PHILADELPHIA (June 27, 2019) – Researchers at Fox Chase Cancer Center have developed a new classification scheme and nomenclature for the structural states of protein kinases, which play an important role in signaling pathways and can be targeted by cancer treatments.
“Humans have about 500 genes called kinases that add phosphate groups to the surface of other proteins, changing their function,” said Roland L. Dunbrack, Jr, PhD, professor in the Molecular Therapeutics Program at Fox Chase. “Adding that phosphate to the protein can make it function in overdrive and if that chemical function is not regulated then the cell is unable to deal with the dysregulation and will divide and metastasize.”
Currently, there are quite a few drugs available that are designed to inhibit kinases, according to Dunbrack. One of the most commonly known is imatinib, a drug that targets the protein kinase BCR-ABL as a treatment for leukemia.
Protein kinases can adopt at least two conformations; an active or “on” conformation and an inactive or “off” conformation. When designing inhibitors for protein kinases, researchers must know the exact molecular configuration of the active or inactive site of the kinase where the inhibitor would bond.
In the past, the broad structural terms DFGin and DFGout – referring to the position of its activation loop – have been used as the basis for grouping inhibitors developed to target the active site of these proteins. For example, dasatinib is a type I inhibitor binding to DFGin conformations, and imatinib is a type II inhibitor binding to the DFGout conformations.
Previous attempts have been made to better catalog these kinase conformations, but a rigorous and intuitive catalog does not exist to date, according to Dunbrack.
Dunbrack and a post-doctoral fellow, Vivek Modi, PhD, recently published a paper detailing a clustering scheme and nomenclature developed to better categorize the conformations in human protein kinases. The paper, “Defining a new nomenclature for the structures of active and inactive kinases” was published in PNAS.
“The nomenclature that we developed is pretty simple and should be intuitive for any structural biologist,” Dunbrack said. “We looked at it and tried to strip it down to the fewest syllables and letters possible.”
The system includes eight labels that clearly define the geometry of the active site and distinguish closely related inactive states, which were not previously characterized. The system was based on the location of the DFG Phe side chain (DFGin, DFGout, and DFGinter) and the orientation of the activation loop using the dihedral angles that determine the placement of the Phe side chain.
The conformations are labeled based on the Ramachandran regions (A, alpha; B, beta; L, left) of the amino acids in the XDF motif and the Phe rotamer (minus, plus, trans). There are six DFGin structures (BLAminus, BLAplus, ABAminus, BLBminus, BLBplus, and BLBtrans) and two DFGout structures (BBAminus, and BABtrans).
Dunbrack described it using a lock and key analogy, with inhibitors as the key.
“We are hoping the appeal to this system is that it is easy and intuitive for structural biologists to calculate and understand the structure of the active site; you might call that the ‘lock’,” he said. “We need to know what the lock looks like to know how to make the key.”
This research was funded by National Institutes of Health Grants R01 GM084453 and R35 GM122517.