Computational Analysis Of The Nek Family Of Proteins Reveals Unique Structural Features And Interactions With Other Cancer-Related Proteins.

Abstract The human Never In Mitosis A-like kinase (NEK) protein family consists of serine/threonine kinases that are implicated in the assembly of the mitotic spindle, regulation of the disjunction of the centrosome, and the functioning of the primary cilium. Protein kinases that regulate the centrosome cycle are often abnormally controlled in tumor cells, as are NEK family members. NEK2 was first identified in pediatric solid tumors and also has elevated expression levels in breast, pancreatic and colorectal cancer. NEK1, NEK3, and NEK5 are highly expressed in thyroid tumors, NEK8 is overexpressed in primary human breast tumors, and NEK11's expression is upregulated in early-stage colorectal cancers. To effectively exploit NEKs as drug targets, it is critical to understand their structure-function relationships to help elucidate their mechanism of action. However, structural information for most NEKs and the range and breadth of their interactions with other proteins are still widely unknown. In this study, we use an integrated computational approach which includes the prediction of the 3D structure using homology modeling, threading, and ab initio techniques, the biophysical/biochemical characterization of the theoretical models, followed by in silico protein-protein predictions and docking analysis to present a comprehensive computational analysis of all eleven NEK proteins. Our results reveal unique structural features in some of NEK family members, such as the armadillo (ARM)-like fold in NEK10 and RCC1 repeats found in NEK8 and NEK9. In addition, we present detailed investigations of four predicted protein-protein interaction scenarios involving NEK1, NEK7, NEK8, and NEK9 using docking analysis. This analysis lends support to new, previously unreported interactions of these NEKs with other cancer-related proteins i.e., TNF alpha with NEK7, GEF2 with NEK9, LRRK2 with NEK1, and ARA9 with NEK8. The details of the residues involved in the interaction interfaces from our proposed interaction scenarios provide valuable data for designing rational experiments to validate these interactions. Overall, this study uncovers novel and intriguing information about the NEK protein family, unique protein-protein interaction predictions, and lays the groundwork for elucidating their molecular mechanism as well as for investigating their potential as therapeutic targets. Citation Format: Andriele Silva, Shaneen Singh. Computational analysis of the NEK family of proteins reveals unique structural features and interactions with other cancer-related proteins [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 172.