Discovery of Klotho peptide antagonists against Wnt3 and Wnt3a target proteins using combination of protein engineering, protein–protein docking, peptide docking and molecular dynamics simulations

Abstract

The Klotho is known as lifespan enhancing protein involved in antagonizing the effect of Wnt proteins. Wnt proteins are stem cell regulators, and uninterrupted exposure of Wnt proteins to the cell can cause stem and progenitor cell senescence, which may lead to aging. Keeping in mind the importance of Klotho in Wnt signaling, in silico approaches have been applied to study the important interactions between Klotho and Wnt3 and Wnt3a (wingless-type mouse mammary tumor virus (MMTV) integration site family members 3 and 3a). The main aim of the study is to identify important residues of the Klotho that help in designing peptides which can act as Wnt antagonists. For this aim, a protein engineering study is performed for Klotho, Wnt3 and Wnt3a. During the theoretical analysis of homology models, unexpected role of number of disulfide bonds and secondary structure elements has been witnessed in case of Wnt3 and Wnt3a proteins. Different in silico experiments were carried out to observe the effect of correct number of disulfide bonds on 3D protein models. For this aim, total of 10 molecular dynamics (MD) simulations were carried out for each system. Based on the protein–protein docking simulations of selected protein models of Klotho with Wnt3 and Wnt3a, different peptides derived from Klotho have been designed. Wnt3 and Wnt3a proteins have three important domains: Index finger, N-terminal domain and a patch of ∼10 residues on the solvent exposed surface of palm domain. Protein–peptide docking of designed peptides of Klotho against three important domains of palmitoylated Wnt3 and Wnt3a yields encouraging results and leads better understanding of the Wnt protein inhibition by proposed Klotho peptides. Further in vitro studies can be carried out to verify effects of novel designed peptides as Wnt antagonists.

Klotho expression is a prerequisite for proper muscle stem cell function and regeneration of skeletal muscle

“…sKlotho is a known inhibitor of canonical Wnt signaling [ 42 ]. The KL1 domain of sKlotho was recently mapped as the interaction domain of sKlotho with Wnt3a [ 43 ]. This evidence prompted us to speculate if sKlotho could be an inhibitor of canonical Wnt signaling in muscle stem cells.…”

Common and unique transcriptional responses to dietary restriction and loss of insulin receptor substrate 1 (IRS1) in mice

“…This is in line with whole transcriptome analysis of WAT from WT mice following short-term DR [ 50 ]. Wnt signalling has been implicated in aging at both the cellular and whole animal level [ 51 , 52 ], and reduced Wnt signalling is implicated in the lifespan extension noted in C. elegans [ 53 ] and Klotho transgenic mice [ 52 , 54 ]. GO categories related to ribosomal biogenesis were identified in the up-regulated gene sets of liver and muscle in WT DR mice, with a large number of GO categories linked to lipid metabolic processes over-represented in muscle.…”

Emerging Roles of Wnt Ligands in Human Colorectal Cancer

“…Wnt3 and Wnt3a are highly homologous proteins with 85% amino acid sequence identity. However, 15% of difference exerts a great influence on protein structure and dynamics under the same condition, which eventually leads to different biological functions (88). Wnt3 was highly expressed in colon cancer tissues, and autocrine Wnt3 secretion via Evi/Wls was required to maintain the Wnt activity in colon cancer cells.…”