In silico evaluation of missense SNPs in cancer-associated Cystatin A protein and their potential to disrupt Cathepsin B interaction
Shafaat Hossain,
Omar Hamza Bin Manjur,
Mst Sharmin Sultana Shimu,
Tamanna Sultana,
Mustafizur Rahman Naim,
Shahariar Siddique,
Abdullah Al Mamun,
Md Miftaur Rahman,
Md Abu Saleh,
Md Rakibul Hasan,
Tania Rahman
Affiliations
Shafaat Hossain
Department of Biology & Biochemistry, University of Houston, USA
Omar Hamza Bin Manjur
Department of Biochemistry & Molecular Biology, University of Dhaka, Bangladesh; Bangladesh Reference Institute for Chemical Measurements (BRiCM), Bangladesh
Mst Sharmin Sultana Shimu
Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
Tamanna Sultana
Department of Biochemistry & Molecular Biology, University of Dhaka, Bangladesh
Mustafizur Rahman Naim
Biomedical and Toxicological Research Institute (BTRI), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
Shahariar Siddique
Institute of Food Science and Technology (IFST), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
Abdullah Al Mamun
Department of Biochemistry & Biotechnology, University of Science and Technology, Chittagong, Bangladesh; Institute of Technology Transfer and Innovation (ITTI), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
Md Miftaur Rahman
Bangladesh Dental College, Dhaka, Bangladesh
Md Abu Saleh
Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
Md Rakibul Hasan
Institute of Technology Transfer and Innovation (ITTI), Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
Tania Rahman
Department of Biochemistry & Molecular Biology, University of Dhaka, Bangladesh; Corresponding author.
Cystatin A (CSTA) functions as a cysteine protease inhibitor by forming tight complexes with the cathepsins. Pathogenic mutations in the CSTA gene can disrupt this interaction, potentially leading to physiological ailments. In this study, eight bioinformatics tools (SIFT, PolyPhen-2, PROVEAN, P-Mut, MutPred2, SNAP2, SNPs & GO, and PHD-SNP) were implemented to analyze non-synonymous SNPs from the dbSNP database. Five mutations (Y43C, Y43N, V48F, Y53H, and E94K) located in the conserved region were found to be highly deleterious and less stabilizing. The protein-protein interaction network found that Cathepsin B (CTSB) interacts highly with CSTA. Mutated CSTAs were created by homology modeling, and their altered binding with CTSB was examined through molecular docking and dynamics simulations. Among these, the Y53H (rs1448459675) and E94K (rs200394711) mutants were recognized as weaker inhibitors because they had 2.5 % and an 8 % lower binding affinity, respectively. Moreover, the E94K-CTSB complex, with a root mean square deviation (RMSD) above 5 Å, was found to be highly unstable during molecular dynamics. The root mean square fluctuation (RMSF) of the E94K mutant showed insufficient flexibility, indicating a reduced capacity to suppress CTSB. These findings suggest that the E94K mutation could affect the protein structure and cathepsin B interaction, potentially leading to pathological consequences as evidenced by colorectal adenocarcinoma patients in the COSMIC (Catalogue of Somatic Mutations in Cancer) database.
