Synthesis and SAR of novel, potent and orally bioavailable benzimidazole inhibitors of poly(ADP-ribose) polymerase (PARP) with a quaternary methylene-amino substituent Gui-Dong Zhu a, * , Viraj B. Gandhi a , Jianchun Gong a , Sheela Thomas a , Yan Luo a , Xuesong Liu a , Yan Shi a , Vered Klinghofer a , Eric F. Johnson a , David Frost a , Cherrie Donawho a , Ken Jarvis a , Jennifer Bouska a , Kennan C. Marsh b , Saul H. Rosenberg a , Vincent L. Giranda a , Thomas D. Penning a a Cancer Research, GPRD, Abbott Laboratories, Abbott Park, IL 60064, USA b Preclinical Safety, GPRD, Abbott Laboratories, Abbott Park, IL 60064, USA article info Article history: Received 15 May 2008 Revised 5 June 2008 Accepted 5 June 2008 Available online 12 June 2008 Keywords: PARP Poly(ADP-ribose) polymerase Inhibitor Benzimidazole Anticancer abstract Poly(ADP-ribose) polymerases (PARPs) play significant roles in various cellular functions including DNA repair and control of RNA transcription. PARP inhibitors have been demonstrated to potentiate the effect of cytotoxic agents or radiation in a number of animal tumor models. Utilizing a benzimidazole carbox- amide scaffold in which the amide forms a key intramolecular hydrogen bond for optimal interaction with the enzyme, we have identified a novel series of PARP inhibitors containing a quaternary methy- lene-amino substituent at the C-2 position of the benzimidazole. Geminal dimethyl analogs at the meth- ylene-amino substituent were typically more potent than mono-methyl derivatives in both intrinsic and cellular assays. Smaller cycloalkanes such as cyclopropyl or cyclobutyl were tolerated at the quaternary carbon while larger rings were detrimental to potency. In vivo efficacy data in a B16F10 murine flank melanoma model in combination with temozolomide (TMZ) are described for two optimized analogs. Ó 2008 Elsevier Ltd. All rights reserved. Poly(ADP-ribose) polymerases (PARPs) are a family of DNA- binding proteins found in nearly all eukaryotic cells. 1 When acti- vated by nicks in DNA occurring during inflammation, ischemia, neurodegeneration, or cancer therapy, PARPs catalyze the transfer of ADP-ribose units from nicotinamide adenine dinucleotide (NAD + ) to the acceptor proteins with NAD + as substrate, leading to formation of protein-bound ADP-ribose polymers and dramatic cellular ATP depletion. 2 This cellular ADP-ribose transfer process is pivotal for DNA repair machinery and maintenance of genomic sta- bility. 1,2 PARP-1, the most abundant member of the PARP family, is therefore regarded as a promising target for treating diseases re- lated to inflammation and ischemia-reperfusion injury. This DNA repair mechanism also contributes to the drug resistance that often develops after cancer therapy. 3 In addition, enhanced PARP expres- sion and/or activation has been observed in a number of hemato- logical and solid tumors as compared to normal cells, suggesting a potential selectivity of PARP inhibitors against tumor cells. Inhi- bition of PARP-1 would retard the intracellular DNA repair and therefore sensitize tumor cells to cytotoxic agents or ionizing radi- ation. 4–8 There have been a plethora of PARP inhibitors developed in the past two decades. 9 The majority of the known inhibitors bind to the nicotinamide binding site and structurally mimic the binding mode of nicotinamide, where the amide functional group forms multiple hydrogen bonds with Gly-863 and Ser-904. 9 One struc- tural class of inhibitors, namely benzimidazole carboxamide, was first developed by researchers at the University of Newcastle. 10 This series of compounds displayed relatively high intrinsic po- tency against PARP-1, but suffered from poor activity in a whole cell assay. Herein, utilizing the same benzimidazole carboxamide scaffold, we incorporated a basic amino functionality to the C-2 po- sition of the pharmacophore, and discovered a series of PARP inhibitors with greater cellular activity. Two optimized analogs, 9b and 9k, with a quaternary methylene-amino substituent, dis- played excellent intrinsic and cellular potency, adequate pharma- ceutical properties, and potentiated the efficacy of cytotoxic agent temozolomide (TMZ) in a B16F10 flank melanoma model. Outlined in Scheme 1 are general syntheses of the PARP inhib- itors with a representative structure 6 or 7. 2,3-Diaminobenzamide dihydrochloride 1 11 was first coupled to an appropriately protected amino acid 2 to provide mono-acylated 3. The 1,1 0 -carbonyldiimid- azole (CDI)-mediated amidation proceeded predominately at the 3-amino group. A 1:1 mixture of anhydrous DMF and pyridine was typically used as solvent in which pyridine freed up the 0960-894X/$ - see front matter Ó 2008 Elsevier Ltd. All rights reserved. doi:10.1016/j.bmcl.2008.06.023 * Corresponding author. Tel.: +1 847 935 1305; fax: +1 847 935 5165. E-mail address: Gui-Dong.Zhu@abbott.com (G.-D. Zhu). Bioorganic & Medicinal Chemistry Letters 18 (2008) 3955–3958 Contents lists available at ScienceDirect Bioorganic & Medicinal Chemistry Letters journal homepage: www.elsevier.com/locate/bmcl