnic acid as potential inhibitors of BCL2 and P13K protein through network pharmacology-based analysis, molecular docking and molecular dynamic simulation
K.K.V. Wong, Miah Roney, Nazim Uddin, Syahrul Imran, Ahmad Mahfuz Gazali, Normaiza Zamri, Kamal Rullah & Mohd Fadhlizil Fasihi Mohd Aluwi
Pages: 13632-13645
Published online: 16 Feb 2023
AbstractforUsnic acid as potential inhibitors of BCL2 and P13K protein through network pharmacology-based analysis, molecular docking and molecular dynamic simulation | Full Text | References | PDF (2.2 MB) | EPUB
  • 358 Views
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Article
In silico design of novel CDK2 inhibitors through QSAR, ADMET, molecular docking and molecular dynamics simulation studies
Mohamed Moussaoui, Mouna Baassi, Soukayna Baammi, Hatim Soufi, Mohammed Salah, Rachid Daoud, Achraf EL Allali, M.E. Belghiti & Said Belaaouad
Pages: 13646-13662
Published online: 19 May 2023
AbstractforIn silico design of novel CDK2 inhibitors through QSAR, ADMET, molecular docking and molecular dynamics simulation studies | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 309 Views
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Article
Molecular docking and dynamics simulation of Orthosiphon stamineus against SGLT1 and SGLT2
Usha Subbiah, Athira Ajith & Harini Venkata Subbiah
Pages: 13663-13678
Published online: 30 Mar 2023
AbstractforMolecular docking and dynamics simulation of Orthosiphon stamineus against SGLT1 and SGLT2 | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 126 Views
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Article
Novel phytochemical inhibitors targeting monkeypox virus thymidine and serine/threonine kinase: integrating computational modeling and molecular dynamics simulation
Mitesh Patel, Abdulrahman S. Bazaid, Esam I. Azhar, Hattan S. Gattan, Naif K. Binsaleh, Mirav Patel, Malvi Surti & Mohd Adnan
Pages: 13679-13695
Published online: 28 Feb 2023
AbstractforNovel phytochemical inhibitors targeting monkeypox virus thymidine and serine/threonine kinase: integrating computational modeling and molecular dynamics simulation | Full Text | References | PDF (2.4 MB) | EPUB
  • 216 Views
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Article
Molecular dynamics and absolute binding free energy studies of piperine derivatives as potential inhibitors of SARS-CoV-2 main protease
Karteek Rao Amperayani, Govinda Varadhi, Baswanth Oruganti & Uma Devi Parimi
Pages: 13696-13706
Published online: 30 Mar 2023
AbstractforMolecular dynamics and absolute binding free energy studies of piperine derivatives as potential inhibitors of SARS-CoV-2 main protease | Full Text | References | PDF (1.8 MB) | EPUB
  • 212 Views
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Article
Molecular dynamics simulations and bioinformatics’ analysis of deleterious missense single nucleotide polymorphisms in Glyoxalase-1 gene
Nida Ali Syed, Attya Bhatti & Peter John
Pages: 13707-13717
Published online: 22 Feb 2023
AbstractforMolecular dynamics simulations and bioinformatics’ analysis of deleterious missense single nucleotide polymorphisms in Glyoxalase-1 gene | Full Text | References | PDF (1.1 MB) | EPUB
  • 256 Views
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Letter to the Editor

Letter
Molecular dynamics of α-helical structure: poly-l-glutamic acid
Y. N. Chirgadze, I. V. Likhachev, N. K. Balabaev & E. V. Brazhnikov
Pages: 13718-13723
Published online: 27 Feb 2023
AbstractforMolecular dynamics of α-helical structure: poly-l-glutamic acid | Full Text | References | PDF (1.1 MB) | EPUB
  • 98 Views
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Research Articles

Article
Synthesis, spectral characterization of pyrazole derived Schiff base analogs: molecular dynamic simulation, antibacterial and DNA binding studies
Razia Sultana, Asghar Ali, Charmy Twala, Rabiya Mehandi, Manish Rana, Daraksha Yameen, Mohammad Abid & Rahisuddin
Pages: 13724-13751
Published online: 24 Feb 2023
AbstractforSynthesis, spectral characterization of pyrazole derived Schiff base analogs: molecular dynamic simulation, antibacterial and DNA binding studies | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 361 Views
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Article
Lawsonia inermis flower aqueous extract expressed better anti-alpha-glucosidase and anti-acetylcholinesterase activity and their molecular dynamics
Ismail Shahanaj, Jaganathan Ramakrishnan, Kumaradhas Poomani & Natarajan Devarajan
Pages: 13752-13765
Published online: 11 Mar 2023
AbstractforLawsonia inermis flower aqueous extract expressed better anti-alpha-glucosidase and anti-acetylcholinesterase activity and their molecular dynamics | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 161 Views
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Article
Machine-learning technique, QSAR and molecular dynamics for hERG–drug interactions
Nilima Rani Das, Tripti Sharma, Andrey A. Toropov, Alla P. Toropova, Manish Kumar Tripathi & P. Ganga Raju Achary
Pages: 13766-13791
Published online: 05 Apr 2023
AbstractforMachine-learning technique, QSAR and molecular dynamics for hERG–drug interactions | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 349 Views
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Article
The coat protein of tobacco mosaic virus as an anti-tobacco mosaic virus: a molecular dynamics simulation
Narjes Sheibani, Seyed Shahriar Arab & Mohammad Kamalvand
Pages: 13792-13797
Published online: 01 Mar 2023
AbstractforThe coat protein of tobacco mosaic virus as an anti-tobacco mosaic virus: a molecular dynamics simulation | Full Text | References | PDF (1.1 MB) | EPUB
  • 190 Views
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Article
Molecular modeling study of pyrrolidine derivatives as novel myeloid cell leukemia-1 inhibitors through combined 3D-QSAR, molecular docking, ADME/Tox and MD simulation techniques
Kamal Tabti, Soukayna Baammi, Abdelouahid Sbai, Hamid Maghat, Tahar Lakhlifi & Mohammed Bouachrine
Pages: 13798-13814
Published online: 25 Feb 2023
AbstractforMolecular modeling study of pyrrolidine derivatives as novel myeloid cell leukemia-1 inhibitors through combined 3D-QSAR, molecular docking, ADME/Tox and MD simulation techniques | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 208 Views
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Article
Anti-inflammatory potential of selective small compounds by targeting TNF-α & NF-kB signaling: a comprehensive molecular docking and simulation study
Prachi Agnihotri, Hemchandra Deka, Debolina Chakraborty, Monu, Mohd Saquib, Uma Kumar & Sagarika Biswas
Pages: 13815-13828
Published online: 04 Apr 2023
AbstractforAnti-inflammatory potential of selective small compounds by targeting TNF-α & NF-kB signaling: a comprehensive molecular docking and simulation study | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 336 Views
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Article
Structure-based drug design, molecular dynamics simulation, ADMET, and quantum chemical studies of some thiazolinones targeting influenza neuraminidase
Mustapha Abdullahi, Adamu Uzairu, Gideon Adamu Shallangwa, Paul Andrew Mamza, Muhammad Tukur Ibrahim, Iqrar Ahmad & Harun Patel
Pages: 13829-13843
Published online: 09 May 2023
AbstractforStructure-based drug design, molecular dynamics simulation, ADMET, and quantum chemical studies of some thiazolinones targeting influenza neuraminidase | Full Text | References | PDF (3 MB) | EPUB
  • 317 Views
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Article
Ligand-based virtual screening, molecular dynamics, and biological evaluation of repurposed drugs as inhibitors of Trypanosoma cruzi proteasome
Suzane Quintana Gomes, Leonardo Bruno Federico, Guilherme Martins Silva, Carla Duque Lopes, Sérgio de Albuquerque & Carlos Henrique Tomich de Paula da Silva
Pages: 13844-13856
Published online: 24 Feb 2023
AbstractforLigand-based virtual screening, molecular dynamics, and biological evaluation of repurposed drugs as inhibitors of Trypanosoma cruzi proteasome | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 244 Views
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Article
Inhibitory effect of natural compounds on Dihydropteroate synthase of Mycobacterium leprae: Molecular dynamic study
Mahvish Khan, Saif Khan, Nashwa Zaki Ali Bushara, Rafat Ali, Zainab Tabassum, Romana Ishrat, Hussein Abdel-Aziz Marouf, Subuhi Sherwani, Shadab Mirza & Shafiul Haque
Pages: 13857-13872
Published online: 17 Apr 2023
AbstractforInhibitory effect of natural compounds on Dihydropteroate synthase of Mycobacterium leprae: Molecular dynamic study | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 94 Views
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Article
Structural, spectroscopic, molecular docking, ADME, molecular dynamics studies of Val-Trp dipeptide
Bilge Bicak
Pages: 13873-13890
Published online: 27 Feb 2023
AbstractforStructural, spectroscopic, molecular docking, ADME, molecular dynamics studies of Val-Trp dipeptide | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 368 Views
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Article
Molecular dynamics simulation of phosphatidylcholine membrane in low ionic strengths of sodium chloride
Wissam Mahmoud Abdel-gawad, Mahmoud Abdelmohsen, Mohamed Hasanen Gaber, Wafaa Muhammad Ahmed Khalil & Mohammed Said Mohammed Abu-Elmagd
Pages: 13891-13901
Published online: 22 Feb 2023
AbstractforMolecular dynamics simulation of phosphatidylcholine membrane in low ionic strengths of sodium chloride | Full Text | References | PDF (1.9 MB) | EPUB
  • 194 Views
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Article
Design and simulation of a caprylic acid enzymatically modified phosphatidylcholine micelle using a coarse-grained molecular dynamics simulations approach
Dalia Santos-Luna, Yudibeth Sixto-López, Diego Bravo-Alfaro, Cynthia Cano-Sarmiento, Hugo García & José Correa-Basurto
Pages: 13902-13913
Published online: 24 Feb 2023
AbstractforDesign and simulation of a caprylic acid enzymatically modified phosphatidylcholine micelle using a coarse-grained molecular dynamics simulations approach | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 117 Views
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Article
Identification of potential novel inhibitors against glutamine synthetase enzyme of Leishmania major by using computational tools
Mohammad Kashif & Naidu Subbarao
Pages: 13914-13922
Published online: 06 Feb 2023
AbstractforIdentification of potential novel inhibitors against glutamine synthetase enzyme of Leishmania major by using computational tools | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 213 Views
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Article
Virtual screening of bioactive anti-SARS-CoV natural products and identification of 3β,12-diacetoxyabieta-6,8,11,13-tetraene as a potential inhibitor of SARS-CoV-2 virus and its infection related pathways by MD simulation and network pharmacology
A.K.M. Moyeenul Huq, Miah Roney, Syahrul Imran, Shafi Ullah Khan, Md. Nazim Uddin, Thet Thet Htar, Atif Amin Baig, Mohiuddin Ahmed Bhuiyan, Zainul Amiruddin Zakaria, Mohd Fadhlizil Fasihi Mohd Aluwi & Saiful Nizam Tajuddin
Pages: 13923-13936
Published online: 14 Feb 2023
AbstractforVirtual screening of bioactive anti-SARS-CoV natural products and identification of 3β,12-diacetoxyabieta-6,8,11,13-tetraene as a potential inhibitor of SARS-CoV-2 virus and its infection related pathways by MD simulation and network pharmacology | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 214 Views
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Article
Evaluation of SNPs from human IGFBP6 associated with gene expression: an in-silico study
Shubham Ramdas Wanarase, Shivam Vinayakrao Chavan, Sameer Sharma & Susha D.
Pages: 13937-13949
Published online: 22 Mar 2023
AbstractforEvaluation of SNPs from human IGFBP6 associated with gene expression: an in-silico study | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 131 Views
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Article
Combination of bendamustine-azacitidine against Syk target of breast cancer: an in silico study
Sankar Muthumanickam, Balajee Ramachandran, Pandi Boomi, Jeyaraman Jeyakanthan, Halliah Gurumallesh Prabu, Sonamuthu Jegatheswaran & Kumpati Premkumar
Pages: 13950-13962
Published online: 26 Apr 2023
AbstractforCombination of bendamustine-azacitidine against Syk target of breast cancer: an in silico study | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 115 Views
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Article
Exploring the potential and identifying Withania somnifera alkaloids as novel dihydrofolate reductase (DHFR) inhibitors by the AlteQ method
Krishnamoorthy Gurushankar, Hrvoje Rimac, Palko Nadezhda & Maria Grishina
Pages: 13963-13976
Published online: 10 Feb 2023
AbstractforExploring the potential and identifying Withania somnifera alkaloids as novel dihydrofolate reductase (DHFR) inhibitors by the AlteQ method | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 93 Views
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Article
Potential drug candidates as P-glycoprotein inhibitors to reverse multidrug resistance in cancer: an in silico drug discovery study
Mahmoud A. A. Ibrahim, Khlood A. A. Abdeljawaad, Laila A. Jaragh-Alhadad, Hesham Farouk Oraby, Mohamed A. M. Atia, Othman R. Alzahrani, Gamal A. H. Mekhemer, Mahmoud F. Moustafa, Ahmed M. Shawky, Peter A. Sidhom & Alaa H. M. Abdelrahman
Pages: 13977-13992
Published online: 08 Mar 2023
AbstractforPotential drug candidates as P-glycoprotein inhibitors to reverse multidrug resistance in cancer: an in silico drug discovery study | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 330 Views
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Article
Identification and validation of novel non-nucleoside class of molecules inhibiting the dengue virus replication
Kuldeep K. Roy, Deeti Jyothi, Udita Paul & Soumi Sukla
Pages: 13993-14002
Published online: 27 Mar 2023
AbstractforIdentification and validation of novel non-nucleoside class of molecules inhibiting the dengue virus replication | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 324 Views
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Article
Targeting Olokizumab-Interleukin 6 interaction interface to discover novel IL-6 inhibitors
Que-Huong Tran, Hoang-Nhi Cao, Dac-Nhan Nguyen, Thi-Thuy-Nga Tran, Minh-Tri Le, Quoc-Thai Nguyen, Van-Thanh Tran, Viet-Hung Tran & Khac-Minh Thai
Pages: 14003-14015
Published online: 30 Mar 2023
AbstractforTargeting Olokizumab-Interleukin 6 interaction interface to discover novel IL-6 inhibitors | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 247 Views
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Article
Designing of new tetrahydro-β-carboline-based ABCG2 inhibitors using 3D-QSAR, molecular docking, and DFT tools
Shahnawaz Ahmad, Dinesh Gupta, Tanzeel Ahmed & Asimul Islam
Pages: 14016-14027
Published online: 08 Feb 2023
AbstractforDesigning of new tetrahydro-β-carboline-based ABCG2 inhibitors using 3D-QSAR, molecular docking, and DFT tools | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 263 Views
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Article
In silico analysis of substitution mutations in the β-globin gene in Turkish population of β-thalassemia
Sima Alkilani & Tuba Sevimoglu
Pages: 14028-14035
Published online: 08 Feb 2023
AbstractforIn silico analysis of substitution mutations in the β-globin gene in Turkish population of β-thalassemia | Full Text | References | PDF (1.3 MB) | EPUB | Supplemental
  • 257 Views
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Article
Structural and biochemical analysis of human inositol monophosphatase-1 inhibition by ebselen
Areej Abuhammad, Nicola Laurieri, Alistair Rice, Edward D. Lowe, Nisha Singh, Saleem M. Naser, Samer S. Ratrout & Grant C. Churchill
Pages: 14036-14048
Published online: 10 Feb 2023
AbstractforStructural and biochemical analysis of human inositol monophosphatase-1 inhibition by ebselen | Full Text | References | PDF (1.8 MB) | EPUB
  • 158 Views
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Article
Structural insight into TIPE1 functioning as a lipid transfer protein
Sujian Cao, Ye Zhang, Haoqian Jiang, Xuben Hou & Wei Wang
Pages: 14049-14062
Published online: 10 Mar 2023
AbstractforStructural insight into TIPE1 functioning as a lipid transfer protein | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 202 Views
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Article
Anastrozole-mediated modulation of mitochondrial activity by inhibition of mitochondrial permeability transition pore opening: an initial perspective
Somesh Kumar, Neha Choudhary, Mohammed Faruq, Arun Kumar, Ravindra K. Saran, Prem Kumar Indercanti, Vikram Singh, Haseena Sait, Sunita Jaitley, Martin Valis, Kamil Kuca, Sunil K. Polipalli, Manoj Kumar, Tejveer Singh, Prashanth Suravajhala, Rohit Sharma & Seema Kapoor
Pages: 14063-14079
Published online: 23 Feb 2023
AbstractforAnastrozole-mediated modulation of mitochondrial activity by inhibition of mitochondrial permeability transition pore opening: an initial perspective | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 204 Views
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Article
Investigating the antibacterial mechanism of Ampelopsis cantoniensis extracts against methicillin-resistant Staphylococcus aureus via in vitro and in silico analysis
Van Ngo Thai Bich, Tan Khanh Nguyen, Thao Dao Thi Thu, Linh Thuy Thi Tran, Sa Vo Duong Nguyen, Ho Le Han, Long-Hung Dinh Pham, Trung Hoang Thanh, Van Hoa Duong, Tuan Anh Trieu, Manh Hung Tran & Phu Tran Vinh Pham
Pages: 14080-14091
Published online: 08 Mar 2023
AbstractforInvestigating the antibacterial mechanism of Ampelopsis cantoniensis extracts against methicillin-resistant Staphylococcus aureus via in vitro and in silico analysis | Full Text | References | PDF (1.4 MB) | EPUB | Supplemental
  • 233 Views
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Article
Identification of novel potential inhibitor of thymidylate kinase from Variola virus
Prashasti Sinha & Anil Kumar Yadav
Pages: 14092-14102
Published online: 12 Mar 2023
AbstractforIdentification of novel potential inhibitor of thymidylate kinase from Variola virus | Full Text | References | PDF (1.8 MB) | EPUB
  • 114 Views
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Article
In silico investigation of the structural stability as the origin of the pathogenicity of α-synuclein protofibrils
Jeseong Yoon, MinJun Lee, Yunsu Park, Kyunghee Lee & Seokmin Shin
Pages: 14103-14115
Published online: 10 Apr 2023
AbstractforIn silico investigation of the structural stability as the origin of the pathogenicity of α-synuclein protofibrils | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 219 Views
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Article
Design of multi-epitope based vaccine against Mycobacterium tuberculosis: a subtractive proteomics and reverse vaccinology based immunoinformatics approach
Subhashree Subhasmita Nayak, Guneswar Sethi & Krishna Ramadas
Pages: 14116-14134
Published online: 12 Feb 2023
AbstractforDesign of multi-epitope based vaccine against Mycobacterium tuberculosis: a subtractive proteomics and reverse vaccinology based immunoinformatics approach | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 589 Views
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Article
Integrating network pharmacology approaches for the investigation of multi-target pharmacological mechanism of 6-shogaol against cervical cancer
Abdelbaset Mohamed Elasbali, Waleed Abu Al-Soud, Afnan Elayyan Mousa Elayyan, Ziad H. Al-Oanzi, Hassan H. Alhassan, Bashir M. Mohamed, Hamad H. Alanazi, Mohammad Saquib Ashraf, Shadman Moiz, Mitesh Patel, Mirav Patel & Mohd Adnan
Pages: 14135-14151
Published online: 21 Mar 2023
AbstractforIntegrating network pharmacology approaches for the investigation of multi-target pharmacological mechanism of 6-shogaol against cervical cancer | Full Text | References | PDF (2.7 MB) | EPUB
  • 347 Views
  • 3 CrossRef citations
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Article
Surfactin-like lipopeptides from Bacillus clausii efficiently bind to spike glycoprotein of SARS-CoV-2
Piyush Baindara, Trinath Chowdhury, Dinata Roy, Mahitosh Mandal & Santi M. Mandal
Pages: 14152-14163
Published online: 06 Apr 2023
AbstractforSurfactin-like lipopeptides from Bacillus clausii efficiently bind to spike glycoprotein of SARS-CoV-2 | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 320 Views
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Article
Prediction of dual NF-κB/IκB inhibitors using an integrative in-silico approaches
Maryam Abbasi, Mohammad Mahboubi-Rabbani, Khosrow Kashfi & Hojjat Sadeghi-Aliabadi
Pages: 14164-14178
Published online: 15 Feb 2023
AbstractforPrediction of dual NF-κB/IκB inhibitors using an integrative in-silico approaches | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 141 Views
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Article
Computational analysis of structural and functional evaluation of the deleterious missense variants in the human CTLA4 gene
Meryem Bouqdayr, Anass Abbad, Hanâ Baba, Asmae Saih, Lahcen Wakrim & Anass Kettani
Pages: 14179-14196
Published online: 10 Feb 2023
AbstractforComputational analysis of structural and functional evaluation of the deleterious missense variants in the human CTLA4 gene | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 169 Views
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Article
Virtual screening, structure based pharmacophore mapping, and molecular simulation studies of pyrido[2,3-d]pyrimidines as selective thymidylate synthase inhibitors
Adarsh Kumar, Jurica Novak, Ankit Kumar Singh, Harshwardhan Singh, Suresh Thareja, Prateek Pathak, Maria Grishina, Amita Verma & Pradeep Kumar
Pages: 14197-14211
Published online: 08 May 2023
AbstractforVirtual screening, structure based pharmacophore mapping, and molecular simulation studies of pyrido[2,3-d]pyrimidines as selective thymidylate synthase inhibitors | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 143 Views
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Article
Removal of Erythrosine B dye from wastewater by Penicillium italicum: experimental, DFT, and molecular docking studies
Serap Çetinkaya, Volkan Eyupoglu, Halil İbrahim Çetintaş, Ali Fazıl Yenidünya, Özgür Kebabcı & Burak Tüzün
Pages: 14212-14223
Published online: 08 Mar 2023
AbstractforRemoval of Erythrosine B dye from wastewater by Penicillium italicum: experimental, DFT, and molecular docking studies | Full Text | References | PDF (2.4 MB) | EPUB
  • 460 Views
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Article
Comparison and monitoring of antibody response in convalescent and healthy vaccinated individuals against RBD and PCS of SARS-CoV-2 spike protein
Seyed Amir Hossein Mohammadzadeh Hosseini Moghri, Mojtaba Ranjbar, Hadi Hassannia & Fatemeh Khakdan
Pages: 14224-14231
Published online: 24 Mar 2023
AbstractforComparison and monitoring of antibody response in convalescent and healthy vaccinated individuals against RBD and PCS of SARS-CoV-2 spike protein | Full Text | References | PDF (972.9 KB) | EPUB
  • 102 Views
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Article
Bioinformatics and cheminformatics approaches to identify pathways, molecular mechanisms and drug substances related to genetic basis of cervical cancer
K. M. Salim Andalib, Md Habibur Rahman & Ahsan Habib
Pages: 14232-14247
Published online: 28 Feb 2023
AbstractforBioinformatics and cheminformatics approaches to identify pathways, molecular mechanisms and drug substances related to genetic basis of cervical cancer | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
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Article
Vibrational spectroscopy simulation of solvation effects on a G-quadruplex
Davide Moscato, Fabio Gabas, Riccardo Conte & Michele Ceotto
Pages: 14248-14258
Published online: 01 Mar 2023
AbstractforVibrational spectroscopy simulation of solvation effects on a G-quadruplex | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 79 Views
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Article
In silico discovery of potent inhibitors against monkeypox’s major structural proteins
Kiran Bharat Lokhande, Ashish Shrivastava & Ashutosh Singh
Pages: 14259-14274
Published online: 25 Feb 2023
AbstractforIn silico discovery of potent inhibitors against monkeypox’s major structural proteins | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 468 Views
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Article
Synthesis, X-ray crystal structure, Hirshfeld surface analysis and computational investigation into the potential inhibitory action of novel 6-(p-tolyl)-2-((p-tolyl)thio)methyl-7H-[1.2.4]triazolo[5,1-b][1,3,4]thiadiazine inhibits the main protease of COVID-19
Shaaban K. Mohamed, El Hassane Anouar, Sajjad Ahmad, Mohamed S. Abbady, Fatma K. Abdel-Wadood, Maha Q. M. Qahtan, Joel T. Mague & Youness El Bakri
Pages: 14275-14284
Published online: 16 Feb 2023
AbstractforSynthesis, X-ray crystal structure, Hirshfeld surface analysis and computational investigation into the potential inhibitory action of novel 6-(p-tolyl)-2-((p-tolyl)thio)methyl-7H-[1.2.4]triazolo[5,1-b][1,3,4]thiadiazine inhibits the main protease of COVID-19 | Full Text | References | PDF (2.1 MB) | EPUB
  • 136 Views
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Article
Identification of geographic origins of Morus alba Linn. through surfaced enhanced Raman spectrometry and machine learning algorithms
Zhang-Wen Ma, Jia-Wei Tang, Qing-Hua Liu, Jing-Yi Mou, Rui Qiao, Yan Du, Chang-Yu Wu, Dao-Quan Tang & Liang Wang
Pages: 14285-14298
Published online: 20 Feb 2023
AbstractforIdentification of geographic origins of Morus alba Linn. through surfaced enhanced Raman spectrometry and machine learning algorithms | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 268 Views
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Article
Evaluation of the size effect of hydrophobic ring substitution on 9-O position of berberine on DNA binding
Munira Khatun, Gopal Chandra Jana, Sk Nayim, Asima Dhal, Anirudha Patra & Maidul Hossain
Pages: 14299-14307
Published online: 21 Feb 2023
AbstractforEvaluation of the size effect of hydrophobic ring substitution on 9-O position of berberine on DNA binding | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 101 Views
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Article
Venetoclax analogs as promising anticancer therapeutics via targeting Bcl-2 protein: in-silico drug discovery study
Nahlah Makki Almansour, Khaled S. Allemailem, Abeer Abas Abd El Aty, Dhouha Boussoufa, Ekram Ismail Fagiree & Mahmoud A. A. Ibrahim
Pages: 14308-14324
Published online: 23 Feb 2023
AbstractforVenetoclax analogs as promising anticancer therapeutics via targeting Bcl-2 protein: in-silico drug discovery study | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 256 Views
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Article
Exploiting the co-crystal ligands shape, features and structure-based approaches for identification of SARS-CoV-2 Mpro inhibitors
Numan Yousaf, Yaruq Jabeen, Muhammad Imran, Muhammad Saleem, Moazur Rahman, Abbas Maqbool, Mazhar Iqbal & Muhammad Muddassar
Pages: 14325-14338
Published online: 22 Mar 2023
AbstractforExploiting the co-crystal ligands shape, features and structure-based approaches for identification of SARS-CoV-2 Mpro inhibitors | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 195 Views
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Article
In silico analysis of dietary polyphenols and their gut microbial metabolites suggest inhibition of SARS-CoV-2 infection, replication, and host inflammatory mediators
Esther Mezhibovsky, Skyler H. Hoang, Samantha Szeto & Diana E. Roopchand
Pages: 14339-14357
Published online: 20 Feb 2023
AbstractforIn silico analysis of dietary polyphenols and their gut microbial metabolites suggest inhibition of SARS-CoV-2 infection, replication, and host inflammatory mediators | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
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Article
Molecular modeling of pyrrolo-pyrimidine based analogs as potential FGFR1 inhibitors: a scientific approach for therapeutic drugs
Ali Raza, Tahir Ali Chohan, Muhammad Sarfraz, Talha Ali Chohan, Muhammad Imran Sajid, Rakesh Kumar Tiwari, Siddique Akber Ansari, Hamad M. Alkahtani, Shabana Yasmeen Ansari, Umair Khurshid & Hammad Saleem
Pages: 14358-14371
Published online: 10 Mar 2023
AbstractforMolecular modeling of pyrrolo-pyrimidine based analogs as potential FGFR1 inhibitors: a scientific approach for therapeutic drugs | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
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Article
Improving the selective naked-eye detection of COVID-19 mediated by simultaneously using three different target oligonucleotides coated on plasmonic AuNPs/hexagonal Ag@AuNPs
Neda Hosseinpour Moghadam, Rezvan Najafi, Ali Ghanbariasad, Amin Shiralizadeh Dezfuli & Akram Jalali
Pages: 14372-14381
Published online: 30 Mar 2023
AbstractforImproving the selective naked-eye detection of COVID-19 mediated by simultaneously using three different target oligonucleotides coated on plasmonic AuNPs/hexagonal Ag@AuNPs | Full Text | References | PDF (1.2 MB) | EPUB
  • 104 Views
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Article
Triad pyrazole–thiazole–coumarin heterocyclic core effectively inhibit HSP and drive cancer cells to apoptosis
Mehmet Gümüş, İrfan Koca, Yusuf Sert, Ali Dişli, Ezgi Nurdan Yenilmez Tunoğlu, Lütfi Tutar & Yusuf Tutar
Pages: 14382-14397
Published online: 24 Feb 2023
AbstractforTriad pyrazole–thiazole–coumarin heterocyclic core effectively inhibit HSP and drive cancer cells to apoptosis | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
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Article
Design peptide and multi-epitope protein vaccine candidates against monkeypox virus using reverse vaccinology approach: an in-silico study
Hamid Reza Jahantigh, Behzad Shahbazi, Hamed Gouklai, Hans Van der Weken, Zahra Gharibi, Zahra Rezaei, Mehri Habibi & Khadijeh Ahmadi
Pages: 14398-14418
Published online: 08 May 2023
AbstractforDesign peptide and multi-epitope protein vaccine candidates against monkeypox virus using reverse vaccinology approach: an in-silico study | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
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Article
Characterization of the coupling mechanism of scorpion β-neurotoxins on the voltage-gated sodium channel hNav1.6
Pavel Andrei Montero-Dominguez & Gerardo Corzo
Pages: 14419-14427
Published online: 22 Feb 2023
AbstractforCharacterization of the coupling mechanism of scorpion β-neurotoxins on the voltage-gated sodium channel hNav1.6 | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 550 Views
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Article
Long-range communication between transmembrane- and nucleotide-binding domains does not depend on drug binding to mutant P-glycoprotein
Cátia A. Bonito, Ricardo J. Ferreira, Maria-José U. Ferreira, Jean-Pierre Gillet, M. Natália D. S. Cordeiro & Daniel J. V. A. dos Santos
Pages: 14428-14437
Published online: 01 Mar 2023
AbstractforLong-range communication between transmembrane- and nucleotide-binding domains does not depend on drug binding to mutant P-glycoprotein | Full Text | References | PDF (1.2 MB) | EPUB | Supplemental
  • 436 Views
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Open Access
Article
Computational approaches screening DNA aptamers against conserved outer membrane protein W of Vibrio cholerae O1- an investigation expanding the potential for point-of-care detection with aptasensors
Lipi Poojara, Ram K & Rakesh M. Rawal
Pages: 14438-14449
Published online: 22 Feb 2023
AbstractforComputational approaches screening DNA aptamers against conserved outer membrane protein W of Vibrio cholerae O1- an investigation expanding the potential for point-of-care detection with aptasensors | Full Text | References | PDF (2.4 MB) | EPUB
  • 282 Views
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Article
An in silico quest for next-generation antimalarial drugs by targeting Plasmodium falciparum hexose transporter protein: a multi-pronged approach
Ali Altharawi, Yassine Riadi & Muhammad Tahir ul Qamar
Pages: 14450-14459
Published online: 22 Feb 2023
AbstractforAn in silico quest for next-generation antimalarial drugs by targeting Plasmodium falciparum hexose transporter protein: a multi-pronged approach | Full Text | References | PDF (1.4 MB) | EPUB | Supplemental
  • 173 Views
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Article
Identifying novel and potent inhibitors of EGFR protein for the drug development against the breast cancer
Arif Jamal Siddiqui, Sadaf Jahan, Mitesh Patel, Abdelmushin Abdelgadir, Wael Alturaiki, Fevzi Bardakci, Manojkumar Sachidanandan, Riadh Badraoui, Mejdi Snoussi & Mohd Adnan
Pages: 14460-14472
Published online: 24 Feb 2023
AbstractforIdentifying novel and potent inhibitors of EGFR protein for the drug development against the breast cancer | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 196 Views
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Article
Retinoic acid shows direct parasiticidal activity by targeting ergosterol pathway in Leishmania donovani: a potential therapeutic advancement
Satya Prakash & Ambak Kumar Rai
Pages: 14473-14483
Published online: 28 Mar 2023
AbstractforRetinoic acid shows direct parasiticidal activity by targeting ergosterol pathway in Leishmania donovani: a potential therapeutic advancement | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 142 Views
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Article
In silico investigation and potential therapeutic approaches of isoquinoline alkaloids for neurodegenerative diseases: computer-aided drug design perspective
Riyadh Ahmed Atto Al-Shuaeeb, H.R. Abd El-Mageed, Shimaa Ahmed, Hussein S. Mohamed, Zeinab S. Hamza, Md. Oliullah Rafi, Iqrar Ahmad & Harun Patel
Pages: 14484-14496
Published online: 15 May 2023
AbstractforIn silico investigation and potential therapeutic approaches of isoquinoline alkaloids for neurodegenerative diseases: computer-aided drug design perspective | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 189 Views
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Article
In silico screening of inhibitors against human dihydrofolate reductase to identify potential anticancer compounds
Asma Soofi, Mostafa Rezaei-Tavirani & Nahid Safari-Alighiarloo
Pages: 14497-14509
Published online: 08 Mar 2023
AbstractforIn silico screening of inhibitors against human dihydrofolate reductase to identify potential anticancer compounds | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 142 Views
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Article
Identification of potential biological target for trypanocidal sesquiterpene lactones derivatives
Tonino G. Adessi, Jorge Cantero, Andrés Ballesteros-Casallas, Manuela E. García, Viviana E. Nicotra & Margot Paulino
Pages: 14510-14523
Published online: 01 Mar 2023
AbstractforIdentification of potential biological target for trypanocidal sesquiterpene lactones derivatives | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 152 Views
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Article
Investigation of novel ligand targeting bromodomain-containing protein 4 (BRD4) for cancer drug discovery: complete pharmacophore approach
Vaishnavi Shanmugam & Soundararajn Muthukrishnan
Pages: 14524-14539
Published online: 25 Feb 2023
AbstractforInvestigation of novel ligand targeting bromodomain-containing protein 4 (BRD4) for cancer drug discovery: complete pharmacophore approach | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 248 Views
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Article
A theoretical survey to find potential natural compound for inhibition of binding the RBD domain to ACE2 receptor based on plant antivirals
Karim Mahnam & Seyed Mehdi Rajaee
Pages: 14540-14565
Published online: 28 Mar 2023
AbstractforA theoretical survey to find potential natural compound for inhibition of binding the RBD domain to ACE2 receptor based on plant antivirals | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 120 Views
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Article
Structural-based design of HD-TAC7 PROteolysis TArgeting chimeras (PROTACs) candidate transformations to abrogate SARS-CoV-2 infection
Sana Zahid, Yasir Ali & Sajid Rashid
Pages: 14566-14581
Published online: 25 Feb 2023
AbstractforStructural-based design of HD-TAC7 PROteolysis TArgeting chimeras (PROTACs) candidate transformations to abrogate SARS-CoV-2 infection | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 440 Views
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Review Articles

Review Article
An overview of mechanism and chemical inhibitors of shikimate kinase
Bharath Kumar Chagaleti, M. B. Rahul Reddy, Venkatesan Saravanan, Shanthakumar B.Priya D.P. Senthil Kumar & M. K. Kathiravan
Pages: 14582-14598
Published online: 28 Mar 2023
AbstractforAn overview of mechanism and chemical inhibitors of shikimate kinase | Full Text | References | PDF (2.7 MB) | EPUB
  • 317 Views
  • 1 CrossRef citations
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Review Article
A review on medicinally important heterocyclic compounds and importance of biophysical approach of underlying the insight mechanism in biological environment
Subramani Karthikeyan, Maria Grishina, Saravanan Kandasamy, Rajendiran Mangaiyarkarasi, Anitha Ramamoorthi, Shanmugavel Chinnathambi, Ganesh N. Pandian & L. John Kennedy
Pages: 14599-14619
Published online: 13 Mar 2023
AbstractforA review on medicinally important heterocyclic compounds and importance of biophysical approach of underlying the insight mechanism in biological environment | Full Text | References | PDF (2.8 MB) | EPUB
  • 448 Views
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