Targeting human secretory phospholipase A2 with designed peptide inhibitors for inflammatory therapy

References

• Ashley NT, Weil ZM, Nelson RJ. Inflammation: mechanisms, costs, and natural variation. Annu Rev Ecol Evol Syst 2012;43:385–406
   Web of Science ®Google Scholar
• Burke JE, Dennis EA. Phospholipase A2 structure/function, mechanism, and signaling. J Lipid Res 2009;50:S237–42
   PubMed Web of Science ®Google Scholar
• Meyer MC, Rastogi P, Beckett CS, McHowat J. Phospholipase A2 inhibitors as potential anti-inflammatory agents. Curr Pharm Des 2005;11:1301–12
   PubMed Web of Science ®Google Scholar
• Mahalka AK, Kinnunen PK. Class specific peptide inhibitors for secretory phospholipases A2. Biochem Biophys Res Commun 2013;436:349–53
   PubMed Web of Science ®Google Scholar
• Zhou P, Wang C, Ren Y, et al. Computational peptidology: a new and promising approach to therapeutic peptide design. Curr Med Chem 2013;20:1985–96
   PubMed Web of Science ®Google Scholar
• Chandra V, Kaur P, Srinivasan A, Singh TP. Three-dimensional structure of a presynaptic neurotoxic phospholipase A2 from Daboia russelli pulchella at 2.4 Å resolution. J Mol Biol 2000;296:1117–26
   PubMed Web of Science ®Google Scholar
• Chandra V, Jasti J, Kaur P, et al. Design of specific peptide inhibitors of phospholipase A2: structure of a complex formed between Russell's viper phospholipase A2 and a designed peptide Leu-Ala-Ile-Tyr-Ser (LAIYS). Acta Crystallogr D 2002;58:1813–19
   PubMed Web of Science ®Google Scholar
• Singh RK, Ethayathulla AS, Jabeen T, et al. Aspirin induces its anti-inflammatory effects through its specific binding to phospholipase A2: crystal structure of the complex formed between phospholipase A2 and aspirin at 1.9 angstroms resolution. J Drug Target 2005;13:113–19
   PubMed Web of Science ®Google Scholar
• Singh RK, Somvanshi N, Sharma S, et al. Structural elements of ligand recognition site in secretory phospholipase A2 and structure-based design of specific inhibitors. Curr Top Med Chem 2007;7:757–64
   PubMed Web of Science ®Google Scholar
• Singh RK, Vikram P, Makker J, et al. Design of specific peptide inhibitors for group I phospholipase A2: structure of a complex formed between phospholipase A2 from Naja naja sagittifera (group I) and a designed peptide inhibitor Val–Ala–Phe–Arg–Ser (VAFRS) at 1.9 Å resolution reveals unique features. Biochemistry 2003;42:11701–6
   PubMed Web of Science ®Google Scholar
• Jorens PG, Sibille Y, Goulding NJ, et al. Potential role of Clara cell protein, an endogenous phospholipase A2 inhibitor, in acute lung injury. Eur Respir J 1995;8:1647–53
   PubMed Web of Science ®Google Scholar
• Hansford KA, Reid RC, Clark CI, et al. D-tyrosine as a chiral precusor to potent inhibitors of human nonpancreatic secretory phospholipase A2 (IIa) with antiinflammatory activity. Chembiochem 2003;4:181–5
   PubMed Web of Science ®Google Scholar
• Thwin MM, Ong WY, Fong CW, et al. Secretory phospholipase A2 activity in the normal and kainate injected rat brain, and inhibition by a peptide derived from python serum. Exp Brain Res 2003;150:427–33
   PubMed Web of Science ®Google Scholar
• Umland TC, Swaminathan S, Furey W, et al. Refined structure of rat Clara cell 17 kDa protein at 3.0 Å resolution. J Mol Biol 1992;224:441–8
   PubMed Web of Science ®Google Scholar
• Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003;52:80–7
   PubMed Web of Science ®Google Scholar
• Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 1999a;285:1735–47
   PubMed Web of Science ®Google Scholar
• Rostkowski M, Olsson MH, Søndergaard CR, Jensen JH. Graphical analysis of pH-dependent properties of proteins predicted using PROPKA. BMC Struct Biol 2011;11:6
   PubMed Web of Science ®Google Scholar
• London N, Raveh B, Cohen E, et al. Rosetta FlexPepDock web server – high resolution modeling of peptide-protein interactions. Nucleic Acids Res 2011;39:W249–53
   PubMed Web of Science ®Google Scholar
• Raveh B, London N, Schueler-Furman O. Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins 2010;78:2029–40
   PubMed Web of Science ®Google Scholar
• Duan Y, Wu C, Chowdhury S, et al. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 2003;24:1999–2012
   PubMed Web of Science ®Google Scholar
• Darden T, York D, Pedersen L. Particle mesh Ewald and N.log(N) method for Ewald sums in large systems. J Chem Phys 1993;98:10089–92
   Web of Science ®Google Scholar
• Ryckaert J, Ciccotti G, Berendsen HJC. Numerical-integration of Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327–41
   Web of Science ®Google Scholar
• Kollman PA, Massova I, Reyes C, et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 2000;33:889–97
   PubMed Web of Science ®Google Scholar
• Pierce BG, Wiehe K, Hwang H, et al. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinformatics 2014;30:1771–3
   PubMed Web of Science ®Google Scholar
• Church WB, Inglis AS, Tseng A, et al. A novel approach to the design of inhibitors of human secreted phospholipase A2 based on native peptide inhibition. J Biol Chem 2001;276:33156–64
   PubMed Web of Science ®Google Scholar
• Thwin MM, Satyanarayanajois SD, Nagarajarao LM, et al. Novel peptide inhibitors of human secretory phospholipase A2 with antiinflammatory activity: solution structure and molecular modeling. J Med Chem 2007;50:5938–50
   PubMed Web of Science ®Google Scholar
• Word JM, Lovell SC, LaBean TH, et al. Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol 1999b;285:1711–33
   PubMed Web of Science ®Google Scholar
• Stein A, Aloy P. Contextual specificity in peptide-mediated protein interactions. PLoS One 2008;3:e2524
   PubMed Web of Science ®Google Scholar
• Morrison KL, Weiss GA. Combinatorial alanine-scanning. Curr Opin Chem Biol 2001;5:302–7
   PubMed Web of Science ®Google Scholar
• Bi J, Yang H, Yan H, et al. Knowledge-based virtual screening of HLA-A*0201-restricted CD8+ T-cell epitope peptides from herpes simplex virus genome. J Theor Biol 2011;281:133–9
   PubMed Web of Science ®Google Scholar
• Xiang Z, Honig B. Extending the accuracy limits of prediction of side-chain conformations. J Mol Biol 2001;311:421–30
   PubMed Web of Science ®Google Scholar
• Hou T, Chen K, McLaughlin WA, et al. Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. PLoS Comput Biol 2006;2:e1
   PubMed Web of Science ®Google Scholar
• Ni Z, Chen H, Qi X, Jin R. Why is substrate peptide binding unsusceptible to multidrug-resistant mutations in HIV-1 protease? A structural and energetic analysis. Int J Pept Res Ther 2014;20:43–51
   Web of Science ®Google Scholar
• Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995;8:127–34
   PubMedGoogle Scholar
• Zhou P, Zou J, Tian F, Shang Z. Fluorine bonding – how does it work in protein-ligand interactions? J Chem Inf Model 2009;49:2344–55
   PubMed Web of Science ®Google Scholar
• Zhou P, Huang J, Tian F. Specific noncovalent interactions at protein-ligand interface: implications for rational drug design. Curr Med Chem 2012;19:226–38
   PubMed Web of Science ®Google Scholar