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

Abstract

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