Komar CM (2005) Peroxisome proliferator-activated receptors (PPARs) and ovarian function—implications for regulating steroidogenesis, differentiation, and tissue remodeling. Reprod Biol Endocrinol 3:41

Article  PubMed  PubMed Central  Google Scholar 

Wang Y, Lei F, Lin Y, Han Y, Yang L, Tan H (2023) Peroxisome proliferator-activated receptors as therapeutic target for cancer. J Cell Mol Med 28:e17931

Article  PubMed  PubMed Central  Google Scholar 

Cariou B, Charbonnel B, Staels B (2012) Thiazolidinediones and PPARγ agonists: time for a reassessment. Trends Endocrinol Metab 23:205–215

Article  CAS  PubMed  Google Scholar 

Wagner KD, Wagner N (2010) Peroxisome proliferator-activated receptor beta/delta (PPARβ/δ) acts as regulator of metabolism linked to multiple cellular functions. Pharmacol Ther 125:423–435

Article  CAS  PubMed  Google Scholar 

Liu Y, Colby JK, Zuo X, Jaoude J, Wei D, Shureiqi I (2018) The role of PPAR-δ in metabolism, inflammation, and cancer: many characters of a critical transcription factor. Int J Mol Sci 19:3339

Article  PubMed  PubMed Central  Google Scholar 

Poulsen L, Siersbæk M, Mandrup S (2012) PPARs: fatty acid sensors controlling metabolism. Semin Cell Dev Biol 23:631–639

Article  PubMed  Google Scholar 

Berger J, Moller DE (2002) The mechanisms of action of PPARs. Annu Rev Med 53:409–435

Article  CAS  PubMed  Google Scholar 

Kahremany S, Livne A, Gruzman A, Senderowitz H, Sasson S (2015) Activation of PPARδ: from computer modelling to biological effects. Br J Pharmacol 172:754–770

Article  CAS  PubMed  Google Scholar 

Fyffe SA, Alphey MS, Buetow L, Smith TK, Ferguson MA, Sørensen MD, Björkling F, Hunter WN (2006) Recombinant human PPAR-β/δ ligand-binding domain is locked in an activated conformation by endogenous fatty acids. J Mol Biol 356:1005–1013

Article  CAS  PubMed  Google Scholar 

Shearer BG, Steger DJ, Way JM, Stanley TB, Lobe DC, Grillot DA, Iannone MA, Lazar MA, Willson TM, Billin AN (2008) Identification and characterization of a selective peroxisome proliferator-activated receptor beta/delta (NR1C2) antagonist. Mol Endocrinol 22:523–529

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lieber S, Scheer F, Meissner W, Naruhn S, Adhikary T, Müller-Brüsselbach S, Diederich WE, Müller R (2012) (Z)-2-(2-bromophenyl)-3-acrylonitrile (DG172): an orally bioavailable PPARβ/δ-selective ligand with inverse agonistic properties. J Med Chem 55:2858–2868

Article  CAS  PubMed  Google Scholar 

Toth PM, Lieber S, Scheer FM, Schumann T, Schober Y, Nockher WA, Adhikary T, Müller-Brüsselbach S, Müller R, Diederich WE (2016) Design and synthesis of highly active peroxisome proliferator-activated receptor (PPAR) β/δ inverse agonists with prolonged cellular activity. ChemMedChem 11:488–496

Article  CAS  PubMed  Google Scholar 

Shen Y, Chi H, Zhou J, Luo L, Tu Q, Qi C, Gao Z (2019) Structure-based stepwise screening of PPARγ antagonists as potential competitors with NCOA1 coactivator peptide for PPARγ CIS site. Int J Pept Res Ther 25:1369–1377

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 

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 

London N, Raveh B, Movshovitz-Attias D, Schueler-Furman O (2010) Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions? Proteins 78:3140–3149

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li Z, Peng Y, Ye H, Zhang Y, Zhou P (2024) The C-terminal self-binding helical peptide of human estrogen-related receptor γ can be druggably targeted by a novel class of rationally designed peptidic antagonists. J Comput Chem 45:27473

Article  Google Scholar 

Artis DR, Lin JJ, Zhang C, Wang W, Mehra U, Perreault M, Erbe D, Krupka HI, England BP, Arnold J, Plotnikov AN, Marimuthu A, Nguyen H, Will S, Signaevsky M, Kral J, Cantwell J, Settachatgull C, Yan DS, Fong D, Oh A, Shi S, Womack P, Powell B, Habets G, West BL, Zhang KY, Milburn MV, Vlasuk GP, Hirth KP, Nolop K, Bollag G, Ibrahim PN, Tobin JF (2009) Scaffold-based discovery of indeglitazar, a PPAR pan-active anti-diabetic agent. Proc Natl Acad Sci USA 106:262–267

Article  CAS  PubMed  Google Scholar 

Word JM, Lovell SC, Richardson JS, Richardson DC (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285:1735–1747

Article  CAS  PubMed  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 

Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, Onufriev A (2005) H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res 33:W368–W371

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schöning-Stierand K, Diedrich K, Ehrt C, Flachsenberg F, Graef J, Sieg J, Penner P, Poppinga M, Ungethüm A, Rarey M (2022) ProteinsPlus: a comprehensive collection of web-based molecular modeling tools. Nucleic Acids Res 50:W611–W615

Article  PubMed  PubMed Central  Google Scholar 

Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C (2015) ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J Chem Theory Comput 11:3696–3713

Article  CAS  PubMed  PubMed Central  Google Scholar 

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

Article  CAS  Google Scholar 

Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25:1157–1174

Article  CAS  PubMed  Google Scholar 

Baily C, Cieplak P, Cornell WD, Kollman PA (1993) A well-behaved electrostatic potential-based method using charge restraints for deriving atomic charge. J Phys Chem 97:10269–10280

Article  Google Scholar 

Darden T, York D, Pedersen L (1993) Particale mesh Ewald and N.log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092

Article  CAS  Google Scholar 

Ryckaert JP, Ciccotti G, Berendsen HJC (1997) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327–341

Article  Google Scholar 

Liu R, Liu L (2023) Use of Apatinib as a bait to fish its unexpected kinase targets from the hepatocellular carcinoma druggable kinome. J Comput Biophys Chem 22:439–451

Article  CAS