An analysis of hydrophobic interactions of thymidylate synthase with methotrexate: free energy calculations involving mutant and native structures bound to methotrexate

Cationic Micelle-like Nanoparticles as the Carrier of Methotrexate for Glioblastoma Treatment

In the present study, ultra-small, magnetic, oleyl amine-coated Fe3O4 nanoparticles were synthesized and stabilized with a cationic ligand, cetyltrimethylammonium bromide, and an anticancer drug, methotrexate, was incorporated into a micelle-like nanoparticle structure for glioblastoma treatment. Nanoparticles were further characterized for their physicochemical properties using spectroscopic methods. Drug incorporation efficiency, drug loading, and drug release profile of the nanoparticles were investigated. According to the results, max incorporation efficiency% of 89.5 was found for 25 µg/mL of methotrexate-loaded nanoparticles. The cumulative amount of methotrexate released reached 40% at physiological pH and 85% at a pH of 5.0 up to 12 h. The toxicity and anticancer efficacy of the nanoparticles were also studied on U87 cancer and L929 cells. IC50 concentration of nanoparticles reduced cell viability to 49% in U87 and 72% in L929 cells. The cellular uptake of nanoparticles was found to be 1.92-fold higher in U87 than in L929 cells. The total apoptosis% in U87 cells was estimated to be ~10-fold higher than what was observed in the L929 cells. Nanoparticles also inhibited the cell motility and prevented the metastasis of U87 cell lines. Overall, designed nanoparticles are a promising controlled delivery system for methotrexate to the cancer cells to achieve better therapeutic outcomes.

Application of per-residue energy decomposition to identify the set of amino acids critical for in silico prediction of COX-2 inhibitory activity

The enormous magnitude of scientific research carried out in the field of NSAIDs and cyclooxygenases (COXs) is known. They are crucial in pain management. COX-2 inhibitors have evolved over the years; from traditional NSAIDs to isoform-specific. The present study is aimed to identify a cluster of amino acids in the catalytic site whose energy contribution can better explain COX-2 inhibitory activity accurately than the binding energy of the whole protein. Initially, MD simulations (25 ns) and MM-PBSA calculations were performed for 8 diarylheterocyclic inhibitors. Per-residue energy decomposition studies were carried out to elucidate the energy contribution of each amino acid, and their correlation with COX-2 inhibitory activity was enumerated. A cluster of catalytic amino acids whose free energy sum has a high correlation with biological data was identified. The cluster of Gln178, Ser339, Tyr341, Arg499, Phe504, Val509 and Ala513 showed the correlation of -0.60. Further, the study was extended to a total of 26 COX-2 inhibitors belonging to different classes to validate the applicability of the cluster of amino acids identified. Results clearly suggest that the cluster of amino acids identified provide accurate screening method, and can be applied to predict COX-2 inhibitory activity of small molecules.

Atom and receptor based 3D QSAR models for generating new conformations from pyrazolopyrimidine as IL-2 inducible tyrosine kinase inhibitors

In the current study, quantitative three-dimensional structure-activity-relationship (3D-QSAR) method was performed to design a model for new chemical entities by utilizing pyrazolopyrimidines. Their inhibiting activity on receptor IL-2 Itk correlates descriptors based on topology and hydrophobicity. The best model developed by ligand-based (atom-based) approach has correlation-coefficient of r²: 0.987 and cross-validated squared correlation-coefficient of q²: 0.541 with an external prediction capability of r²: 0.944. Whereas the best selected model developed by structured-based (receptor-based) approach has correlation-coefficient of r²: 0.987, cross-validated squared correlation-coefficient of q²: 0.637 with an external predictive ability of r²: 0.941. The statistical parameters prove that structure-based gave a better model to design new chemical scaffolds. The results achieved indicated that hydrophobicity at R₁ location play a vital role in the inhibitory activity and introduction of appropriately bulky and strongly hydrophobic-groups at position 3 of the terminal phenyl-group which is highly significant to enhance the activity. Six new pyrazolopyrimidine derivatives were designed. Docking simulation study was carried out and their inhibitory activity was predicted by the best structure based model with predictive activity of ranging from 8.43 to 8.85 log unit. The interacting residues PHE435, ASP500, LYS391, GLU436, MET438, CYS442, ILE369, VAL377 of PDB 4HCT were studied with respect to type of bonding with the new compounds. This study was aimed to search out more potent inhibitors of IL-2 Itk.

Prediction and evaluation of the lipase inhibitory activities of tea polyphenols with 3D-QSAR models

The extraordinary hypolipidemic effects of polyphenolic compounds from tea have been confirmed in our previous study. To gain compounds with more potent activities, using the conformations of the most active compound revealed by molecular docking, a 3D-QSAR pancreatic lipase inhibitor model with good predictive ability was established and validated by CoMFA and CoMISA methods. With good statistical significance in CoMFA (r²_cv = 0.622, r² = 0.956, F = 261.463, SEE = 0.096) and CoMISA (r²_cv = 0.631, r² = 0.932, F = 75.408, SEE = 0.212) model, we summarized the structure-activity relationship between polyphenolic compounds and pancreatic lipase inhibitory activities and find the bulky substituents in R₂, R₄ and R₅, hydrophilic substituents in R₁ and electron withdrawing groups in R₂ are the key factors to enhance the lipase inhibitory activities. Under the guidance of the 3D-QSAR results, (2R,3R,2′R,3′R)-desgalloyloolongtheanin-3,3′-O-digallate (DOTD), a potent lipase inhibitor with an IC50 of 0.08 μg/ml, was obtained from EGCG oxidative polymerization catalyzed by crude polyphenol oxidase. Furthermore, DOTD was found to inhibit lipid absorption in olive oil-loaded rats, which was related with inhibiting the activities of lipase in the intestinal mucosa and contents.

Insight into the interactions between novel isoquinolin-1,3-dione derivatives and cyclin-dependent kinase 4 combining QSAR and molecular docking

Several small-molecule CDK inhibitors have been identified, but none have been approved for clinical use in the past few years. A new series of 4-[(3-hydroxybenzylamino)-methylene]-4H-isoquinoline-1,3-diones were reported as highly potent and selective CDK4 inhibitors. In order to find more potent CDK4 inhibitors, the interactions between these novel isoquinoline-1,3-diones and cyclin-dependent kinase 4 was explored via in silico methodologies such as 3D-QSAR and docking on eighty-one compounds displaying potent selective activities against cyclin-dependent kinase 4. Internal and external cross-validation techniques were investigated as well as region focusing, bootstraping and leave-group-out. A training set of 66 compounds gave the satisfactory CoMFA model (q² = 0.695, r² = 0.947) and CoMSIA model (q² = 0.641, r² = 0.933). The remaining 15 compounds as a test set also gave good external predictive abilities with r²_pred values of 0.875 and 0.769 for CoMFA and CoMSIA, respectively. The 3D-QSAR models generated here predicted that all five parameters are important for activity toward CDK4. Surflex-dock results, coincident with CoMFA/CoMSIA contour maps, gave the path for binding mode exploration between the inhibitors and CDK4 protein. Based on the QSAR and docking models, twenty new potent molecules have been designed and predicted better than the most active compound 12 in the literatures. The QSAR, docking and interactions analysis expand the structure-activity relationships of constrained isoquinoline-1,3-diones and contribute towards the development of more active CDK4 subtype-selective inhibitors.