Article
Biochemistry & Molecular Biology
Nizar Al-Shar'i, Sondos S. Musleh
Summary: In this study, novel CHK1 inhibitors targeting its allosteric pocket were identified using computational drug design techniques to overcome chemoresistance caused by CHK1 overexpression. A 1 μs MD simulation was run to study the enzyme's native dynamics for designing potential allosteric inhibitors. Structure-based pharmacophore models were generated and applied in virtual screening to select 20 compounds for biological evaluation against CHK1 enzyme, with moderate activities observed.
MOLECULAR DIVERSITY
(2022)
Article
Biochemistry & Molecular Biology
Fateme Zare, Aida Solhjoo, Hossein Sadeghpour, Amirhossein Sakhteman, Ali Dehshahri
Summary: Glucocorticoids have wide therapeutic effects but are limited by side effects. This study identified three novel compounds with potential glucocorticoid effects through virtual screening and molecular docking. Molecular dynamics simulations confirmed their binding stability.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Muthu Kumar Thirunavukkarasu, Ramanathan Karuppasamy
Summary: The study screened a candidate with high binding affinity in MEK protein from a library of 11,808 compounds, and suggested that Nebivolol may be an excellent candidate for MEK inhibition in NSCLC patients in the future.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Shivani Chandel, Rajveer Singh, Anupam Gautam, Velayutham Ravichandiran
Summary: The study demonstrates that gedunin may act as an effective GSK-3 beta inhibitor for the management of neuroblastoma by inducing apoptosis and inhibiting cell proliferation. Further preclinical and clinical investigation is needed to validate these findings.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Trupti S. Chitre, Purvaj V. Hirode, Deepak K. Lokwani, Aniket L. Bhatambrekar, Sayli G. Hajare, Shubhangi B. Thorat, D. Priya, Kunal B. Pradhan, Kalyani D. Asgaonkar, Shirish P. Jain
Summary: A significant three descriptor QSAR model was established to predict the Hec1/Nek2 inhibitory activity of 2-aminothiazoles derivatives, based on which new lead molecules were designed and further studied through ADMET and molecular docking. The study provides insights into the key interactions between the derivatives and Hec1/Nek2 protein, facilitating the development of potential anticancer molecules.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Krishnendu Bera
Summary: Drug repurposing using in silico studies identified ravidasvir as a potential inhibitor of 3-Chymotrypsin-like protease (3CL(pro)) of SARS-CoV-2, with promising binding energy and potential for further drug development and optimization in combating COVID-19 pandemic.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Vishal K. Singh, Ritika Srivastava, Parth Sarthi Sen Gupta, Farha Naaz, Himani Chaurasia, Richa Mishra, Malay Kumar Rana, Ramendra K. Singh
Summary: The newly designed NNRTIs compounds have high binding affinity with HIV-1 RT and lower toxicity, showing potential as inhibitors against HIV-1 RT.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Abdulrahman Ghasemlou, Vuk Uskokovic, Yahya Sefidbakht
Summary: The impact of 10 mutations and 5 proximity-related mutations on the main protease of SARS-COV-2 was investigated, providing a new target for drug design against COVID-19. Multiple new compounds were obtained through docking and structure-based design, and the best compounds were selected through screening and prediction. Among them, NE1 compound, modified from Nelfinavir, showed the highest affinity and is the best candidate for further Mpro inhibition and drug development studies.
BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Aina Hazimah Bahaman, Roswanira Abdul Wahab, Azzmer Azzar Abdul Hamid, Khairul Bariyyah Abd Halim, Yilmaz Kaya
Summary: The study investigated the selectivity of beta-glucosidase and xylanase enzymes from Trichoderma asperellum UC1 in degrading lignin, hemicellulose, and cellulose in oil palm leaves for nanocellulose production. Molecular docking and simulations revealed strong interactions between the enzymes and specific substrates, highlighting the cellulose preference of beta-glucosidase and the hemicellulose preference of xylanase. The findings contribute to understanding the molecular mechanisms involved in the production of nanocellulose from oil palm leaves.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Biochemistry & Molecular Biology
Rohit Shukla, Tiratha Raj Singh
Summary: Alzheimer's disease (AD) is a complex global disease characterized by amyloid beta and neurofibrillary tangles. This study screened compounds against CDK5 and identified two potential lead compounds through pharmacokinetics analysis.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Biochemistry & Molecular Biology
Yingqi Qiu, Yuanmeng Wang, Jiahao Lu, Qinghua Zhu, Li Jia, Fuhou Lei, Liqun Shen, Lihe Jiang, Aiqun Wu
Summary: This study involved the chemical modification of curcumin to obtain tetrahydrocurcumin and demonstrated its enhanced physiological and antioxidant activities compared to curcumin. The computational pharmacology techniques provided a theoretical basis for the development and modification of high-efficiency, low-toxicity drugs that interact with various targets of curcumin in the future.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Zouhair Elkarhat, Hicham Charoute, Lamiae Elkhattabi, Abdelhamid Barakat, Hassan Rouba
Summary: This study investigated the key viral enzyme nsp12 of SARS-cov-2 and its interactions with ligands using various tools. The results showed high conservation of multiple motifs in nsp12 and low binding energies between the ligands and nsp12. Molecular dynamics simulations demonstrated the stability of certain ligand-nsp12 complexes.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Pharmacology & Pharmacy
Yuwei Wang, Yifan Guo, Shaojia Qiang, Ruyi Jin, Zhi Li, Yuping Tang, Elaine Lai Han Leung, Hui Guo, Xiaojun Yao
Summary: In this study, the structure-activity relationships and binding modes of a series of anthraquinone derivatives targeting PGAM1 were investigated using 3D-QSAR, molecular docking, and molecular dynamics simulations, which showed satisfactory predictive ability. Molecular dynamics simulations revealed key residues and dominant interactions, as well as stable hydrogen bond formations during the ligand binding process. Overall, the study provided theoretical guidance for the design of new anthraquinone derivatives as PGAM1 inhibitors.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Chemistry, Physical
Jonatas M. Negreiro, Akenaton O. C. V. Gomes, Ricardo A. Marques, Davila Zampieri, Fatima M. Nunes, Francisco G. Barbosa, Jair Mafezoli, Marcos C. Mattos, Cristiano S. Lima, Francisco L. S. Oliveira, Geancarlo Zanatta, Maria C. F. Oliveira
Summary: This study investigates the catalytic activity of lipase from the fungus Fusarium oxysporum f. sp. tracheiphilum using in silico methods. The biotransformation of the natural product Annonalide (1) and its semisynthetic derivatives was studied to explain the experimental results. The study found that lipase-mediated hydrolysis of the O-acyl group was observed in substrates 3-5, and the acyl chain length favored the catalytic activity of lipase.
MOLECULAR CATALYSIS
(2023)
Article
Biology
Leonardo Bruno Federico, Guilherme Martins Silva, Suzane Quintana Gomes, Isaque Antonio Galindo Francischini, Mariana Pegrucci Barcelos, Cleydson Breno Rodrigues dos Santos, Luciano T. Costa, Joaquin Maria Campos Rosa, Carlos Henrique Tomich de Paula da Silva
Summary: Microtubules play a crucial role in cancer treatment, especially due to their unique structure and the colchicine binding site (CBS). Through virtual screening and molecular dynamics simulations, four promising CBS inhibitors were identified, offering potential for the development of safer drugs.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)