Structure–Activity Relationships of the Peptide Deformylase Inhibitor BB-3497: Modification of the Methylene Spacer and the P1 0 Side Chain StephenJ.Davies,* AndrewP.Ayscough,R.PaulBeckett,RyanA.Bragg, JohnM.Clements,SheilaDoel,ChristineGrew,StevenB.Launchbury, GemmaM.Perkins,LisaM.Pratt,HelenK.Smith,Zoe¨ M.Spavold,S.WayneThomas, RichardS.ToddandMarkWhittaker British Biotech Pharmaceuticals Limited, Watlington Road, Oxford OX4 6LY, UK Received 26 March 2003; revised 19 May 2003; accepted 22 May 2003 Abstract—StructuralmodificationstothepeptidedeformylaseinhibitorBB-3497aredescribed.Inthispaper,wedescribetheinitial SARaroundthisleadformodificationstothemethylenespacerandtheP1 0 sidechain.Enzymeinhibitionandantibacterialactivity data revealed that the optimum distance between the N-formyl hydroxylamine metal binding group and the P1 0 side chain is one unsubstituted methylene unit. Additionally, lipophilic P1 0 side chains that closely mimic the methionine residue in the substrate provided compounds with the best microbiological profile. # 2003ElsevierLtd.Allrightsreserved. Ribosomal protein synthesis in bacteria is initiated by N-formylation of methionyl-tRNA by formyl- transferase. Most mature proteins, however, do not retain the N-formyl group or the terminal methionine residue. Deformylation is therefore a crucial step in bacterial protein biosynthesis and the metalloenzyme responsible, peptide deformylase (PDF), is essential for bacterial growth. 1 Bacterial PDF is now widely recognised as an attractive target for antibacterial chemotherapy. 2 We reported previously 3 that the N-formyl hydroxyl- amine BB-3497 (Fig.1)isaneffectiveinhibitor(IC 50 =7 nM) of the Escherichia coli PDF . Ni enzyme, exhibiting potentantibacterialactivitybothinvitroandinvivo.In a subsequent communication, 4 we identified the N-for- myl hydroxylamine and hydroxamic acid structural motifs to be the optimum metal binding groups on the pseudopeptidic backbone of BB-3497. Further to this study, we have conducted a systematic modification of the other sites indicated in Figure 1. In this communi- cation the optimum distance between the metal binding group and the P1 0 side chain is evaluated and the pre- ferred P1 0 substituents for enzyme binding affinity and antibacterial activity are discussed. During the course of this investigation, several X-ray crystal structures of PDF enzymes were elucidated. 5 8 The structural information provided by these studies 0960-894X/03/$ - see front matter # 2003 Elsevier Ltd. All rights reserved. doi:10.1016/S0960-894X(03)00532-8 Bioorganic & Medicinal Chemistry Letters 13 (2003) 2709–2713 Figure 1. BB-3497 structure–activity relationships. *Corresponding author. Tel.: +44-1235-441732; fax: +44-1235- 441509;e-mail: stephen.davies@evotecoai.com