3D Modeling of G-Protein Coupled Receptors. G-protein coupled receptors (GPCRs) are essential players in myriad biological processes, including olfaction, photoreception, taste, hormone signaling, neurotransmitter activation, etc., and are the targets of numerous pharmaceutical agents. It has been estimated that over 50% of therapeutic compounds in use act on GPCRs. During last several years I have developed a variety of modeling tools allowing extensive sampling of conformational possibilities of transmembrane GPCRs and their complexes with peptide ligands. This approach allows 3D modeling of receptors belonging to rhodopsin-like family as well as to other families. The most innovative features of the developed approach are as follows:

1. Sampling involving large movements of transmembrane (TM) helices (as opposed to short molecular dynamics runs)
2. Accounting for flexibility of the extracellular and intracellular loops that is not addressed by any other approach
3. Step-by-step validation of modeling results by site-directed mutagenesis

The approach was validated by rationalizing experimental structural and mutagenic results obtained for rhodopsin, angiotensin-type I receptor (AT-1 receptor), CXCR4 receptor and C5a receptor. New efficient constitutively active mutants were predicted for AT-1 receptor and C5a receptor.

 Sen, S, Baranski, TJ, Nikiforovich, GV. Conformational movement of F251A contributes to the molecular mechanism of constitutive activation in the C5a receptor, Chemical Biology & Drug Design, 2008; in press.

 Nikiforovich, GV, Marshall, GR, Baranski, TJ. Modeling molecular mechanisms of binding of the anaphylotoxin C5a to the C5a receptor, Biochemistry, 2008; in press.

 Hagemann, IS, Miller, D, Klco, JM, Nikiforovich, GV, Baranski, TJ. Structure of the complement factor 5a (C5a) receptor/ligand complex studied by disulfide trapping and molecular modeling, J. Biol. Chem., 2008; in press.

 Taylor, CM, Nikiforovich, GV, Marshall, GR. Defining the interface between the C-terminal fragment of α-transducin and photoactivated rhodopsin. Biophys J, 2007; 92:4325-4334. [PDF]

 Nikiforovich, GV, Taylor, CM, Marshall, GR. Modeling of the complex between transducin and photoactivated rhodopsin, a prototypical G-protein-coupled receptor. Biochemistry, 2007; 46(16):4734-4744. [PDF]

 Matsumoto, ML, Narzinski, K, Nikiforovich, GV, Baranski, TJ. A Comprehensive structure-function map of the intracellular surface of the human C5a receptor II. Elucidation of G protein specificity determinants. J. Biol. Chem., 2007; 282(5):3122-3133. [PDF]

 Matsumoto, ML, Narzinski, K, Kiser, PD, Nikiforovich, GV, Baranski, TJ. A Comprehensive structure-function map of the intracellular surface of the human C5a receptor I. Identification of critical residues. J. Biol. Chem., 2007; 282(5):3105-3121. [PDF]

 Våbenø, J, Nikiforovich, GV, Marshall, GR. Insight into the binding mode for cyclopentapeptide antagonists of the CXCR4 receptor. Chemical Biology & Drug Design 2006; 67:346-354. [PDF]

 Våbenø, J, Nikiforovich, GV, Marshall, GR. A minimalistic 3D pharmacophore model for cyclopentapeptide CXCR4 antagonists. Biopolymers, 2006; 84:459-471. [PDF]

 Klco, JM, Nikiforovich, GV, Baranski, TJ. Genetic analysis of the first and third extracellular loops of the C5a receptor reveals an essential WXFG motif in the first loop. J. Biol. Chem., 2006; 281(17):12010-12019. [PDF]

 Hagemann, IS, Nikiforovich, GV, Baranski, TJ. Comparison of the retinitis pigmentosa mutations in rhodopsin with a functional map of the C5a receptor. Vision Research, 2006; 46:4519-4531. [PDF]

 Nikiforovich, GV, Zhang, M, Yang, Q, Jagadeesh, G, Chen, HC, Hunyady, L, Marshall, GR, and Catt, KJ. Interactions between conserved residues in transmembrane helices 2 and 7 during angiotensin AT1 receptor activation. Chemical Biology & Drug Design, 2006; 68, 239-249. [PDF]

 Nikiforovich, GV, Marshall, GR. 3D modeling of the activated states of constitutively active mutants of rhodopsin. Biochemical & Biophysical Research Communications, 2006; 345:430-437 . [PDF]

 Nikiforovich GV, Mihalik, B, Catt, KJ, Marshall, GR. Molecular mechanisms of constitutive activity: mutations at position 111 of the angiotensin AT₁ receptor. J. Pept. Res., 2005; 66:236-248. [PDF]

 Nikiforovich GV, Marshall GR. Modeling flexible loops in the dark-adapted and activated states of rhodopsin, a prototypical G-protein coupled receptor. Bioph. J., 2005; 89:3780-3789. [PDF]

 Nikiforovich GV, Marshall GR. 3D model for Meta-II rhodopsin, An activated G-protein-coupled receptor. Biochemistry, 2003; 42:9110-9120. [PDF]

 Galaktionov S, Nikiforovich GV, Marshall GR. Ab initio modeling of small, medium and large loops in proteins. Biopolymers (Peptide Science), 2001; 60:153-168. [PDF]

 Nikiforovich GV, Galaktionov S, Balodis J, Marshall GR. Novel approach to computer modeling of seven-helical transmembrane proteins: Current progress in the test case of bacteriorhodopsin. Acta Biochimica Polonica, 2001; 44:53-64. [PDF]

 Tseitin VM, Nikiforovich GV. Isolated transmembrane helices arranged across a membrane: computational studies. Protein Engineering 1999; 12(4):305-311. [PDF]

 Nikiforovich GV. A Novel Non-Statistical Method for Predicting Breaks in Transmembrane Helices. Protein Engineering 1998; 11:279-283. [PDF]

 Nikiforovich GV, Marshall GR. 3D Model for TM Region of the AT-1 Receptor in Complex with Angiotensin II Independently Validated by Site-Directed Mutagenesis Data. Biochem. Biophys. Res. Commun. 2001; 286:1204-1211. [PDF]

  Drug Design Based on Computational Studies of Peptides. This scientific endeavor has been my hallmark for many years. 3D models of pharmacophores were obtained for angiotensin, delta-opioid peptides, luliberin, alpha-melanocorticotropin, cholecystokinin, bradykinin, and many other peptides. Virtually all of them have been used as templates for chemical synthesis of biologically active cyclic analogs that are prototypical drug candidates. Currently, I employ this approach for design of various compounds to satisfy continuous needs of academic and industrial communities to design new leads to pharmaceuticals, both peptide and non-peptide.

 Nikiforovich, GV, Marshall, GR. Computational approaches in peptide and protein design: an overview. In Peptide and protein design,; Jensen, K., Ed. J. Wiley: 2008; in press.

 Sköld, C, Nikiforovich G, Karlén A. Modeling binding modes of angiotensin II and pseudopeptide analogues to the AT2 receptor. J Mol Graph Model 2008; 26(6):991-1003. [PDF]

 Nikiforovich, GV, Marshall, GR, Achilefu, S. Molecular modeling suggests conformational scaffolds specifically targeting five subtypes of somatostatin receptors. Chemical Biology & Drug Design, 2007; 69(3):163-169. [PDF]

 Zhang, X, Nikiforovich, GV, Marshall, GR. Conformational templates for rational drug design: Flexibility of cyclo(D-Pro1-Ala2-Ala3-Ala4-Ala5) in DMSO solution. J. Med. Chem. 2007; 50(12):2921-2925. [PDF]

 Bloch, S, Xu, B, Ye, Y, Liang, K, Nikiforovich, GV, Achilefu, S. Targeting beta-3 integrin using a linear hexapeptide labeled with a near-infrared fluorescent molecular probe. Mol. Pharmaceutics, 2006; 3(5):539-549. [PDF]

 Nikiforovich, GV, Marshall, GR. 3D modeling of the activated states of constitutively active mutants of rhodopsin. Biochemical and Biophysical Research Communications, 2006; 345(1):430-437. [PDF]

 Ye, Y, Li, WP, Anderson, CJ, Kao, GV, Nikiforovich, GV, Achilefu, S. Synthesis and characterization of a macrocyclic near-infrared optical scaffold. J Am Chem Soc, 2003; 125:7766-7767. [PDF]

 Johanesson P, Lindeberg G, Johanson A, Nikiforovich GV, Gogoll A, Synnergren B, Le Greves M, Nyberg F, Karlen A, Hallberg A. Vinyl Sulfide Cyclized Analogues of Angiotensin II with High Affinity and Full Agonist Activity at the AT1 Receptor. J. Med. Chem. 2002; 45(9):1767-1777. [PDF])