2-Aminobenzimidazoles as potent ITK antagonists: de novo design of a pyrrole system targeting additional hydrogen bonding interaction Ho Yin Lo a, * , Jörg Bentzien a , Andre White a , Chuk C. Man a , Roman W. Fleck a , Steven S. Pullen b , Hnin Hnin Khine b , Josephine King b , Joseph R. Woska Jr. b , John P. Wolak c , Mohammed A. Kashem c , Gregory P. Roth d , Hidenori Takahashi a a Boehringer Ingelheim Pharmaceuticals Inc., Medicinal Chemistry, 900 Ridgebury Rd./PO Box 368, Ridgefield, CT 06877, USA b Boehringer Ingelheim Pharmaceuticals Inc., Immunology and Inflammation, 900 Ridgebury Rd./PO Box 368, Ridgefield, CT 06877, USA c Boehringer Ingelheim Pharmaceuticals Inc., Biomolecular screening, 900 Ridgebury Rd./PO Box 368, Ridgefield, CT 06877, USA d Burnham Institute for Medical Research at Lake Nona, Orlando, FL 32819, USA article info Article history: Received 27 September 2008 Revised 10 October 2008 Accepted 13 October 2008 Available online 17 October 2008 abstract Based on information from molecular modeling, a series of 2-aminobenzimidazoles with pyrrole moieties were designed and synthesized as ITK antagonists. Results showed that a significant improvement of intrinsic and cell-based potency was achieved. X-ray crystallographic analysis of an inhibitor complex with ITK confirmed the prediction from the de novo design that the pyrrole moiety of the inhibitor would form an additional hydrogen bonding interaction with Glu436 in the catalytic domain, and hence improve overall binding affinity of the inhibitor. Ó 2008 Elsevier Ltd. All rights reserved. During the quest for novel anti-inflammatory agents and mech- anisms which could be used on the treatment of inflammatory dis- ease, such as allergic asthma, rheumatoid arthritis, and multiple sclerosis, we pursued Interleukin-2 inducible T-cell kinase (ITK) 1 as a promising target. In our recent search for novel small molecule inhibitors for ITK, 2 we discovered a series of potent, selective ITK antagonists featur- ing 2-aminobenzimidazole scaffold as a key pharmacophore. Lead compound such as 1 (Fig. 1) exhibited a good activity profile: IC 50 ’s were determined to be 140 nM in an ITK DELFIA assay 3a for the intrinsic binding affinity and 780 nM in an Insulin Receptor Ki- nase (IRK) DELFIA assay for the selectivity. However, compound 1 was not active (IC 50 >3 lM) in a DT40/ITK cell assay, 3b which might be due to the relatively low intrinsic potency of the compound. Based on an X-ray co-crystal structure of a structurally related ITK inhibitor bound to the human ITK kinase domain, 4 we realized that beside the double ‘backbone’ hydrogen bonding interactions between the amide carbonyl group of Met 438 and the N–H of the benzimidazole core, Glu 436 might be able to provide an additional hydrogen bonding interaction by its amide moiety. Next to Glu 436 , there was an unoccupied kinase specificity pocket (KSP). The KSP is about 7.3 Å deep (measuring from the ‘gate-keeper’ Phe 435 to Met 410 ) and contains hydrophobic (Leu 418 , Leu, 489 and Val 419 ) and hydrophilic residues (Lys 391 , Glu 406 , Met, 410 and Asp 500 ). In order to access the KSP from the thiophene side of the inhibitor effectively, the design had to take into consideration structural modifications that would avoid creating steric interactions with Phe 435 . Molecular modeling suggested that a compound such as 2 which features a pyrrole moiety off the 2-amide position could potentially act as a hydrogen bonding donor through interactions with the carbonyl group of Glu 436 as shown in Figure 2. Furthermore, an additional hydrogen bond could also be achieved through interactions with Lys 391 and the carbonyl group off the 3-position of the pyrrole ring. Thirdly, the ‘pyrrole-carbonyl-aromatic’ substitution pattern might provide the correct angle necessary to avoid Phe 435 and occupy the KSP. This would provide an opportunity for additional interactions with various amino acids (Ser 499 , Asp, 500 and Glu 406 ) within the pocket. 0040-4039/$ - see front matter Ó 2008 Elsevier Ltd. All rights reserved. doi:10.1016/j.tetlet.2008.10.057 * Corresponding author. Tel.: +1 203 798 4923. E-mail address: ho-yin.lo@boehringer-ingelheim.com (H. Y. Lo). N N N O N N O S 1 Met438 H KSP Phe435 Met410 Asp500 Leu489 Lys391 Glu406 Val419 O Glu436 Figure 1. Illustration of the binding mode of 1 in ITK. Tetrahedron Letters 49 (2008) 7337–7340 Contents lists available at ScienceDirect Tetrahedron Letters journal homepage: www.elsevier.com/locate/tetlet