References
- Butchko HH, Stargel WW, Comer CP, et al. Aspartame: review of safety. Regul Toxicol Pharmacol 2002;35:S1–93
- Laffitte A, Neiers F, Briand L. Functional roles of the sweet taste receptor in oral and extraoral tissues. Curr Opin Clin Nutr Metab Care 2014;17:379–85
- Sigoillot M, Brockhoff A, Meyerhof W, Briand L. Sweet-taste-suppressing compounds: current knowledge and perspectives of application 2012;96:619–30
- Avenoza A, Parísa M, Peregrina JM, et al. Aspartame analogues containing 1-amino-2-phenylcyclohexanecarboxylic acids (c6Phe). Tetrahedron 2002;58:4899–905
- Formaggio F, Crisma M, Valle G. Conformationally restricted analogues of anti-aspartame-type sweeteners. J Chem Soc Perkin Trans 2 1992;2:1945–50
- Walters DE, Prakash I, Desai N. Active conformations of neotame and other high-potency sweeteners. J Med Chem 2000;43:1242–5
- Hruby VJ, Cai M. Design of peptide and peptidomimetic ligands with novel pharmacological activity profiles. Annu Rev Pharmacol Toxicol 2013;53:557–80
- Li T, Shiotani K, Miyazaki A, et al. Bifunctional [2′,6′-dimethyl-l-tyrosine1]endomorphin 2 analogues substituted at position 3 with alkylated phenylalanine derivatives yield potent mixed µ-agonist/δ-antagonist and dual µ-agonist/δ-agonist opioid ligands. J Med Chem 2007;50:2753–66
- Harrison BA, Pasternak GW, Verdine GL. 2,6-Dimethyltyrosine analogues of a stereodiversified ligand library: highly potent, selective, non-peptidic µ opioid receptor agonists. J Med Chem 2003;46:677–80
- Stefanucci A, Pinnen F, Feliciani F, et al. Conformationally constrained histidines in the design of peptidomimetics: strategies for the χ-space control. Int J Mol Sci 2011;12:2853–90
- Torino D, Mollica A, Pinnen F, et al. Synthesis and evaluation of new endomorphin analogues modified at the Pro2 residue. Bioorg Med Chem Lett 2009;19:4115–18
- Torino D, Mollica A, Pinnen F, et al. Synthesis and evaluation of new endomorphin-2 analogues containing (Z)-α,β-Didehydrophenylalanine (ΔZPhe) residue. J Med Chem 2010;53:4550–4
- Mollica A, Feliciani F, Stefanucci A, et al. N-(tert)-butyloxycarbonyl)-beta,beta-cyclopentyl-cysteine (acetamidomethyl)-methyl ester for synthesis of novel peptidomimetic derivatives. Protein Pept Lett 2010;17:925–9
- Karoyan P, Sagan S, Lequin O, et al. Targ Heter Sys 2005;8:216–73
- Zhang F, Klebansky B, Fine RM, et al. Molecular mechanism of the sweet taste enhancers. Proc Nat Acad Sci USA 2010;107:4752–7
- (a) Mollica A, Pinnen F, Azzurra S, Costante R. The evolution of peptide synthesis: from early days to small molecular machines. Curr Bioact Comp 2013;9:184–202. (b) Mollica A, Paglialunga Paradisi M, Torino D, et al. Hybrid α/β-peptides: For–Met–Leu–Phe–OMe analogues containing geminally disubstituted β2,2- and β3,3-amino acids at the central position. Amino Acids 2006;30:453–9
- Dörrich S, Falgner S, Schweeberg S, et al. Silicon-containing dipeptidic aspartame and neotame analogues. Organometallics 2012;31:5903–17
- Muto T, Tsuchiya D, Morikawa K, Jingami H. Structures of the extracellular regions of the group II/III metabotropic glutamate receptors. Proc Nat Acad Sci USA 2007;104:3759–64
- Larkin MA, Blackshields G, Brown NP, et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007;23:2947–8
- McWilliam H, Li W, Uludag M, et al. Analysis tool web services from the EMBL-EBI. Nucleic Acids Res 2013;41:W597–600
- Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Prot Sci 2006;15:2507–24
- Van Der Spoel D, Lindahl E, Hess B, et al. GROMACS: fast, flexible, and free. J Comp Chem 2005;26:1701–18
- Laskowski RA, MacArthur MW, Moss DS, Thornton JM. {PROCHECK}: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993;26:283–91
- Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 2010;31:455–61
- Mirzaie S, Fathi F, Hakhamaneshi MS, et al. Combined 3D-QSAR modeling and molecular docking study on multi-acting quinazoline derivatives as HER2 kinase inhibitors. EXCLI J 2013;12:130–43
- Schuttelkopf AW, van Aalten DM. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Cryst D, Biol Cryst 2004;60:1355–63
- Gasteiger J, Marsili M. Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges. Tetrahedron 1980;36:3219–28
- Wang R, Lai L, Wang S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J Comput-aided Mol Des 2002;16:11–26
- Bas DC, Rogers DM, Jensen JH. Very fast prediction and rationalization of pKa values for protein-ligand complexes. Proteins 2008;73:765–83
- Lemkul JA, Allen WJ, Bevan DR. Practical considerations for building GROMOS-compatible small-molecule topologies. J Chem Inf Mod 2010;50:2221–35
- Mirzaie S, Najafi K, Hakhamaneshi MS. Investigation for antimicrobial resistance-modulating activity of diethyl malate and 1-methyl malate against beta-lactamase class A from Bacillus licheniformis by molecular dynamics, in vitro and in vivo studies. J Biomol Struct Dyn 2015;33:1016–26
- Berendsen HJC, Postma JPM, van Gunsteren WF, et al. Molecular dynamics with coupling to an external bath. J Chem Phys 1984;81:3684–90
- Parrinello M, Rahman A. Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys 1981;52:7182–90
- Darden T, York D, Pedersen L. Particle mesh Ewald: an N log(N) method for Ewald sums in large systems. J Chem Phys 1993;98:10089–92
- Hess B, Bekker H, Berendsen HJC, Fraaije JGEM. LINCS: a linear constraint solver for molecular simulations. J Comput Chem 1997;18:1463–72
- Kumari R, Kumar R, Lynn A. g_mmpbsa – a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model 2014;54:1951–62
- Mollica A, Feliciani F, Stefanucci A, et al. Synthesis and biological evaluation of new active For–Met–Leu–Phe–OMe analogues containing para-substituted Phe residues. J Pept Sci 2012;18:418–26
- Kunishima N, Shimada Y, Tsuji Y, et al. Structural basis of glutamate recognition by a dimeric metabotropic glutamate receptor. Nature 2000;407:971–7
- Tsuchiya D, Kunishima N, Kamiya N, et al. Structural views of the ligand-binding cores of a metabotropic glutamate receptor complexed with an antagonist and both glutamate and Gd3+. Proc Nat Acad Sci USA 2002;99:2660–5
- Gundampati RK, Chikati R, Kumari M, et al. Protein–protein docking on molecular models of Aspergillus niger RNase and human actin: novel target for anticancer therapeutics. J Mol Mod 2012;18:653–62
- Cui M, Jiang P, Maillet E, et al. The heterodimeric sweet taste receptor has multiple potential ligand binding sites. Curr Pharm Des 2006;12:4591–600
- Assadi-Porter FM, Tonelli M, Maillet EL, et al. Interactions between the human sweet-sensing T1R2-T1R3 receptor and sweeteners detected by saturation transfer difference NMR spectroscopy. Biochim Biophys Acta 2010;1798:82–6
- Acher FC, Selvam C, Pin JP, et al. A critical pocket close to the glutamate binding site of mGlu receptors opens new possibilities for agonist design. Neuropharmacology 2011;60:102–7
- Parenti MD, Rastelli G. Advances and applications of binding affinity prediction methods in drug discovery. Biotechnol Adv 2012;30:244–50
- Venken T, Krnavek D, Munch J, et al. An optimized MM/PBSA virtual screening approach applied to an HIV-1 gp41 fusion peptide inhibitor. Proteins 2011;79:3221–35
- Barakat KH, Jordheim LP, Perez-Pineiro R, et al. Virtual screening and biological evaluation of inhibitors targeting the XPA-ERCC1 interaction. PloS One 2012;7:e51329