Blue Ridge Institute for Medical Research
Research at BRIMR focuses on the structure and regulation of protein kinases, their downstream signaling modules, and therapeutic drugs that target these enzymes. Protein kinases catalyze the following reaction:
MgATP1- + protein-O:H → Protein-O:PO32- + MgADP + H+.
I give this stoichiometry in nearly all of my papers on protein kinases following the suggestion of John Westley, an enzymologist and teacher (now deceased) at the University of Chicago, who taught that the stoichiometry is a fundamental enzyme property that should be given in every paper on every enzyme to eliminate any ambiguity. Note that the phosphoryl group (PO32-) and not the phosphate group (OPO32-) is transferred from ATP to the protein substrate. Based upon the nature of the phosphorylated –OH group, these enzymes are classified as protein-serine/threonine kinases and protein-tyrosine kinases. Investigators have identified 478 typical and 40 atypical protein kinase genes in humans (total 518) that correspond to about 2% of all human genes. The family includes 385 protein-serine/threonine kinases, 90 protein-tyrosine kinases, and 43 protein-tyrosine-kinase like proteins. Of the 90 protein-tyrosine kinases, a total of 58 are receptor and 32 are non-receptor in nature. The exons of the protein kinase family account for about 1.3 Mb or 2% the entire coding sequence of human DNA. The protein kinase family is the second largest enzyme family (after proteases) and the fifth largest gene family in humans.
have focused on the targeted inhibition of protein kinases by orally effective
small molecules in the treatment of various disorders. The US FDA has approved
36 such drugs for the treatment of various cancerous, inflammatory, and fibrotic
We have studied the roles of targeted inhibitors of ALK,
the cyclin-dependent protein kinases, EGFR, ERK1/2, the Janus kinases, MEK1/2,
PDGFR, RET, ROS1, Src, and VEGFR1/2/3 in the treatment of various disorders. Imatinib
was the first protein kinase inhibitor that was approved in 2001 by the FDA for
the treatment of Philadelphia chromosome positive chronic myelogenous leukemia.
Its initial success paved the way for the development and approval of an
additional 35 small molecule antagonists that interact directly with the protein
kinase domain. It has subsequently been approved for the treatment of more
maladies than any other targeted protein kinase antagonist and may be considered
as a broad-spectrum antagonist. Imatinib is effective in the treatment of
Philadelphia chromosome positive acute lymphoblastic leukemia, aggressive
systemic mastocytosis, chronic eosinophilic leukemia (CEL), dermatofibrosarcoma
protuberans (DFSP), hypereosinophilic syndrome (HES), gastrointestinal stromal
tumors (GIST), and myelodysplastic/myeloproliferative diseases (MDS/MDP).
We have classified these drugs into seven possible types (I–VI and I½) based upon the structures of the drug-protein kinase complexes. Type I drugs bind to the active conformation of the protein kinase with (i) DFG-Din, (ii) αCin, (iii) an open activation segment, and (iv) a linear R-spine. The type I½ drugs bind to an inactive enzyme conformation with DFG-Din; the activation segment may be closed, the R-spine may be nonlinear, or the αC-helix may be out. The type II drugs bind to their target enzyme with DFG-Dout, which corresponds to a less active conformation. The R-spine RS2 residue is displaced from RS1 and RS3 and the R-spine is broken. The type III inhibitors are allosteric in nature and bind adjacent to the adenine binding pocket. Type IV drugs are also allosteric inhibitor, but they do not bind within the cleft that separates the small and large lobes of protein kinases. Type V inhibitors bind to two different regions of their protein kinase target (e.g., to the ATP and protein substrate binding sites). Type VI inhibitors bind covalently to their target enzyme.
We are systematically studying the nature or the interaction of these antagonists with their target enzyme. Our studies are based upon the X-ray crystallographic results that are in the public domain as well as computer generated models of antagonist binding to their targets. To see the publications corresponding to these studies, click here.
Concentrate only on the biggest and most important biomedical research problems. – James D. Watson
Created 9 March 2008; updated 9 February 2018