Discovery of Potent Vascular Endothelial Growth Factor Receptor‐2 Inhibitors

Substantial evidence over the last decades has implicated uncontrolled angiogenesis with various pathological states, including cancer. Vascular endothelial growth factor (VEGF) plays a critical role in its regulation. Because the tyrosine kinase VEGF receptor‐2 (VEGFR‐2) is the major mediator of the mitogenic, angiogenic, and permeability‐enhancing effects of VEGF, it has become one of the most profound anti‐angiogenesis targets. Inspired by the anthranilamide class of VEGFR‐2 inhibitors, we performed a computational analysis of some potent representative members, using docking and molecular dynamics calculations. Based on the observations drawn from introducing the effect of the receptor's flexibility in implicit aqueous environment, we designed, synthesized, and characterized several new analogues of related scaffolds with modifications in their steric and electronic characteristics. In vitro evaluation of these compounds revealed several novel VEGFR‐2 inhibitors that are less cytotoxic and more potent than the parent compounds.

[1]  B. Ruggeri,et al.  Development of vascular endothelial growth factor receptor (VEGFR) kinase inhibitors as anti-angiogenic agents in cancer therapy. , 2004, Current medicinal chemistry.

[2]  P. Dervan,et al.  Shape selective recognition of T.A base pairs by hairpin polyamides containing N-terminal 3-methoxy (and 3-chloro) thiophene residues. , 2003, Bioorganic & medicinal chemistry.

[3]  Christopher I. Bayly,et al.  Fast, efficient generation of high‐quality atomic charges. AM1‐BCC model: II. Parameterization and validation , 2002, J. Comput. Chem..

[4]  M. Morrison,et al.  Novel 2,3-dihydro-1,4-benzoxazines as potent and orally bioavailable inhibitors of tumor-driven angiogenesis. , 2008, Journal of medicinal chemistry.

[5]  N. Ferrara,et al.  The biology of VEGF and its receptors , 2003, Nature Medicine.

[6]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[7]  Konstantin V Balakin,et al.  VEGF/VEGFR signalling as a target for inhibiting angiogenesis , 2007, Expert opinion on investigational drugs.

[8]  Napoleone Ferrara,et al.  Vascular endothelial growth factor: basic science and clinical progress. , 2004, Endocrine reviews.

[9]  Napoleone Ferrara,et al.  Angiogenesis as a therapeutic target , 2005, Nature.

[10]  J. Kuriyan,et al.  The Conformational Plasticity of Protein Kinases , 2002, Cell.

[11]  T. Mosmann.  Rapid colorimetric assay for cellular growth and survival: application to proliferation and cytotoxicity assays. , 1983, Journal of immunological methods.

[12]  D. Case,et al.  Theory and applications of the generalized born solvation model in macromolecular simulations , 2000, Biopolymers.

[13]  Yutaka Maeda,et al.  Novel 4-amino-furo[2,3-d]pyrimidines as Tie-2 and VEGFR2 dual inhibitors. , 2005, Bioorganic & medicinal chemistry letters.

[14]  Lenwood S. Heath,et al.  H++: a server for estimating pKas and adding missing hydrogens to macromolecules , 2005, Nucleic Acids Res..

[15]  E. Hu,et al.  Discovery of aryl aminoquinazoline pyridones as potent, selective, and orally efficacious inhibitors of receptor tyrosine kinase c-Kit. , 2008, Journal of medicinal chemistry.

[16]  Anselm H. C. Horn,et al.  AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine , 2006, Journal of molecular modeling.

[17]  Stover,et al.  New anilinophthalazines as potent and orally well absorbed inhibitors of the VEGF receptor tyrosine kinases useful as antagonists of tumor-driven angiogenesis , 2000, Journal of medicinal chemistry.

[18]  Valerie J. Gillet,et al.  Comparison of Conformational Analysis Techniques To Generate Pharmacophore Hypotheses Using Catalyst , 2005, J. Chem. Inf. Model..

[19]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[20]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[21]  David S. Goodsell,et al.  Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998 .

[22]  S. Schenone,et al.  Antiangiogenic agents: an update on small molecule VEGFR inhibitors. , 2007, Current medicinal chemistry.

[23]  P. A. Harris,et al.  Discovery of novel benzimidazoles as potent inhibitors of TIE-2 and VEGFR-2 tyrosine kinase receptors. , 2007, Journal of medicinal chemistry.

[24]  Daniel Elbaum,et al.  Design, synthesis, and evaluation of orally active benzimidazoles and benzoxazoles as vascular endothelial growth factor-2 receptor tyrosine kinase inhibitors. , 2007, Journal of medicinal chemistry.

[25]  Holger Gohlke,et al.  Target flexibility: an emerging consideration in drug discovery and design. , 2008, Journal of medicinal chemistry.

[26]  M. Shibuya.  Structure and dual function of vascular endothelial growth factor receptor-1 (Flt-1). , 2001, The international journal of biochemistry & cell biology.

[27]  M. Shibuya,et al.  A single autophosphorylation site on KDR/Flk‐1 is essential for VEGF‐A‐dependent activation of PLC‐γ and DNA synthesis in vascular endothelial cells , 2001, The EMBO journal.

[28]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[29]  G. Neufeld,et al.  Vascular endothelial growth factor (VEGF) and its receptors , 1999, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[30]  Ling Wang,et al.  Naphthamides as novel and potent vascular endothelial growth factor receptor tyrosine kinase inhibitors: design, synthesis, and evaluation. , 2008, Journal of medicinal chemistry.

[31]  J. Mestan,et al.  Anthranilic acid amides: a novel class of antiangiogenic VEGF receptor kinase inhibitors. , 2002, Journal of medicinal chemistry.

[32]  Napoleone Ferrara,et al.  VEGF and the quest for tumour angiogenesis factors , 2002, Nature Reviews Cancer.

[33]  K. Alitalo,et al.  The biology of vascular endothelial growth factors. , 2005, Cardiovascular research.

[34]  L. Johnson,et al.  Active and Inactive Protein Kinases: Structural Basis for Regulation , 1996, Cell.

[35]  Kenneth J. Hillan,et al.  Discovery and development of bevacizumab, an anti-VEGF antibody for treating cancer , 2004, Nature Reviews Drug Discovery.

[36]  P. A. Harris,et al.  Discovery and evaluation of 2-anilino-5-aryloxazoles as a novel class of VEGFR2 kinase inhibitors. , 2005, Journal of medicinal chemistry.

[37]  L. Ellis,et al.  Role of the vascular endothelial growth factor pathway in tumor growth and angiogenesis. , 2005, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[38]  J. P. Bowen,et al.  Molecular design and clinical development of VEGFR kinase inhibitors. , 2007, Current topics in medicinal chemistry.

[39]  Richard Kendall,et al.  Evolution of a highly selective and potent 2-(pyridin-2-yl)-1,3,5-triazine Tie-2 kinase inhibitor. , 2007, Journal of medicinal chemistry.

[40]  G. Giaccone,et al.  Angiogenesis inhibitors. Drug selectivity and target specificity. , 2007, Current pharmaceutical design.

[41]  J. Mestan,et al.  Advances in the structural biology, design and clinical development of VEGF-R kinase inhibitors for the treatment of angiogenesis. , 2004, Biochimica et biophysica acta.

[42]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[43]  B. Mroczkowski,et al.  Crystal structure of the kinase domain of human vascular endothelial growth factor receptor 2: a key enzyme in angiogenesis. , 1999, Structure.

[44]  Alexander D. MacKerell,et al.  Computational identification of inhibitors of protein-protein interactions. , 2007, Current topics in medicinal chemistry.

[45]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .