Peptide deformylase (PDF) is a class of metalloenzyme responsible for catalyzing the removal of the N-formyl group from N-terminal methionine following translation. PDF inhibitors are moving into new phase of drug development. Initially, PDF was considered as an important target in antibacterial drug discovery; however genome database searches have revealed PDF-like sequences in parasites (P. falciparum) and human, widening the utility of this target in antimalarial and anticancer drug discovery along with antibacterial. Using structural and mechanistic information together with high throughput screening, several types of chemical classes of PDF inhibitors with improved efficacy and specificity have been identified. Various drugs like, GSK-1322322 (Phase II), BB-83698 (Phase I), and LBM-415 (Phase I) have entered into clinical developments. Developments in the field have prompted us to review the current aspects of PDFs, especially their structures, different classes of PDF inhibitors, and molecular modeling studies. In nut shell, this review enlightens PDF as a versatile target along with its inhibitors and future perspectives of different PDF inhibitors.

01 May 2008·Biophysical ChemistryQ4 · BIOLOGY

Prediction of the binding modes between BB-83698 and peptide deformylase from Bacillus stearothermophilus by docking and molecular dynamics simulation

Q4 · BIOLOGY

Article

Author: Qiang Wang ; Zhengting Cai ; Weiren Xu ; Jianwu Wang

BB-83698 is a first potent inhibitor of peptide deformylase in this novel class to enter clinical trials. In this study, automated docking, molecular dynamics simulation and binding free energy calculations with the linear interaction energy (LIE) method are first applied to investigate the binding of BB-83698 to the peptide deformylase from Bacillus stearothermophilus. The lowest docking energy structure from each cluster is selected as different representative binding modes. Compared with the experimental data, the results show that the binding of BB-83698 in Mode 1 is the most stable, with a binding free energy of -41.35 kJ/mol. The average structure of the Mode 1 complex suggests that inhibitor interacts with Ile59 and Gly109 by hydrogen bond interaction and with Pro47, Pro57, Ile59 and Leu146 by hydrophobic interaction are essential for the activity of BB-83698. Mode 2 represents a new binding mode. Additionally, if the hydrophilic group is introduced to the benzo-[1,3]-dioxole ring, the binding affinity of BB-83698 to the peptide deformylase from B. stearothermophilus will be greatly improved.

01 Aug 2007·Therapeutics and clinical risk management

Drug forecast - the peptide deformylase inhibitors as antibacterial agents.

Article

Author: Guay, David R P

The relatively rapid development of microbial resistance after the entry of every new antimicrobial into the marketplace necessitates a constant supply of new agents to maintain effective pharmacotherapy. Despite extensive efforts to identify novel lead compounds from molecular targets, only the peptide deformylase inhibitors (PDIs) have shown any real promise, with some advancing to phase I human trials. Bacterial peptide deformylase, which catalyzes the removal of the N-formyl group from N-terminal methionine following translation, is essential for bacterial protein synthesis, growth, and survival. The majority of PDIs are pseudopeptide hydroxamic acids and two of these (IV BB-83698 and oral NVP LBM-415) entered phase I human trials. However, agents to the present have suffered from major potential liabilities. Their in vitro activity has been limited to gram-positive aerobes and some anaerobes and has been quite modest against the majority of such species (MIC(90) values ranging from 1-8 mg/L). They have exerted bacteriostatic, not bacteriocidal, activity, thus reducing their potential usefulness in the management of serious infections in the immunocompromised. The relative ease with which microorganisms have been able to develop resistance and the multiple available mechanisms of resistance (mutations in fmt, defB, folD genes; AcrAB/TolC efflux pump; overexpression of peptide deformylase) are worrisome. These could portend a short timespan of efficacy after marketing. Despite these current liabilities, further pursuit of more potent and broader spectrum PDIs which are less susceptible to bacterial mechanisms of resistance is still warranted.

100 Deals associated with BB-83698

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Indication	Highest Phase	Country/Location	Organization	Date
Bacterial Infections	Phase 1	GB	-	-
Community Acquired Pneumonia	Phase 1	GB	-	-
Healthcare-Associated Pneumonia	Phase 1	-	Oscient Pharmaceuticals Corp.	-
Healthcare-Associated Pneumonia	Phase 1	-	Ligand UK Ltd.	-
Hospital-acquired pneumonia	Phase 1	GB	-	-
Pneumonia, Bacterial	Phase 1	-	Ligand UK Ltd.	-
Pneumonia, Bacterial	Phase 1	-	Oscient Pharmaceuticals Corp.	-

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