Computational and structural based approach to identify malignant nonsynonymous single nucleotide polymorphisms associated with CDK4 gene

PLOS ONE RESEARCH ARTICLE Computational and structural based approach to identify malignant nonsynonymous single nucleotide polymorphisms associated with CDK4 gene Rahatul Islam ID, Mashiur Rahaman ID, Hammadul Hoque, Nazmul Hasan, Shamsul H. Prodhan, Asfia Ruhama, Nurnabi Azad Jewel* Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 OPEN ACCESS Citation: Islam R, Rahaman M, Hoque H, Hasan N, Prodhan SH, Ruhama A, et al. (2021) Computational and structural based approach to identify malignant nonsynonymous single nucleotide polymorphisms associated with CDK4 gene. PLoS ONE 16(11): e0259691. https://doi.org/ 10.1371/journal.pone.0259691 Editor: Avaniyapuram Kannan Murugan, King Faisal Specialist Hospital and Research Center, SAUDI ARABIA * Abstract Cycline-dependent kinase 4 (CDK4), an enzyme of the cycline dependent or Ser/Thr protein kinase family, plays a role in cell cycle progression (G1 phase) by phosphorylating a tumor suppressor protein called pRB. Alteration of this enzyme due to missense mutation/ nonsynonymous single nucleotide polymorphisms (nsSNPs) are responsible for various types of cancer progression, e.g. melanoma, lung cancer, and breast cancer. Hence, this study is designed to identify the malignant missense mutation of CDK4 from the single nucleotide polymorphism database (dbSNP) by incorporating computational algorithms. Out of 239 nsSNPs; G15S, D140Y and D140H were predicted to be highly malignant variants which may have a devastating impact on protein structure or function. We also found defective binding motif of these three mutants with the CDK4 inhibitor ribociclib and ATP. However, by incorporating molecular dynamic simulation, our study concludes that the superiority of G15S than the other two mutants (D140Y and D140H) in destabilizing proteins nature. Received: June 8, 2021 Accepted: October 22, 2021 Published: November 4, 2021 Copyright: © 2021 Islam et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All relevant data are within the manuscript and its Supporting information files. Funding: The author(s) received no specific funding for this work. Competing interests: The authors have declared that no competing interests exist. Introduction Melanoma, particularly malignant melanoma, is a form of skin cancer caused by pigment-producing cells called melanocytes. Although the etiology of the disease is fully complex including different types of genomic alteration in some genes, e.g. MC1R, CDKN2A, and CDK4, nonfunctional CDK4 is the cardinal hallmark of the disease cutaneous malignant melanoma-3 (CMM3). Furthermore, a vast majority of human tumors are now believed to be occurred due to the deregulation of the CDK4/6–cyclin D–INK4–RB pathway [1–3]. Besides, the interference of the CDK4 gene in tumor progression was disclosed by the observations that repression of CDK4 can contribute to terminal differentiation of erythroleukemia cells, whereas overexpression of CDK4 leads to tumorigenesis of different assortment of cancers inluding glioblastomas and sarcomas, lung cancer, and breast cancers [4–7]. However, germline mutations in the CDK4 are quite rare, having recently been discovered in families of hereditary malignant PLOS ONE | https://doi.org/10.1371/journal.pone.0259691 November 4, 2021 1 / 24 PLOS ONE Malignant nonsynonymous single nucleotide polymorphisms identification in CDK4 gene melanoma. Four such cases are known to date where Arg encoded by the 24 codon is converted to either Cys or His after mutations occur [8–10]. The gene (CDK4) positioned on the long arm of 12(q) chromosome is 5 kb long and has 8 exons, one of which is a non-coding exon [10, 11]. The protein product of this gene is a major component of the protein kinase complex essential for the progression of the G1 phase of cell cycle as it phosphorylates and inhibits pRB protein of retinoblastoma gene [12, 13]. The phosphorylation of pRB enables the transcription factor E2F1 to dissociate from the pRB/E2F1 complexes, and eventually, transcription of E2F1 target genes induces G1 phase progression. [13]. However, CDK4 alone cannot phosphorylate pRB protein and enzyme activity requires both phosphorylation at Thr-172 and binding to a D-type cyclin for activation [14]. The daunting task of cancer studies is to discover the effects of SNPs specifically nonsynonymous single nucleotide polymorphisms (nsSNPs) or missense mutations in the coding sequence of tumor suppressor genes. A single nucleotide polymorphism, or SNP, is known as a single nucleotide variation (e.g., A > T / G / C) at DNA level. SNPs (Single Nucleotide Polymorphism) were also estimated to be responsible for more than 90 per cent of sequence variations in the human genome [15]. However, non-synonymous SNP (nsSNPs) are prioritized mainly because of their involvement in most of the human genetic diseases and their role in disease diagnosis as a biomarker [16]. Furthermore, these nsSNPs may induce amino acid substitutions in the protein sequence which can cause destabilizing conditions of the protein, including loss of stability or interaction between proteins [17, 18]. Current advances in human genome science have yielded a wealth of evidence showing tens of millions of human genetic variations across populations, including SNPs. Study of these variations can provide a framework for analyzing the relevance of these variations in disease susceptibility as well as formulating newer treatments. However, analysis of all these substitutions with the help of laboratory-based techniques is time-consuming, costly, and laborious. An effective alternative to this is the use of methods (In silico) based on the biochemical intensity of the amino acid substitution, as well as the protein sequence and/or structural information. Based on this information, various in silico approaches have been developed recently to sort out the functional malignant nsSNPs in the candidate protein by utilizing different prediction algorithms. Functional nsSNPs in various genes like PPARG [19], BCL11A [20], CDK7 [21], STN1 [22], BRAF [23] and BRCA1 [24, 25] were thus successfully identified from a broad range of SNP datasets. In a sense, discovering the effects of nsSNPs in the coding region of the tumor suppressor gene from a large set of data is a challenging task in cancer studies. Thus, this study was conducted with a view to identify the most malignant nsSNPs in the CDK4 genome and further evaluation of the mutants to assess the structural impact of these substitutions on protein structure or interaction. Analysis of this study will aid in shortening of the expens (...truncated)