Molecular modelling approaches predicted 1,2,3-triazolyl ester of ketorolac (15K) to be a novel allosteric modulator of the oncogenic kinase PAK1

A computational approach for structural and functional analyses of disease-associated mutations in the human CYLD gene

Tumor suppressor cylindromatosis protein (CYLD) regulates NF-κB and JNK signaling pathways by cleaving K63-linked poly-ubiquitin chain from its substrate molecules and thus preventing the progression of tumorigenesis and metastasis of the cancer cells. Mutations in CYLD can cause aberrant structure and abnormal functionality leading to tumor formation. In this study, we utilized several computational tools such as PANTHER, PROVEAN, PredictSNP, PolyPhen-2, PhD-SNP, PON-P2, and SIFT to find out deleterious nsSNPs. We also highlighted the damaging impact of those deleterious nsSNPs on the structure and function of the CYLD utilizing ConSurf, I-Mutant, SDM, Phyre2, HOPE, Swiss-PdbViewer, and Mutation 3D. We shortlisted 18 high-risk nsSNPs from a total of 446 nsSNPs recorded in the NCBI database. Based on the conservation profile, stability status, and structural impact analysis, we finalized 13 nsSNPs. Molecular docking analysis and molecular dynamic simulation concluded the study with the findings of two significant nsSNPs (R830K, H827R) which have a remarkable impact on binding affinity, RMSD, RMSF, radius of gyration, and hydrogen bond formation during CYLD-ubiquitin interaction. The principal component analysis compared native and two mutants R830K and H827R of CYLD that signify structural and energy profile fluctuations during molecular dynamic (MD) simulation. Finally, the protein-protein interaction network showed CYLD interacts with 20 proteins involved in several biological pathways that mutations can impair. Considering all these in silico analyses, our study recommended conducting large-scale association studies of nsSNPs of CYLD with cancer as well as designing precise medications against diseases associated with these polymorphisms.

Effect of rhodamine 6G dye molecular interactions on counterintuitive self-assembly of noble metal nanorods

HYPOTHESIS

Self-assembled nanostructures with highly ordered and diversified patterns can be obtained by adding additives that directionally control the interparticle interactions. However, due to the complex non-covalent weak interactions in the self-assembly process, the active mechanism of additives is not fully understood, resulting in the limitation of obtaining the nano-superstructures. The introduction of rhodamine 6G (R6G) enables gold nanorods (GNRs) self-assembled into a counterintuitive tetragonal superlattice, during which the exploration of the influence of R6G molecular interactions on the GNRs self-assembly is of importance.

EXPERIMENTS

We present the detailed investigations of spacial configuration, binding modes, and aggregated degree of R6G molecule on formation of the tetragonal GNRs superlattices by combining the experimental and simulated results.

FINDINGS

By analyzing the peak position and peak intensity in the fluorescent spectra of assembled samples and pure R6G samples, H-dimer is verified as the main cause for inducing the tetragonal superstructures. Molecular dynamics simulations reveal that 2-3 H-dimers adsorbed obliquely in a zigzag chain manner on the surface of GNRs is the most stable state of the self-assembly. This work would contribute to a deeper understanding of the complex colloidal nanoparticle self-assemblies and push forward the development of the bottom-up nanoscale superstructures.

Recent advances in synthesis and anticancer potential of triazole containing scaffolds

Cancer is the most lethal disease that may be found anywhere on the globe. Approximately 10% of individuals die as a result of cancer of various types, with 19.3 million new cancer cases and 10 million deaths expected in 2020. More than 100 medications are commercially available for the treatment of cancer, but only a few candidates have high specificity, resulting in several side effects. The scientific community has spent the past decades focusing on drug discovery. Natural resources are used to isolate pharmaceutically active candidates, which are then synthesized in laboratories. More than 60% of all prescribed drugs are made from natural ingredients. Unique five-membered heteroaromatic center motifs with sulfur, oxygen and nitrogen atoms are found in heterocyclic compounds such as indazole, thiazole, triazole, triazole, and oxazole, and are used as a core scaffold in many medicinally important therapies. Triazole possesses a wide range of pharmacological activities including anticancer, antibacterial, antifungal, antibiotic antiviral, analgesic, anti-inflammatory, anti-HIV, antidiabetic, and antiprotozoal activities. Novel Triazole motifs with a variety of biological characteristics have been successfully synthesized using versatile synthetic methods. We intend here to facilitate the rational design and development of innovative triazole-based anti-cancer medicines with increased selectivity for various cancer cell lines by providing insight into various ligand-receptor interactions.