Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity Leslie W. Tari a,⇑ , Michael Trzoss a , Daniel C. Bensen a , Xiaoming Li a , Zhiyong Chen a , Thanh Lam a , Junhu Zhang a , Christopher J. Creighton a , Mark L. Cunningham a , Bryan Kwan a , Mark Stidham a , Karen J. Shaw a , Felice C. Lightstone b , Sergio E. Wong b , Toan B. Nguyen b , Jay Nix c , John Finn a a Trius Therapeutics, 6310 Nancy Ridge Dr., San Diego, CA 92121, USA b Lawrence Livermore National Laboratory, Physical and Life Sciences Directorate, Livermore, CA 94550, USA c Advanced Light Source, Beamline 4.2.2, 1 Cyclotron Rd., Berkeley, CA 94720, USA article info Article history: Available online 5 December 2012 Keywords: Bacterial topoisomerases GyrB ParE Pyrrolopyrimidine Inhibitor abstract The bacterial topoisomerases DNA gyrase (GyrB) and topoisomerase IV (ParE) are essential enzymes that control the topological state of DNA during replication. The high degree of conservation in the ATP-bind- ing pockets of these enzymes make them appealing targets for broad-spectrum inhibitor development. A pyrrolopyrimidine scaffold was identified from a pharmacophore-based fragment screen with optimiza- tion potential. Structural characterization of inhibitor complexes conducted using selected GyrB/ParE orthologs aided in the identification of important steric, dynamic and compositional differences in the ATP-binding pockets of the targets, enabling the design of highly potent pyrrolopyrimidine inhibitors with broad enzymatic spectrum and dual targeting activity. Ó 2012 Elsevier Ltd. All rights reserved. The increasing prevalence of antibiotic resistant strains of path- ogenic bacteria continues to erode the utility of every major class of antibiotics used in the clinic. 1 To avoid cross-resistance with established classes of antibiotics, new agents must be developed that act via novel mechanisms of action, or against unique binding sites on existing validated targets. Target selection is of critical importance to preemptively minimize the probability of resistance development. Antibacterial agents that target single enzymes can be subject to high-level resistance resulting from single-step muta- tions. Single agents with the capacity to interact with multiple sites on the same target or simultaneously target enzymes from multiple essential pathways have been demonstrated to impair the ability of bacteria to develop resistance. 1 The bacterial topoisomerases DNA gyrase (GyrA/GyrB) and topoisomerase IV (ParC/ParE) are established antibacterial targets 2 that are closely related at the structural and functional levels. Both topoisomerases form A 2 B 2 holoenzymes that control the topologi- cal state of DNA during replication: DNA gyrase is primarily responsible for the initiation of DNA replication and elongation of nascent DNA, while topoisomerase IV is primarily responsible for decatenation of daughter chromosomal DNA at the end of rep- lication. 3 Multiple discrete binding sites on DNA gyrase have been identified as the targets of synthetic and natural product inhibi- tors. 4 The best characterized inhibitor classes are the fluoroquino- lone antibiotics 5 , which act as topoisomerase poisons by stabilizing a covalent GyrA-DNA complex 6 , and the aminocoumarins, catalytic inhibitors of DNA gyrase which act via competitive inhibition of GyrB ATPase activity. 7 The increasing prevalence of fluoroquino- lone resistant strains and problems with side effects are beginning to limit the utility of this widely utilized antibiotic class. 8 Amino- coumarin antibiotics, such as novobiocin, are effective at killing Gram-positive bacteria, but were unsuccessful in the clinic. In addition to issues with safety, their size, poor ligand efficiency, and weak activity against ParE (i.e., inability to dual target) have resulted in a rapid emergence of resistance. 9 A number of struc- ture-based design efforts have been effective in generating ligand efficient small molecule inhibitors superior to novobiocin in po- tency and dual targeting capabilities (reviewed in 2 ), but to date, no synthetic or natural product GyrB/ParE inhibitors have reached the clinic. Thus, the GyrB/ParE ATP-binding subunits represent unexploited targets for the development of novel antibiotics. This manuscript and the following companion manuscript highlight a novel pyrrolopyrimidine inhibitor series with broad spectrum anti- 0960-894X/$ - see front matter Ó 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.bmcl.2012.11.032 ⇑ Corresponding author. Tel.: +1 858 452 0370; fax: +1 858 677 9975. E-mail address: ltari@triusrx.com (L.W. Tari). Bioorganic & Medicinal Chemistry Letters 23 (2013) 1529–1536 Contents lists available at SciVerse ScienceDirect Bioorganic & Medicinal Chemistry Letters journal homepage: www.elsevier.com/locate/bmcl