title: Structural characterization of nonactive site, TrkA-selective kinase inhibitors.
abstract: Current therapies for chronic pain can have insufficient efficacy and lead to side effects, necessitating research of novel targets against pain. Although originally identified as an oncogene, Tropomyosin-related kinase A (TrkA) is linked to pain and elevated levels of NGF (the ligand for TrkA) are associated with chronic pain. Antibodies that block TrkA interaction with its ligand, NGF, are in clinical trials for pain relief. Here, we describe the identification of TrkA-specific inhibitors and the structural basis for their selectivity over other Trk family kinases. The X-ray structures reveal a binding site outside the kinase active site that uses residues from the kinase domain and the juxtamembrane region. Three modes of binding with the juxtamembrane region are characterized through a series of ligand-bound complexes. The structures indicate a critical pharmacophore on the compounds that leads to the distinct binding modes. The mode of interaction can allow TrkA selectivity over TrkB and TrkC or promiscuous, pan-Trk inhibition. This finding highlights the difficulty in characterizing the structure-activity relationship of a chemical series in the absence of structural information because of substantial differences in the interacting residues. These structures illustrate the flexibility of binding to sequences outside of-but adjacent to-the kinase domain of TrkA. This knowledge allows development of compounds with specificity for TrkA or the family of Trk proteins.
authors.affiliation: Global Chemistry, Merck Research Laboratories (MRL), Merck & Co. Inc., West Point, PA 19486; hua-poo_su@merck.com.
authors.forename: Hua-Poo
authors.initials: HP
authors.lastname: Su
authors.affiliation: Screening & Protein Sciences, MRL, Merck & Co. Inc., West Point, PA 19486.
authors.forename: Keith
authors.initials: K
authors.lastname: Rickert
authors.affiliation: In Vitro Pharmacology, MRL, Merck & Co. Inc., West Point, PA 19486.
authors.forename: Christine
authors.initials: C
authors.lastname: Burlein
authors.affiliation: In Vitro Pharmacology, MRL, Merck & Co. Inc., West Point, PA 19486.
authors.forename: Kartik
authors.initials: K
authors.lastname: Narayan
authors.affiliation: In Vitro Pharmacology, MRL, Merck & Co. Inc., West Point, PA 19486.
authors.forename: Marina
authors.initials: M
authors.lastname: Bukhtiyarova
authors.affiliation: Global Chemistry, Merck Research Laboratories (MRL), Merck & Co. Inc., West Point, PA 19486.
authors.forename: Danielle M
authors.initials: DM
authors.lastname: Hurzy
authors.affiliation: Global Chemistry, Merck Research Laboratories (MRL), Merck & Co. Inc., West Point, PA 19486.
authors.forename: Craig A
authors.initials: CA
authors.lastname: Stump
authors.affiliation: Global Chemistry, Merck Research Laboratories (MRL), Merck & Co. Inc., West Point, PA 19486.
authors.forename: Xufang
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Global Chemistry, Merck Research Laboratories (MRL), Merck & Co. Inc., West Point, PA 19486.
authors.forename: John
authors.initials: J
authors.lastname: Reid
authors.affiliation: Neuroscience Discovery, MRL, Merck & Co. Inc., West Point, PA 19486.
authors.forename: Alicja
authors.initials: A
authors.lastname: Krasowska-Zoladek
authors.affiliation: Screening & Protein Sciences, MRL, Merck & Co. Inc., West Point, PA 19486.
authors.forename: Srivanya
authors.initials: S
authors.lastname: Tummala
authors.affiliation: Screening & Protein Sciences, MRL, Merck & Co. Inc., West Point, PA 19486.
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Shipman
authors.affiliation: Screening & Protein Sciences, MRL, Merck & Co. Inc., West Point, PA 19486.
authors.forename: Maria
authors.initials: M
authors.lastname: Kornienko
authors.affiliation: In Vitro Pharmacology, MRL, Merck & Co. Inc., West Point, PA 19486.
authors.forename: Peter A
authors.initials: PA
authors.lastname: Lemaire
authors.affiliation: Screening & Protein Sciences, MRL, Merck & Co. Inc., West Point, PA 19486.
authors.forename: Daniel
authors.initials: D
authors.lastname: Krosky
authors.affiliation: In Vitro Pharmacology, MRL, Merck & Co. Inc., West Point, PA 19486.
authors.forename: Amanda
authors.initials: A
authors.lastname: Heller
authors.affiliation: In Vitro Pharmacology, MRL, Merck & Co. Inc., Boston, MA 02115.
authors.forename: Abdelghani
authors.initials: A
authors.lastname: Achab
authors.affiliation: In Vitro Pharmacology, MRL, Merck & Co. Inc., Boston, MA 02115.
authors.forename: Chad
authors.initials: C
authors.lastname: Chamberlin
authors.affiliation: In Vitro Pharmacology, MRL, Merck & Co. Inc., Boston, MA 02115.
authors.forename: Peter
authors.initials: P
authors.lastname: Saradjian
authors.affiliation: In Vitro Pharmacology, MRL, Merck & Co. Inc., Boston, MA 02115.
authors.forename: Berengere
authors.initials: B
authors.lastname: Sauvagnat
authors.affiliation: In Vitro Pharmacology, MRL, Merck & Co. Inc., Boston, MA 02115.
authors.forename: Xianshu
authors.initials: X
authors.lastname: Yang
authors.affiliation: In Vitro Pharmacology, MRL, Merck & Co. Inc., Boston, MA 02115.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Ziebell
authors.affiliation: In Vitro Pharmacology, MRL, Merck & Co. Inc., Boston, MA 02115.
authors.forename: Elliott
authors.initials: E
authors.lastname: Nickbarg
authors.affiliation: Global Chemistry, Merck Research Laboratories (MRL), Merck & Co. Inc., West Point, PA 19486.
authors.forename: John M
authors.initials: JM
authors.lastname: Sanders
authors.affiliation: Global Chemistry, Merck Research Laboratories (MRL), Merck & Co. Inc., West Point, PA 19486.
authors.forename: Mark T
authors.initials: MT
authors.lastname: Bilodeau
authors.affiliation: In Vitro Pharmacology, MRL, Merck & Co. Inc., West Point, PA 19486.
authors.forename: Steven S
authors.initials: SS
authors.lastname: Carroll
authors.affiliation: Screening & Protein Sciences, MRL, Merck & Co. Inc., West Point, PA 19486.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Lumb
authors.affiliation: Global Chemistry, Merck Research Laboratories (MRL), Merck & Co. Inc., West Point, PA 19486.
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Soisson
authors.affiliation: Neuroscience Discovery, MRL, Merck & Co. Inc., West Point, PA 19486.
authors.forename: Darrell A
authors.initials: DA
authors.lastname: Henze
authors.affiliation: Global Chemistry, Merck Research Laboratories (MRL), Merck & Co. Inc., West Point, PA 19486.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Cooke
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004353:Drug Evaluation, Preclinical; D006801:Humans; D007700:Kinetics; D008562:Membrane Glycoproteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D011487:Protein Conformation; D047428:Protein Kinase Inhibitors / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology*; D020917:Receptor, trkA / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000235:genetics; D020813:Receptor, trkB / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics; D020812:Receptor, trkC / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics; D011994:Recombinant Proteins / Q000737:chemistry / Q000187:drug effects / Q000235:genetics; D013329:Structure-Activity Relationship; D020349:Surface Plasmon Resonance
chemical_list: D008562:Membrane Glycoproteins; C000611485:NTRK1 protein, human; D047428:Protein Kinase Inhibitors; D011994:Recombinant Proteins; D020917:Receptor, trkA; D020813:Receptor, trkB; D020812:Receptor, trkC; C000591259:tropomyosin-related kinase-B, human
keywords: TrkA; inhibition; kinase; pain; selectivity