Elucidating the mutational impact in causing Niemann-Pick disease type C: an in silico approach

Exploring the impact of variations in the mucolipin1 protein that result in mucolipidosis type 4 using the technique of molecular docking and dynamics simulation

Mucolipidosis type IV (MLIV) is classified as an exceptionally autosomal recessive condition due to a change in MCOLN1 that encodes the mucolipin-1 protein. ML-1 is a membrane protein comprising 6 Trans regions, which are situated at the LELs, a serine lipase area, and a nuclear localization sign. The characteristic features of the ML4 patients are mental retardation and skeletal deformities due to an increase in lipid molecules in the brain, other tissues, and organs. The fundamental goal of the work is to identify the most significant amino acid variants via a computational pipeline. The twenty-three amino acid variants that are responsible for the condition were retrieved from the public domain: L106P and L447P amino acid variants, with the following categories: extremely conserved, highly pathogenic, most interfering with protein function, more structurally unstable, and having promising Phenotyping characteristics was scrutinized from the series of bioinformatics tools that denote its significant nature. A docking and dynamics study was initiated to identify the interaction profiling and interatomic simulation between the Native, L106P, and L447P and the ligand ML-SA1 (it was known to ease the fatty acid buildup in lysosomes of cellular models of Mucolipidosis type IV) and had a score of -6.19, -5.12, and -5.21 kcal/mol, followed by a duplicate 100-ns run trajectory results, which assisted in detecting the stable nature of all the complex structures. Hence, this work helps to recognize the significant role of the scrutinized amino acid variants and, on the other hand, the stable nature of the ligand using standard computational tools.

Unravelling the Relacatib activity against the CTSK proteins causing pycnodysostosis: a molecular docking and dynamics approach

Pycnodysostosis is an atypical autosomal recessive condition of Lysosomal storage disorder that originated due to the deficit of the enzyme Cathepsin K which is vital for normal osteoclast action in bone resorption. Abnormal degradation of type 1 collagen and accumulation of toxic undigested collagen fibers in lysosomes of the osteoclast cells resulting in high bone density, brittle bones, and a short stature is caused in CTSK protein-carrying individuals. The broad aim of this study is to identify the most significant variant through various computational pipelines. This study was initiated by retrieving a total number of thirty-six variants from NCBI, HGMD, and UniProt databases, and the Y283C variant was found to be more significant by various standard computational tools. A structural investigation was performed to understand and gain a better knowledge about the interaction profile for the native (1BY8) and variant (Y283C) with Relacatib (a small-molecule drug that blocks the function of Cathepsin K, an enzyme that has been linked to osteoporosis, osteoarthritis, and other bone-degrading diseases). The interaction profile was analyzed using molecular docking. Relacatib (ligand) had an average binding affinity for both native (-7.16 kcal/mol) and Y283C (-6.76 kcal/mol). Finally, Molecular dynamics simulations were done in duplicates to recognize the variant (Y283C) activity of the protein structure against Relacatib for 100 ns. This study assists in comprehending the most pathogenic amino-acid variant, the ligand interaction with the protein structure, and paves the way for understanding the steadiness of the ligand with the native and selected significant amino-acid variant.Communicated by Ramaswamy H. Sarma.

A computational approach to analyzing the functional and structural impacts of Tripeptidyl-Peptidase 1 missense mutations in neuronal ceroid lipofuscinosis

Neuronal ceroid-lipofuscinosis (NCLs) are a group of severe neurodegenerative conditions, most likely present in infantile, late infantile, juvenile, and adult-onset forms. Their phenotypic characteristics comprise eyesight damage, reduced motor activity and cognitive function, and sometimes tend to die in the initial stage. In recent studies, NCLs have been categorized into at least 14 genetic collections (CLN1-14). CLN2 gene encodes Tripeptidyl peptidase 1 (TPP1), which affects late infantile-onset form. In this study, we retrieved a mutational dataset screening for TPP1 protein from various databases (ClinVar, UniProt, HGMD). Fifty-six missense mutants were enumerated with computational methods to perceive the significant mutants (G475R and G501C) and correlated with clinical and literature data. A structure-based screening method was initiated to understand protein-ligand interaction and dynamic simulation. The docking procedure was performed for the native (3EDY) and mutant (G473R and G501C) structures with Gemfibrozil (gem), which lowers the lipid level, decreases the triglycerides amount in the blood circulation, and controls hyperlipidemia. The Native had an interaction score of -5.57 kcal/mol, and the mutants had respective average binding scores of -6.24 (G473R) and - 5.17 (G501C) kcal/mol. Finally, molecular dynamics simulation showed that G473R and G501C mutants had better flexible and stable orientation in all trajectory analyses. Therefore, this work gives an extended understanding of both functional and structural levels of influence for the mutant form that leads to NCL disorder.