New chemotypes for wALADin1-like inhibitors of delta-aminolevulinic acid dehydratase from Wolbachia endobacteria Christian S. Lentz a,c , Dagmar Stumpfe b , Juergen Bajorath b , Michael Famulok c , Achim Hoerauf a , Kenneth M. Pfarr a,⇑ a Institute of Medical Microbiology, Immunology and Parasitology, University Hospital of Bonn, Sigmund-Freud Str. 25, 53127 Bonn, Germany b Department of Life Science Informatics, B-IT, LIMES, Program Unit Medicinal Chemistry and Chemical Biology, Universität Bonn, Dahlmannstr. 2, 53113 Bonn, Germany c LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, Universität Bonn, Gerhard-Domagk-Str. 1, 53121 Bonn, Germany article info Article history: Received 11 June 2013 Revised 9 August 2013 Accepted 11 August 2013 Available online 20 August 2013 Keywords: Delta-aminolevulinic acid dehydratase Wolbachia Brugia malayi Heme biosynthesis wALADin abstract Substituted benzimidazoles of the wALADin1-family have recently been identified as a new class of spe- cies-selective inhibitors of delta-aminolevulinic acid dehydratase (ALAD) from Wolbachia endobacteria of parasitic filarial worms. Due to its Wolbachia-dependent antifilarial activity, wALADin1 is a starting point for the development of new drugs against filarial nematodes. We now present several other chemotypes of ALAD inhibitors that have been identified based upon their molecular similarity to wALADin1. A tricy- clic quinoline derivative (wALADin2) with a different inhibitory mechanism and improved inhibitory potency and selectivity may represent an improved drug lead candidate. Ó 2013 Elsevier Ltd. All rights reserved. The enzyme d-aminolevulinic acid dehydratase (ALAD, also known as porphobilinogen synthase, E.C. 4.2.1.24) catalyzes the condensation of two molecules of 5-aminolevulinic acid (5-ALA) to porphobilinogen as the first common step of heme synthesis. 1 This enzyme has been proposed as a drug target in a variety of hu- man pathogens including the endosymbiotic Wolbachia a-proteo- bacteria of filarial nematodes. 2 These parasitic worms are the causative agents of lymphatic filariasis and onchocerciasis and in- fect more than 150 million people in the tropics and subtropics. 3–5 As these worms are unable to synthesize tetrapyrroles de novo the endobacteria, which have conserved a functional heme biosyn- thetic pathway, are expected to supply their hosts with this essen- tial biomolecule. 2,6–8 Experimental evidence suggests that the worms are indeed dependent upon Wolbachia for heme, as block- ing of the tetrapyrrole biosynthesis enzymes ALAD or ferrochela- tase results in worm death in vitro. 2 The differences in metal cofactor usage between the Mg 2+ -regulated Wolbachia ALAD en- zyme and the Zn 2+ -dependent human ortholog and the corre- sponding differences in protein structure, in principle, enable species-selective inhibition of this pathway. 2,9,10 We have recently reported the discovery of wALADin1 as the most potent member of a new class of trisubstituted benzimid- azole carboxylic acid compounds with species-selective inhibitory activity against ALAD from Wolbachia endobacteria of the filarial worm Brugia malayi (wALAD) but not of the human ortholog (hALAD). 11 Since wALADin1 elicited pronounced antifilarial activ- ity in an ex vivo worm culture assay it holds promise as a lead compound in the development of novel antifilarial drugs. However, the aim of the present study was to identify other specific ALAD inhibitors based on different chemical scaffolds. These alternative chemotypes might offer new possibilities in the design of inhibi- tors with improved potency, specificity and other drug-activity re- lated properties. Based on the structure of wALADin1 (Fig. 1A) and the related benzimidazole compound 24C7 (Fig. 1B), also identified in the ori- ginal high-throughput wALAD activity screen but with weaker inhibitory potency, a fingerprint-based similarity search was con- ducted based on three conceptually different molecular finger- prints: a fragment-based fingerprint, MACCS; 12 an atom- environment fingerprint, ECFP4; 13 and a pharmacophore-based fingerprint, GpiDAPH3. 14 Chemical similarity was quantitatively measured as the fingerprint overlap between reference and 3.75 million vendor catalog molecules using the Tanimoto coeffi- cient. 15 Compounds were ranked according to their similarity val- 0960-894X/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.bmcl.2013.08.052 ⇑ Corresponding author. Tel.: +49 228 287 11207; fax: +49 228 287 11167. E-mail addresses: bajorath@bit.uni-bonn.de (J. Bajorath), pfarr@microbiology- bonn.de (K.M. Pfarr). Bioorganic & Medicinal Chemistry Letters 23 (2013) 5558–5562 Contents lists available at ScienceDirect Bioorganic & Medicinal Chemistry Letters journal homepage: www.elsevier.com/locate/bmcl