Peptide Deformylase Inhibitors Research Articles

Synthesis of the intermediate for fumimycin: a natural peptide deformylase inhibitor

Synthetic efforts toward the potential bacterial peptide deformylase inhibitor fumimycin are reported. The synthetic approach features a tandem Friedel–Crafts alkylation/lactonization access as key reaction to the α, α-disubstituted amino acid unit, and results in the synthesis of an advanced racemic intermediate with an Z configuration propenyl group starting from vanillin with 18 % total yield in five steps.

Structures ofStaphylococcus aureuspeptide deformylase in complex with two classes of new inhibitors

Peptide deformylase (PDF) catalyzes the removal of the formyl group from the N-terminal methionine residue in newly synthesized polypeptides, which is an essential process in bacteria. Four new inhibitors of PDF that belong to two different classes, hydroxamate/pseudopeptide compounds [PMT387 (7a) and PMT497] and reverse-hydroxamate/nonpeptide compounds [PMT1039 (15e) and PMT1067], have been developed. These compounds inhibited the growth of several pathogens involved in respiratory-tract infections, such as Streptococcus pneumoniae, Moraxella catarrhalis and Haemophilus influenzae, and leading nosocomial pathogens such as Staphylococcus aureus and Klebsiella pneumoniae with a minimum inhibitory concentration (MIC) in the range 0.1-0.8 mg ml(-1). Interestingly, the reverse-hydroxamate/nonpeptide compounds showed a 250-fold higher antimicrobial activity towards S.aureus, although the four compounds showed similar K(i) values against S.aureus PDF enzymes, with K(i) values in the 11-85 nM range. To provide a structural basis for the discovery of additional PDF inhibitors, the crystal structures of S. aureus PDF in complex with the four inhibitors were determined at resolutions of 1.90-2.30 Å. The inhibitor-bound structures displayed distinct deviations depending on the inhibitor class. The distance between the Zn(2+) ion and the carbonyl O atom of the hydroxamate inhibitors (or the hydroxyl O atom of the reverse-hydroxamate inhibitors) appears to be correlated to S.aureus inhibition activity. The structural information reported in this study should aid in the discovery of new PDF inhibitors that can be used as novel antibacterial drugs.

Compensatory mutations in agrC partly restore fitness in vitro to peptide deformylase inhibitor-resistant Staphylococcus aureus

To determine how the fitness cost of deformylase inhibitor resistance conferred by fmt mutations can be genetically compensated. Resistant mutants were isolated and characterized with regard to their growth rates in vitro and in neutropenic mice, MIC and DNA sequence. Faster-growing compensated mutants were isolated by serial passage in culture medium, and for a subset of the resistant and compensated mutants whole-genome sequencing was performed. Staphylococcus aureus mutants resistant to the peptide deformylase inhibitor actinonin had mutations in the fmt gene that conferred high-level actinonin resistance and reduced bacterial growth rate. Compensated mutants that remained fully resistant to actinonin and showed increased growth rates appeared within 30-60 generations of growth. Whole-genome sequencing and localized DNA sequencing of mutated candidate genes showed that alterations in the gene agrC were present in the majority of compensated strains. Resistant and compensated mutants grew at similar rates as the wild-type in a mouse thigh infection model. Resistance to deformylase inhibitors due to fmt mutations reduces bacterial growth rates, but these costs can be reduced by mutations in the agrC gene. Mutants defective in fmt (with or without compensatory agrC mutations) grew well in an animal model, implying that they can also cause infection in a host.

Acylprolinamides: A new class of peptide deformylase inhibitors with in vivo antibacterial activity

A new class of PDF inhibitor with potent, broad spectrum antibacterial activity is described. Optimization of blood stability and potency provided compounds with improved pharmacokinetics that were suitable for in vivo experiments. Compound 5c, which has robust antibacterial activity, demonstrated efficacy in two respiratory tract infection models.

New peptide deformylase inhibitors and cooperative interaction: a combination to improve antibacterial activity

Bacterial drug resistance is a worrying public health problem and there is an urgent need for research and development to provide new antibacterial molecules. Peptide deformylase (PDF) is now a well-described intracellular target selected for the design of a new antibiotic group, PDF inhibitors (PDFIs). The initial bacterial susceptibility to an inhibitor of a cytoplasmic target is directly associated with the diffusion of the compound through the membrane barrier of Gram-negative bacteria and with its cytosolic accumulation at the required concentration. We have recently demonstrated that the activity of different PDFIs is strongly dependent on the accumulation of the active molecules by using permeabilizing agents, efflux inhibitors or efflux-mutated strains. In this work we assessed various combination protocols using different putative inhibitors (PDFIs, methionine aminopeptidase inhibitors etc.) to improve antibacterial activity against various resistant Gram-negative bacteria. The maximum effect was observed when combining actinonin with a dual inhibitor of methionine aminopeptidase and PDF, this molecule being also able to interact with the target while actinonin is bound to the PDF active site. Such a combination of inhibitors acting on two tightly associated metabolic steps results in a cooperative effect on bacterial cells and opens an original way to combat multidrug-resistant bacteria.

Flavimycins A and B, Dimeric 1,3-Dihydroisobenzofurans with Peptide Deformylase Inhibitory Activity from Aspergillus flavipes

Flavimycins A (1) and B (2), novel dimeric 1,3-dihydroisobenzofurans, were isolated as inhibitors of peptide deformylase from cultures of Aspergillus flavipes. Their chemical structures were established by NMR and MS data analysis. Compounds 1 and 2 exist as epimeric mixtures at C-1 through fast hemiacetal-aldehyde tautomerism. Compounds 1 and 2 inhibited Staphylococcus aureus peptide deformylase with IC₅₀ values of 35.8 and 100.1 μM, respectively. Consistent with their PDF inhibition, 1 showed two times stronger antibacterial activity than 2 on S. aureus including MRSA, with MIC values of 32-64 μg/mL.

Determination of Disk Diffusion and MIC Quality Control Ranges for GSK1322322, a Novel Peptide Deformylase Inhibitor

GSK1322322 is a novel peptide deformylase inhibitor in the early phase of development for treatment of complicated bacterial skin and skin structure infection and hospitalized community-acquired pneumonia. This quality control (QC) study was performed to establish broth microdilution and disk diffusion QC ranges for strains Staphylococcus aureus ATCC 29213 (MIC range, 1 to 4 μg/ml), Haemophilus influenzae ATCC 49247 (MIC and disk diffusion zone diameter ranges, 0.5 to 4 μg/ml and 20 to 28 mm, respectively), Streptococcus pneumoniae ATCC 49619 (MIC and disk diffusion zone diameter ranges, 0.12 to 0.5 μg/ml and 23 to 30 mm, respectively), and S. aureus ATCC 25923 (disk diffusion zone diameter range, 18 to 26 mm). These ranges are crucial for evaluating GSK1322322 potency as it progresses through clinical trials.

Non-coding nucleotides and amino acids near the active site regulate peptide deformylase expression and inhibitor susceptibility in Chlamydia trachomatis

Chlamydia trachomatis, an obligate intracellular bacterium, is a highly prevalent human pathogen. Hydroxamic-acid-based matrix metalloprotease inhibitors can effectively inhibit the pathogen both in vitro and in vivo, and have exhibited therapeutic potential. Here, we provide genome sequencing data indicating that peptide deformylase (PDF) is the sole target of the inhibitors in this organism. We further report molecular mechanisms that control chlamydial PDF (cPDF) expression and inhibition efficiency. In particular, we identify the σ66-dependent promoter that controls cPDF gene expression and demonstrate that point mutations in this promoter lead to resistance by increasing cPDF transcription. Furthermore, we show that substitution of two amino acids near the active site of the enzyme alters enzyme kinetics and protein stability.

ChemInform Abstract: Design, Synthesis and Antibacterial Activity of 3‐Methylenepyrrolidine Formyl Hydroxyamino Derivatives as Novel Peptide Deformylase Inhibitors.

AbstractStructural modification of a recently developed PDF inhibitor by replacing the pyrrolidine functionality with 3‐methylenepyrrolidine leads to the discovery of derivatives (I) exhibiting better in vitro antibacterial activity than the reference compounds against drug‐resistant clinical isolates including MRSA, PRSP, and H.

Pharmacokinetics and Unexpected Safety Issues of LBM415, a Novel Oral Peptide Deformylase Inhibitor

Peptide deformylase (PDF) inhibitors represent a potential new class of antibiotics targeting a large number of bacterial species. We studied the pharmacokinetics and safety of LBM415, a novel PDF inhibitor, administered as a single oral dose at 100-3,000 mg in the fasted state and at 1,000 mg in the fed state in healthy volunteers. LBM415 was then administered at dosages ranging from 100 mg q.d. to 1,000 mg t.i.d. for 11 days. Dose-proportional pharmacokinetics was observed, with a peak plasma concentration (C(max)) of 17.85 ± 5.96 µg/ml at 1,000 mg b.i.d. (the projected therapeutic dose) and an area under the concentration-time curve (AUC)(0-24h) of 36.83 ± 10.36 µg/ml·h. The half-life, as determined after a 1,000-mg single dose, was 2.18 ± 0.61 h. The compound was well tolerated at low doses, but at the highest dose, 1,000 mg t.i.d., reversible cyanosis and low oxygen saturation, attributable to methemoglobinemia, were detected on day 11. Oxygen saturation was as low as 88% in one subject on day 11.

Identification of benzofuran-4,5-diones as novel and selective non-hydroxamic acid, non-peptidomimetic based inhibitors of human peptide deformylase

Selective inhibitors of human peptide deformylase (HsPDF) are predicted to constitute a new class of antitumor agents. We report the identification of benzofuran-4,5-diones as the first known selective HsPDF inhibitors and we describe their selectivity profile in a panel of metalloproteases. We characterize their structure-activity relationships for antitumor activity in a panel of cancer cell lines, and we assess their in vivo efficacy in a mouse xenograft model. Our results demonstrate that selective HsPDF inhibitors based on the benzofuran-4,5-dione scaffold constitute a novel class of antitumor agents that are potent in vitro and in vivo.

3D-QSAR and molecular docking studies of hydroxamic acids as peptide deformylase inhibitors

Comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), and molecular docking study were conducted on hydroxamic acids as potent peptide deformylase (PDF) inhibitors. The optimal CoMFA model gave statistically significant results with q2 and r2 values of 0.568 and 0.956, respectively. The optimal CoMSIA model with combination of steric, hydrophobic and H-bond donor fields resulted in the best results with q2 and r2 values of 0.722 and 0.958, respectively. These two models were validated by an external test set of eight compounds with satisfactory predictive r2 values of 0.810 and 0.820, respectively. The contour plots of molecular fields indicated that electrostatic and bulky groups substituted at the R1 position, and electropositive and small substituted at R2 position were favorable for the inhibitory activity. In addition, FlexX docking was employed to investigate the binding mode between PDF and its inhibitors. It was found that hydrogen bond interactions might be an important factor for binding affinity of inhibitors in the hydrophobic cavity. Based on the optimal CoMSIA model and FlexX docking, a series of PDF inhibitors with high predictive activities have been designed. This work might provide valuable information in designing more promising PDF inhibitors.

Expression, purification, and activity assay of peptide deformylase from Escherichia coli and Staphylococcus aureus

Peptide deformylase (PDF) is considered an attractive target for screening novel antibiotics. The PDF from Escherichia coli and Staphylococcus aureus are representative of the gram-negative species type of PDF (type I PDF) and the gram-positive species type of PDF (type II PDF), respectively. They could be used for screening broad-spectrum antibiotics. Herein, we cloned the def gene by PCR, inserted it into plasmid pET-22b-def, and transformed the plasmid into E. coli BL21 (DE3) cells, then the cells were induced by IPTG to express PDF. E. coli Ni(2+)-PDF was extracted and purified by ion-exchange chromatography and gel filtration chromatography. S. aureus PDFs were extracted and purified using the MagExtractor kit. The nickel form of S. aureus PDF was obtained by adding NiCl(2) to all reagents used for purification. Iron-enriched S. aureus PDF was obtained by adding FeCl(3) to the growth medium for E. coli BL21 (DE3) cells and adding FeCl(3) and catalase to all reagents used for purification. The activities of PDFs were analyzed, compared, and grouped according to the experimental conditions that produced optimal activity, and we used actinonin as an inhibitor of PDF and calculated the IC(50) value. We obtained high expression of E. coli and S. aureus PDF with high activity and stability. The function of PDFs was inhibited by actinonin in a dose-dependent manner. Results may be helpful for future mechanistic investigations of PDF as well as high-throughput screening for other PDF inhibitors.

Insights from ligand and structure based methods in virtual screening of selective Ni-peptide deformylase inhibitors

In recent years, there has been a growing interest in developing bacterial peptide deformylase (PDF) inhibitors as novel antibiotics. The purpose of the study is to generate a three-dimensional (3D) pharmacophore model by using diverse PDF inhibitors which is useful for designing of potential antibiotics. Twenty one structurally diverse compounds were considered for the generation of quantitative pharmacophore model using HypoGen of Catalyst, further model was validated using 78 compounds. Pharmacophore model demonstrated the importance of two acceptors, one donor and one hydrophobic feature toward the biological activity. The inhibitors were also docked into the binding site of PDF to comprehend the structural insights of the active site. Combination of ligand and structure based methods were used to find the potential antibiotics.

Peptidomimetic inhibitors of bacterial peptide deformylase

A series of N-formyl hydroxylamine peptide deformylase inhibitors containing a cyclic azaamino acid moiety between the P1' and P3' substituents are presented. Selected compounds display antibacterial activity against pathogens associated with respiratory tract infections with representative compounds showing excellent MICs against Haemophilus influenzae.

Design, synthesis and antibacterial activity of 3-methylenepyrrolidine formyl hydroxyamino derivatives as novel peptide deformylase inhibitors

The synthesis and antibacterial activity of 3-methylenepyrrolidine formyl hydroxyamino derivatives are reported. The antibacterial activities of these derivatives were evaluated to discover SAR at P(1') and P(3') positions, and most of these derivatives exhibit better in vitro antibacterial activity than existing drugs against drug-resistant clinical isolates including MRSA, PRSP, and Haemophilus influenzae.

High tolerance to mutations in a Chlamydia trachomatis peptide deformylase loop

To determine if and how a loop region in the peptide deformylase (PDF) of Chlamydia trachomatis regulates enzyme function. Molecular dynamics simulation was used to study a structural model of the chlamydial PDF (cPDF) and predict the temperature factor per residue for the protein backbone atoms. Site-directed mutagenesis was performed to construct cPDF variants. Catalytic properties of the resulting variants were determined by an enzyme assay using formyl-Met-Ala-Ser as a substrate. In silico analysis predicted a significant increase in atomic motion in the DGELV sequence (residues 68-72) of a loop region in a cPDF mutant, which is resistant to PDF inhibitors due to two amino acid substitutions near the active site, as compared to wild-type cPDF. The D68R and D68R/E70R cPDF variants demonstrated significantly increased catalytic efficiency. The E70R mutant showed only slightly decreased efficiency. Although deletion of residues 68-72 resulted in a nearly threefold loss in substrate binding, this deficiency was compensated for by increased catalytic efficiency. Movement of the DGELV loop region is involved in a rate-limiting conformational change of the enzyme during catalysis. However, there is no stringent sequence requirement for this region for cPDF enzyme activity.

Synthesis and in vitro antibacterial activity of oxazolidine LBM-415 analogs as peptide deformylase inhibitors

The drug resistant bacteria pose a severe threat to human health. The increasing resistance of those pathogens to traditional antibacterial therapy renders the identification of new antibacterial agents with novel antibacterial mechanisms an urgent need. In this study, a series of (2S)-N-substituted-1-[(formyhydroxyamino)methyl]-1-oxohexyl]-2-oxazolidinecarboxamides were designed, synthesized and evaluated for in vitro antibacterial activity. Most of these compounds displayed good activities against Gram-positive organisms comparable to reference agent LBM-415.

Peptide deformylase inhibitors with non-peptide scaffold: Synthesis and structure–activity relationships

Peptide deformylase (PDF), which removes the formyl group at the N-terminal methionine residue of nascent protein, has been recognized as a potent target for antibacterial therapy. We report herein the synthesis and structure–activity relationship studies of non-peptide PDF inhibitors.

Over-expression of peptide deformylase in chloroplasts confers actinonin resistance, but is not a suitable selective marker system for plastid transformation

Arabidopsis thaliana peptide deformylase PDF1B was expressed in tobacco chloroplasts using spectinomycin as the selective agent. The foreign protein accumulated in chloroplasts (6% of the total soluble protein) and was enzymatically active. Transplastomic plants were evaluated for resistance to the peptide deformylase inhibitor actinonin. In vitro seed germination in the presence of actinonin and in planta application of the inhibitor demonstrated the resistance of the transformed plants. In addition, transgenic leaf explants were able to develop shoots via organogenesis in the presence of actinonin. However, when the combination of the PDF1B gene and actinonin was used as the primary selective marker system for chloroplast transformation of tobacco, all developed shoots were escapes. Therefore, under the experimental conditions tested, the use of this system for plastid transformation would be limited to function as a secondary selective marker.