Computational design and experimental confirmation of a disulfide-stapled YAP helixα1-trap derived from TEAD4 helical hairpin to selectively capture YAP α1-helix with potent antitumor activity

Harvey KF, Zhang X, Thomas DM (2013) The Hippo pathway and human cancer. Nat Rev Cancer 13:246–257

Article  CAS  PubMed  Google Scholar 

Cunningham R, Hansen CG (2022) The Hippo pathway in cancer: YAP/TAZ and TEAD as therapeutic targets in cancer. Clin Sci 136:197–222

Article  CAS  Google Scholar 

Zhou Y, Huang T, Cheng AS, Yu J, Kang W, To KF (2016) The TEAD family and its oncogenic role in promoting tumorigenesis. Int J Mol Sci 17:138

Article  PubMed  PubMed Central  Google Scholar 

Hong W, Guan KL (2012) The YAP and TAZ transcription co-activators: key downstream effectors of the mammalian Hippo pathway. Semin Cell Dev Biol 23:785–793

Article  CAS  PubMed  PubMed Central  Google Scholar 

Santucci M, Vignudelli T, Ferrari S, Mor M, Scalvini L, Bolognesi ML, Uliassi E, Costi MP (2015) The Hippo pathway and YAP/TAZ-TEAD protein–protein interaction as targets for regenerative medicine and cancer treatment. J Med Chem 58:4857–4873

Article  CAS  PubMed  Google Scholar 

Luo M, Xu Y, Chen H, Wu Y, Pang A, Hu J, Dong X, Che J, Yang H (2022) Advances of targeting the YAP/TAZ-TEAD complex in the hippo pathway for the treatment of cancers. Eur J Med Chem 244:114847

Article  CAS  PubMed  Google Scholar 

Wang S, Ye H, Shang S, Li Z, Peng Y, Zhou P (2024) A structure-based data set of protein-peptide affinities and its nonredundant benchmark: potential applications in computational peptidology. Curr Med Chem 26:1–10

Google Scholar 

Mesrouze Y, Bokhovchuk F, Meyerhofer M, Fontana P, Zimmermann C, Martin T, Delaunay C, Erdmann D, Schmelzle T, Chène P (2017) Dissection of the interaction between the intrinsically disordered YAP protein and the transcription factor TEAD. Elife 6:e25068

Article  PubMed  PubMed Central  Google Scholar 

Furet P, Salem B, Mesrouze Y, Schmelzle T, Lewis I, Kallen J, Chène P (2019) Structure-based design of potent linear peptide inhibitors of the YAP–TEAD protein–protein interaction derived from the YAP Ω-loop sequence. Bioorg Med Chem Lett 29:2316–2319

Article  CAS  PubMed  Google Scholar 

He B, Wu T, He P, Lv F, Liu H (2021) Structure-based derivation and optimization of YAP-like coactivator-derived peptides to selectively target TEAD family transcription factors by hydrocarbon stapling and cyclization. Chem Biol Drug Des 97:1129–1136

Article  CAS  PubMed  Google Scholar 

Mesrouze Y, Gubler H, Villard F, Boesch R, Ottl J, Kallen J, Reid PC, Scheufler C, Marzinzik AL, Chène P (2023) Biochemical and structural characterization of a peptidic inhibitor of the YAP:TEAD interaction that binds to the α-helix pocket on TEAD. ACS Chem Biol 18:643–651

Article  CAS  PubMed  Google Scholar 

Pobbati AV, Rubin BP (2020) Protein–protein interaction disruptors of the YAP/TAZ–TEAD transcriptional complex. Molecules 25:6001

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bai Z, Hou S, Zhang S, Li Z, Zhou P (2017) Targeting self-binding peptides as a novel strategy to regulate protein activity and function: a case study on the proto-oncogene tyrosine protein kinase c-Src. J Chem Inf Model 57:835–845

Article  CAS  PubMed  Google Scholar 

Zhou P, Hou S, Bai Z, Li Z, Wang H, Chen Z, Meng Y (2018) Disrupting the intramolecular interaction between proto-oncogene c-Src SH3 domain and its self-binding peptide PPII with rationally designed peptide ligands. Artif Cells Nanomed Biotechnol 46:1122–1131

Article  CAS  PubMed  Google Scholar 

Zhang D, He D, Pan X, Liu L (2020) Rational design and intramolecular cyclization of hotspot peptide segments at YAP–TEAD4 complex interface. Protein Pept Lett 27:999–1006

Article  CAS  PubMed  Google Scholar 

Zhang D, Wu H, Zhao J (2021) Computational design and experimental substantiation of conformationally constrained peptides from the complex interfaces of transcriptional enhanced associate domains with their cofactors in gastric cancer. Comput Biol Chem 94:107569

Article  CAS  PubMed  Google Scholar 

Gu H, Liu L (2021) Molecular modeling and rational design of noncovalent halogen∙∙∙oxygen∙∙∙hydrogen motif at the complex interface of EGFR kinase domain with RALT peptide. Chem Phys 550:111309

Article  CAS  Google Scholar 

Zhang D, He D, Pan X, Xu Y, Liu L (2019) Structural analysis and rational design of orthogonal stacking system in an E. coli DegP PDZ1–peptide complex. Chem Pap 73:2469–2476

Article  CAS  Google Scholar 

Mesrouze Y, Bokhovchuk F, Izaac A, Meyerhofer M, Zimmermann C, Fontana P, Schmelzle T, Erdmann D, Furet P, Kallen J, Chène P (2018) Adaptation of the bound intrinsically disordered protein YAP to mutations at the YAP:TEAD interface. Protein Sci 27:1810–1820

Article  CAS  PubMed  PubMed Central  Google Scholar 

Krivov GG, Shapovalov MV, Dunbrack RL (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins 77:778–795

Article  CAS  PubMed  PubMed Central  Google Scholar 

Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24:1999–2012

Article  CAS  PubMed  Google Scholar 

Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4:435–447

Article  CAS  PubMed  Google Scholar 

Zhou P, Yan F, Miao Q, Chen Z, Wang H (2021) Why the first self-binding peptide of human c-Src kinase does not contain class II motif but can bind to its cognate Src homology 3 domain in class II mode? J Biomol Struct Dyn 39:310–318

Article  CAS  PubMed  Google Scholar 

Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935

Article  CAS  Google Scholar 

Ni J, Zhong Z, Lu W, Li S, Shao X, Hang L (2024) Systematic profiling of mitogen-inducible gene 6 and its derived peptides binding to receptor tyrosine kinases in bone cancers at molecular and cellular levels. Int J Pept Res Ther 30:8

Article  CAS  Google Scholar 

Yang C, Zhang S, He P, Wang C, Huang J, Zhou P (2015) Self-binding peptides: folding or binding? J Chem Inf Model 55:329–342

Article  CAS  PubMed  Google Scholar 

Yang C, Zhang S, Bai Z, Hou S, Wu D, Huang J, Zhou P (2016) A two-step binding mechanism for the self-binding peptide recognition of target domains. Mol Biosyst 12:1201–1213

Article  CAS  PubMed  Google Scholar 

Darden T, York D, Pedersen L (1993) Particle Mesh Ewald: an N∙Log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092

Article  CAS  Google Scholar 

Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: a linear constraint solver for molecular simulations. J Comput Chem 18:1463–1472

Article  CAS  Google Scholar 

Genheden S, Ryde U (2015) The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin Drug Discov 10:449–461

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chang CE, Chen W, Gilson MK (2005) Evaluating the accuracy of the Quasiharmonic approximation. J Chem Theory Comput 1:1017–1028

Article 

Comments (0)

No login
gif