Competitive Disruption of the Intermolecular Interaction Between Anesthetic PKC Isozyme ζ and its Cognate Substrates using Halogenated Peptidic Inhibitors with Affinity Improved by a Designer Halogen(X)/Hydrogen(H)-Bonding (dgr[XHB]) System

Andrea JE, Sutherland C, Winter CK, Walsh MP (1998) Substrate-dependent activation requirements and kinetic properties of protein kinase C. FEBS Lett 429:73–77

Article  CAS  PubMed  Google Scholar 

Auffinger P, Hays FA, Westhof E, Ho PS (2004) Halogen bonds in biological molecules. Proc Natl Acad Sci USA 101:16789–16794

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 

Bondi A (1964) van der Waals volumes and radii. J Phys Chem 68:441–451

Article  CAS  Google Scholar 

Boys SF, Bernardi F (1970) The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Mol Phys 19:553–566

Article  CAS  Google Scholar 

Chung LW, Sameera WM, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K (2015) The ONIOM method and its applications. Chem Rev 115:5678–5796

Article  CAS  PubMed  Google Scholar 

Cui YH, Chen J, Xu T, Tian HL (2015) Structure-based grafting and identification of kinase-inhibitors to target mTOR signaling pathway as potential therapeutics for glioblastoma. Comput Biol Chem 54:57–65

Article  CAS  PubMed  Google Scholar 

Fosgerau K, Hoffmann T (2015) Peptide therapeutics: current status and future directions. Drug Discov Today 20:122–128

Article  CAS  PubMed  Google Scholar 

Freeley M, Kelleher D, Long A (2011) Regulation of protein kinase C function by phosphorylation on conserved and non-conserved sites. Cell Signal 23:753–762

Article  CAS  PubMed  Google Scholar 

Garg R, Benedetti LG, Abera MB, Wang H, Abba M, Kazanietz MG (2014) Protein kinase C and cancer: what we know and what we do not. Oncogene 33:5225–5237

Article  CAS  PubMed  Google Scholar 

Goldey M, Dutoi A, Head-Gordon M (2013) Attenuated second-order Møller-Plesset perturbation theory: performance within the aug-cc-pVTZ basis. Phys Chem Chem Phys 15:15869–15875

Article  CAS  PubMed  Google Scholar 

Guo X, He D, Liu L, Kuang R, Liu L (2012) Use of QM/MM scheme to reproduce macromolecule-small molecule noncovalent binding energy. Comput Theor Chem 991:134–140

Article  CAS  Google Scholar 

He X, Fusti-Molnar L, Cui G, Merz KM (2009) Importance of dispersion and electron correlation in ab initio protein folding. J Phys Chem B 113:5290–5300

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hemmings HC (1998) General anesthetic effects on protein kinase C. Toxicol Lett 100–101:89–95

Article  PubMed  Google Scholar 

Hirai T, Chida K (2003) Protein kinase Czeta (PKCζ): activation mechanisms and cellular functions. J Biochem 133:1–7

Article  CAS  PubMed  Google Scholar 

Hou T, Zhang W, Case DA, Wang W (2008) Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain. J Mol Biol 376:1201–1214

Article  CAS  PubMed  Google Scholar 

Johansson MU, Zoete V, Michielin O, Guex N (2012) Defining and searching for structural motifs using DeepView/Swiss-PdbViewer. BMC Bioinformatics 13:173

Article  PubMed  PubMed Central  Google Scholar 

Kang JH, Toita R, Kim CW, Katayama Y (2012) Protein kinase C (PKC) isozyme-specific substrates and their design. Biotechnol Adv 30:1662–1672

Article  CAS  PubMed  Google Scholar 

Kaspar AA, Reichert JM (2013) Future directions for peptide therapeutics development. Drug Discov Today 18:807–817

Article  CAS  PubMed  Google Scholar 

Kazi JU (2011) The mechanism of protein kinase C regulation. Front Biol 6:328–336

Article  CAS  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 

Kuang R, Li Y, Zhang C, Zhao Q, Tan J, Ji S, Zhang W (2024) Computational design and experimental validation of an orthogonal system to improve the binding affinity and recognition specificity between anesthetic protein kinase Cι and its pseudosubstrate peptide. J Comput Biophys Chem 23:971–982

Article  CAS  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 45:2771–2777

Article  CAS  PubMed  Google Scholar 

Lian F, Wang Z, Zhou Z, Xu G (2020) Identification, characterization, and comparison of n-alkanols and anesthetics binding to the C1b subdomain of protein kinase Cα: similar function with different binding sites. J Recept Signal Transduct Res 40:109–116

Article  CAS  PubMed  Google Scholar 

Lill MA, Danielson ML (2011) Computer-aided drug design platform using PyMOL. J Comput Aided Mol des 25:13–19

Article  CAS  PubMed  Google Scholar 

Lin J, Wang S, Wen L, Ye H, Shang S, Li J, Shu J, Zhou P (2023a) Targeting peptide-mediated interactions in omics. Proteomics 23:e2200175

Article  PubMed  Google Scholar 

Lin J, Wen L, Zhou Y, Wang S, Ye H, Su J, Li J, Shu J, Huang J, Zhou P (2023b) PepQSAR: a comprehensive data source and information platform for peptide quantitative structure-activity relationships. Amino Acids 55:235–242

Article  CAS  PubMed  Google Scholar 

Liu S, Jiang Y, Cao J, Liu F, Ma L, Zhao Y (2005) Inhibitors of protein kinase C. Chin Sci Bull 50:1293–1304

Article  CAS  Google Scholar 

Liu H, Dou SF, Zhang X, Wang Y, Wen QL, Mu YN (2016) Rational improvement of peptide affinity to human pregnancy-related serine protease HtrA3 PDZ domain by introducing a halogen bond to the domain-peptide complex interface. Int J Pept Res Ther 22:371–376

Article  CAS  Google Scholar 

Lu Y, Zou J, Fan J, Zhao W, Jiang Y, Yu Q (2009) Ab initio calculations on halogen-bonded complexes and comparison with density functional methods. J Comput Chem 30:725–732

Article  CAS  PubMed  Google Scholar 

Mackay HJ, Twelves CJ (2007) Targeting the protein kinase C family: are we there yet? Nat Rev Cancer 7:554–562

Article  CAS  PubMed  Google Scholar 

Mochly-Rosen D, Das K, Grimes KV (2012) Protein kinase C, an elusive therapeutic target? Nat Rev Drug Discov 11:937–957

Article  CAS  PubMed  PubMed Central  Google Scholar 

Moerke NJ (2009) Fluorescence polarization (FP) assays for monitoring peptide-protein or nucleic acid-protein binding. Curr Protoc Chem Biol 1:1–15

Article 

Comments (0)

No login
gif