Discovery of 7-azaindole based anaplastic lymphoma kinase (ALK) inhibitors: Wild type and mutant (L1196M) active compounds with unique binding mode Venkateshwar Rao Gummadi a,  , Sujatha Rajagopalan a,  , Chung-Yeng Looi b , Mohammadjavad Paydar b , Girish Aggunda Renukappa a , Bharathi Raja Ainan a , Narasimha Rao Krishnamurthy a , Sunil Kumar Panigrahi a , Kumari Mahasweta a , Sangeetha Raghuramachandran a , Manoj Rajappa a , Anuradha Ramanathan a , Anirudha Lakshminarasimhan a , Murali Ramachandra a , Pooi-Fong Wong b , Mohammad Rais Mustafa b , Srinivas Nanduri a , Subramanya Hosahalli a,⇑ a Aurigene Discovery Technologies Ltd., #39/40, KIADB Industrial Area, Hosur Road, Electronic City Phase-II, Bangalore 560100, India b Department of Pharmacology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia article info Article history: Received 21 March 2013 Revised 3 June 2013 Accepted 25 June 2013 Available online 4 July 2013 Keywords: Anaplastic lymphoma kinase (ALK) 7-Azaindole Anaplastic large cell lymphoma (ALCL) Cancer Karpas299 abstract We have identified a novel 7-azaindole series of anaplastic lymphoma kinase (ALK) inhibitors. Com- pounds 7b, 7m and 7n demonstrate excellent potencies in biochemical and cellular assays. X-ray crystal structure of one of the compounds (7k) revealed a unique binding mode with the benzyl group occupying the back pocket, explaining its potency towards ALK and selectivity over tested kinases particularly Aur- ora-A. This binding mode is in contrast to that of known ALK inhibitors such as Crizotinib and NVP- TAE684 which occupy the ribose binding pocket, close to DFG motif. Ó 2013 Elsevier Ltd. All rights reserved. Anaplastic lymphoma kinase (ALK) is a transmembrane recep- tor tyrosine kinase that belongs to the insulin receptor superfam- ily. Physiologically ALK is involved in the early development and function of nervous system. However its expression is restricted to the central nervous system in normal adults. 1 Several fusion/ mutant proteins of ALK have been implicated in oncogenesis. Nucleophosmin (NPM)-ALK was the first fusion protein to be iden- tified, with the N-terminus of NPM fused to the intracellular do- main of ALK. NPM–ALK is present in 30–50% of advanced stage anaplastic large cell lymphoma (ALCL) patients. Echinoderm microtubule associated protein like 4 (EML4)-ALK, which is identified in 3–7% of lung tumors, has EML4 fused to the intracel- lular domain of ALK. 2 ALK fusion protein has also been implicated in 30–60% of inflammatory myofibroblastic tumors (IMT). 3 These fusion proteins mediate ligand-independant oligomerization lead- ing to autophosphorylation and hence constitutive activation of ALK. In addition, overexpression or activating mutations of the pro- tein have been identified in 5–15% of neuroblastoma. 4,5 Recent re- ports have also identified ALK amplification in 75% of inflammatory breast cancer (IBC) tumor samples that respond to ALK inhibition in pre-clinical models. 6 Oncogenic ALK mediates its effects through activation of PI3K/Akt, Jak/Stat, Raf/Mek/Erk and the PLCc path- ways 7 , resulting in increased cell proliferation and resistance to apoptosis. Knock-out studies and the use of selective ALK inhibi- tors in pre-clinical models have validated this kinase as a potent oncogenic driver in cancers dependant on ALK. Recently Crizotinib a c-Met/ALK dual inhibitor has been given accelerated approval for the treatment of ALK-dependant cancers, further validating the tar- get and the potential therapeutic application of inhibiting this oncogenic kinase. Hence there is compelling evidence for targeting ALK-dependant hematological and solid tumors. In patients, initial response to Crizotinib has been exceptional. However resistance has been known to develop within a year of starting therapy. Sev- eral examples of resistance to tyrosine kinase inhibitors (TKIs) have been reported earlier. 8,9 One of the most common mutations has been with the gatekeeper residue observed in TKs such as EGFR (T790M mutation) and BCR–ABL (T315I mutation). Among the first identified resistant mutations in patients treated with Crizotinib 0960-894X/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.bmcl.2013.06.071 ⇑ Corresponding author. Tel.: +91 80 71025316; fax: +91 80 28526285. E-mail address: hosahalli_s@aurigene.com (S. Hosahalli).   These authors have contributed equally to this work. Bioorganic & Medicinal Chemistry Letters 23 (2013) 4911–4918 Contents lists available at SciVerse ScienceDirect Bioorganic & Medicinal Chemistry Letters journal homepage: www.elsevier.com/locate/bmcl