Rational design of DKK3 structure-based small peptides as antagonists of Wnt signaling pathway and in silico evaluation of their efficiency

• Published in: PloS one Vol. 12; no. 2; p. e0172217
• Main Authors: Poorebrahim, Mansour, Sadeghi, Solmaz, Rahimi, Hamzeh, Karimipoor, Morteza, Azadmanesh, Kayhan, Mazlomi, Mohammad Ali, Teimoori-Toolabi, Ladan
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 24-02-2017; Public Library of Science (PLoS)
• Subjects: Amino acids; Antagonists; Antineoplastic Agents - chemistry; Binding Sites; Bioinformatics; Biology and Life Sciences; Biotechnology; Cancer; Cellular signal transduction; Computer applications; Computer Simulation; Design; Disease susceptibility; Drug Design; Dynamic stability; Electrostatic properties; Embryos; Evaluation; Genetic aspects; Health aspects; Heparan sulfate; Homology; Humans; Imaging, Three-Dimensional; Intercellular Signaling Peptides and Proteins - chemistry; Ligands; Low Density Lipoprotein Receptor-Related Protein-5 - antagonists & inhibitors; Low Density Lipoprotein Receptor-Related Protein-5 - chemistry; Low Density Lipoprotein Receptor-Related Protein-6 - antagonists & inhibitors; Low Density Lipoprotein Receptor-Related Protein-6 - chemistry; LRP5 protein; Medicine; Molecular biology; Molecular docking; Molecular Docking Simulation; Molecular dynamics; Molecular Dynamics Simulation; Packaging; Pathogenesis; Peptide inhibitors; Peptide Library; Peptides; Physical Sciences; Physicochemical properties; Protein Binding; Protein Domains; Protein Engineering - methods; Proteins; Servers; Signal Transduction; Signaling; Stability analysis; Static Electricity; Thermodynamics; Wnt protein; Wnt Proteins - antagonists & inhibitors; Wnt Proteins - chemistry; Wnt Signaling Pathway - drug effects; Iran
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0172217

Dysregulated Wnt signaling pathway is highly associated with the pathogenesis of several human cancers. Dickkopf proteins (DKKs) are thought to inhibit Wnt signaling pathway through binding to lipoprotein receptor-related protein (LRP) 5/6. In this study, based on the 3-dimensional (3D) structure of DKK3 Cys-rich domain 2 (CRD2), we have designed and developed several peptide inhibitors of Wnt signaling pathway. Modeller 9.15 package was used to predict 3D structure of CRD2 based on the Homology modeling (HM) protocol. After refinement and minimization with GalaxyRefine and NOMAD-REF servers, the quality of selected models was evaluated utilizing VADAR, SAVES and ProSA servers. Molecular docking studies as well as literature-based information revealed two distinct boxes located at CRD2 which are actively involved in the DKK3-LRP5/6 interaction. A peptide library was constructed conducting the backrub sequence tolerance scanning protocol in Rosetta3.5 according to the DKK3-LRP5/6 binding sites. Seven tolerated peptides were chosen and their binding affinity and stability were improved by some logical amino acid substitutions. Molecular dynamics (MD) simulations of peptide-LRP5/6 complexes were carried out using GROMACS package. After evaluation of binding free energies, stability, electrostatic potential and some physicochemical properties utilizing computational approaches, three peptides (PEP-I1, PEP-I3 and PEP-II2) demonstrated desirable features. However, all seven improved peptides could sufficiently block the Wnt-binding site of LRP6 in silico. In conclusion, we have designed and improved several small peptides based on the LRP6-binding site of CRD2 of DKK3. These peptides are highly capable of binding to LRP6 in silico, and may prevent the formation of active Wnt-LRP6-Fz complex.