Potent Peptide Deformylase Inhibitors Research Articles

Design, one-pot synthesis, molecular docking study, and antibacterial evaluation of novel 2H-chromene based imidazo[1,2-a]pyridine derivatives as potent peptide deformylase inhibitors

An efficient, environmentally friendly, one-pot three-component synthesis of a series of 2H-chromene-based imidazo[1,2-a]pyridines had been designed and were synthesized. This protocol was developed by the reaction of substituted 2H-chromene aldehydes and 2-aminopyridine in a mixture of nitroalkane and DMF under microwave irradiation at 60W, 100°C in 15 min with the presence of FeCl3 as the catalyst. The products were obtained in excellent yields with high functional group tolerance. All these compounds had been investigated further in vitro for evaluation of antibacterial potency by agar-well diffusion method against human pathogenic Gram-positive and Gram-negative bacteria, with the determination of minimum inhibitory concentration (MIC) values. Indeed, compound 13i strongly inhibited peptide deformylase (MIC = 16 μg/ml) in the Gram-negative Escherichia coli, in silico. From structure-activity relationships based on the biological and molecular docking results and the potent antibacterial activities, it could be stated that the selected synthetic compounds could be used as potent drugable antibacterial agents.

Biphenyl tetrazole-thiazolidinediones as novel bacterial peptide deformylase inhibitors: Synthesis, biological evaluations and molecular docking study.

Herein, we report the synthesis and screening of biphenyl tetrazole-thiazolidinediones 14(a-j) as bacterial Peptide deformylase (PDF) enzyme inhibitors. The compounds 14b (IC50 value=16.25μM), 14c (IC50 value=18.00μM) and 14h (IC50 value=17.25μM) had shown good PDF inhibition activity. The compounds 14b (MIC range=20.75-35.41μg/mL), 14c (MIC range=19.41-26.00μg/mL) and 14d (MIC range=8.41-8.58μg/mL) had also shown potent antibacterial activity when compared with standard ciprofloxacin (MIC range=25-50μg/mL). Thus, the active derivatives were not only potent PDF inhibitors but also efficient antibacterial agents. In order to gain more insight on the binding mode of the compounds with PDF enzyme, the synthesized compounds 14(a-j) were docked against PDF enzyme of E. coli and compounds exhibited good binding properties. The results suggest that this class of compounds have been potential for development and use in a future as antibacterial drugs.

Ligand and Structure-Based Approaches for the Identification of Peptide Deformylase Inhibitors as Antibacterial Drugs.

Peptide deformylase (PDF) is a metalloprotease catalyzing the removal of a formyl group from newly synthesized proteins, which makes it an important antibacterial drug target. Given the importance of PDF inhibitors like actinonin in antibacterial drug discovery, several reported potent PDF inhibitors were used to develop pharmacophore models using the Galahad module of Sybyl 7.1 software. Generated pharmacophore models were composed of two donor atom centers, four acceptor atom centers and two hydrophobic groups. Model-1 was screened against the Zinc database and several compounds were retrieved as hits. Compounds with Qfit values of more than 60 were employed to perform a molecular docking study with the receptor Escherichia coli PDF, then compounds with docking score values of more than 6 were used to predict the in silico pharmacokinetic and toxicity risk via OSIRIS property explorer. Two known PDF inhibitors were also used to perform a molecular docking study with E. coli PDF as reference molecules. The results of the molecular docking study were validated by reproducing the crystal structure of actinonin. Molecular docking and in silico pharmacokinetic and toxicity prediction studies suggested that ZINC08740166 has a relatively high docking score of 7.44 and a drug score of 0.78.

Bacterial Peptide deformylase inhibition of cyano substituted biaryl analogs: Synthesis, in vitro biological evaluation, molecular docking study and in silico ADME prediction

Herein, we report the synthesis and screening of cyano substituted biaryl analogs 5(a–m) as Peptide deformylase (PDF) enzyme inhibitors. The compounds 5a (IC50 value=13.16μM), 5d (IC50 value=15.66μM) and 5j (IC50 value=19.16μM) had shown good PDF inhibition activity. The compounds 5a (MIC range=11.00–15.83μg/mL), 5b (MIC range=23.75–28.50μg/mL) and 5j (MIC range=7.66–16.91μg/mL) had also shown potent antibacterial activity when compared with ciprofloxacin (MIC range=25–50μg/mL). Thus, the active derivatives were not only potent PDF inhibitors but also efficient antibacterial agents. In order to gain more insight on the binding mode of the compounds with PDF, the synthesized compounds 5(a–m) were docked against PDF enzyme of Escherichia coli and compounds exhibited good binding properties. In silico ADME properties of synthesized compounds were also analyzed and showed potential to develop as good oral drug candidates.

Synthesis, antibacterial activity, and biological evaluation of formyl hydroxyamino derivatives as novel potent peptide deformylase inhibitors against drug-resistant bacteria

Peptide deformylase (PDF) has been identified as a promising target for novel antibacterial agents. In this study, a series of novel formyl hydroxyamino derivatives were designed and synthesized as PDF inhibitors and their antibacterial activities were evaluated. Among the potent PDF inhibitors (1o, 1q, 1o′, 1q′, and 1x), in vivo studies showed that compound 1q possesses mild toxicity, a good pharmacokinetic profile and protective effects. The good in vivo efficacy and low toxicity suggest that this class of compounds has potential for development and use in future antibacterial drugs.

Penetration of GSK1322322 into Epithelial Lining Fluid and Alveolar Macrophages as Determined by Bronchoalveolar Lavage

GSK1322322 is a potent peptide deformylase inhibitor with in vitro and in vivo activity against multidrug-resistant skin and respiratory pathogens. This report provides plasma and intrapulmonary pharmacokinetics, safety, and tolerability of GSK1322322 after repeat (twice daily intravenous dosing for 4 days) dosing at 1,500 mg. Plasma samples were collected over the last 12-hour dosing interval of repeat dosing following the day 4 morning dose (the last dose). Bronchoalveolar lavage samples were collected once in each subject, either before or at 2 or 6 h after the last intravenous dose. Plasma area under the concentration-time curve (AUC0-τ) was 66.7 μg · h/ml, and maximum concentration of drug in serum (Cmax) was 25.4 μg/ml following repeat doses of intravenous GSK1322322. The time course of epithelial lining fluid (ELF) and alveolar macrophages (AM) mirrored the plasma concentration-time profile. The AUC0-τ for ELF and AM were 78.9 μg · h/ml and 169 μg · h/ml, respectively. The AUC0-τ ratios of ELF and AM to total plasma were 1.2 and 2.5, respectively. These ratios increased to 3.5 and 7.4, respectively, when unbound plasma was considered. These results are supportive of GSK1322322 as a potential antimicrobial agent for the treatment of lower respiratory tract bacterial infections caused by susceptible pathogens. (This study has been registered at ClinicalTrials.gov under registration number NCT01610388.).

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.

Discovery and Refinement of a New Structural Class of Potent Peptide Deformylase Inhibitors

New classes of antibiotics are urgently needed to counter increasing levels of pathogen resistance. Peptide deformylase (PDF) was originally selected as a specific bacterial target, but a human homologue, the inhibition of which causes cell death, was recently discovered. We developed a dual-screening strategy for selecting highly effective compounds with low inhibition effect against human PDF. We selected a new scaffold in vitro that discriminated between human and bacterial PDFs. Analyses of structure-activity relationships identified potent antibiotics such as 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide (6b) with the same mode of action in vivo as previously identified PDF inhibitors but without the apoptotic effects of these inhibitors in human cells.

Synthesis and Biological Evaluation of N-Formyl Hydroxylamine Derivatives as Potent Peptide Deformylase Inhibitors

Antibacterial resistance to hospital-acquired Grampositive bacterial pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), penicillin-resistant Streptococcus pneumoniae (PRSP), and vancomycin-resistant enterococci (VRE), has been increasing at an alarming rate. Therefore there is an urgent need to identify novel antibacterial drugs with new modes of action. Peptide deformylase (PDF), which catalyzes the removal of the N-terminal formyl group from newly synthesized polypeptides and is essential in a variety of pathogenic bacteria but is not required for cytoplasmic protein synthesis in eukaryotes, is an attractive target for the discovery of novel antibiotics. Many PDF inhibitors have been reported in recent years, some of which showed excellent antibacterial activity in vitro and in animal models. Amongst these inhibitors, NVPPDF-713 (2, Vicuron and Novartis) and BB-83698 (3, Vernalis) are currently in phase I clinical trials for the treatment of respiratory tract infections (Fig. 1). Based on the mechanism of deformylation of peptides and the pharmacophore requirements for PDF inhibitor, a new series of arylamidopiperidine derivatives at the P3' position was designed and synthesized. We chose tert-leucine as the P2' residue because other PDF inhibitors containing this P2' residue have shown excellent antibacterial activity and bioavailability. We report here the synthesis and preliminary in vitro evaluation of a new series of PDF inhibitors having an arylamidopiperidine at P3' position. The general route for the synthesis of the arylamidopiperidine derivatives is outlined in Scheme 1. The 1-Boc-4aminopiperidine 6 was prepared in two steps from commercially available N-Boc-piperidin-4-one 5 by reductive amination with benzyl amine followed by hydrogenolysis of the benzyl group. Acylation of the 4-amino group was readily accomplished by treating 6 with p-substituted benzoyl chloride to yield intermediate 7. The piperidine hydrochloride 7 was subsequently coupled by standard peptide coupling conditions using N-Boc-L-tert-leucine to give amide 8. Removal of the N-Boc group with HCl (g)/EtOAc gave amine hydrochloride 9. The N-formyl hydroxylamine analogues were synthesized as shown in Scheme 2. The required chiral intermediate 11 containing the P1' residue was prepared by using Evan’s asymmetric alkylation methodology described previously literature. Reaction of (S)-4-benzyl-2-oxazolidinone with acid 10 in the presence of n-BuLi provided the corresponding oxazolidinone amide. Trichlorotitanium enolate of oxazolidinone amide in CH2Cl2 was obtained by treatment of the amide successively with 1.1 equiv each of TiCl4 and Et3N. Subsequent treatment of this enolate with 2.0 equiv of benzyl chloromethyl ether provided 11 selectively in 90% yield. Removal of the auxiliary group of 11 by hydrolysis under

The Crystal Structure of Mitochondrial (Type 1A) Peptide Deformylase Provides Clear Guidelines for the Design of Inhibitors Specific for the Bacterial Forms

Peptide deformylase (PDF) inhibitors have a strong potential to be used as a new class of antibiotics. However, recent studies have shown that the mitochondria of most eukaryotes, including humans, contain an essential PDF, PDF1A. The crystal structure of the Arabidopsis thaliana PDF1A (AtPDF1A), considered representative of PDF1As in general, has been determined. This structure displays several similarities to that of known bacterial PDFs. AtPDF1A behaves as a dimer, with the C-terminal residues responsible for linking the two subunits. This arrangement is similar to that of Leptospira interrogans PDF, the only other dimeric PDF identified to date. AtPDF1A is the first PDF for which zinc has been identified as the catalytic ion. However, the zinc binding pocket does not differ from the binding pockets of PDFs with iron rather than zinc. The crystal structure of AtPDF1A in complex with a substrate analog revealed that the substrate binding pocket of PDF1A displays strong modifications. The S1' binding pocket is significantly narrower, due to the creation of a floor from residues present in all PDF1As but not in bacterial PDFs. A true S3' pocket is created by the residues of a helical CD-loop, which is very long in PDF1As. Finally, these modified substrate binding pockets modify the position of the substrate in the active site. These differences provide guidelines for the design of bacterial PDF inhibitors that will not target mitochondrial PDFs.

Therapeutic potential of peptide deformylase inhibitors

Peptide deformylase (PDF) is an attractive target for antibacterial drug discovery. Progress in the biological characterisation of the enzyme, coupled with newly obtained mechanistic and structural insight, enabled the pharmaceutical industry to discover potent PDF inhibitors that can be considered as clinical development candidates for this new class of antibacterial agents. The in vitro and in vivo data for several lead PDF inhibitors suggest that the current PDF inhibitors are most suitable for the treatment of respiratory tract infections and they are not cross-resistant to the current clinically used antibiotics. Two PDF inhibitors, BB-83698 and VIC-104959, have progressed to Phase I clinical trials by intravenous and oral administration, respectively. Both of these compounds show promising in vitro and in vivo efficacy and an excellent safety profile. The pharmacokinetics in humans for both of the compounds suggest the possibility of a twice-daily dosing regimen for clinical use. Thus far, all of the data suggest a promising future for this new class of antibacterial agents.

Bacterial Peptide Deformylase Inhibitors: A New Class of Antibacterial Agents

Peptide deformylase (PDF) is a prokaryotic metalloenzyme that is essential for bacterial growth but is not required by mammalian cells. Thus, it represents a selective and promising target for the development of new antibacterial agents. Since deformylase inhibitors have yet to be used clinically as antibacterial drugs, compounds targeting this enzyme should avoid cross-resistance with currently used antibacterial agents. The PDF enzyme is a ferrous ion-containing metallohydrolase, but a nickel-containing surrogate is routinely used in the laboratory for testing inhibitors due to its better stability. Enzymes from several bacterial species have been cloned and both their three-dimensional structures and co-crystal structures with bound inhibitor have been determined. As a metallo enzyme, PDF lends itself to the well-precedented mechanism-based rational drug design approach. Using structural and mechanistic information together with high throughput screening, several types of potent PDF inhibitors have been identified. PDF inhibitors identified to date share a common structural feature of a "chelator + peptidomimetic" scaffold. Although compounds with many different chelators inhibit the cell free enzyme, only compounds containing hydroxamic acid or N-formyl hydroxylamine exhibit appreciable antibacterial activity. Several lead inhibitors have demonstrated in vivo efficacy and an excellent safety profile. Two PDF inhibitors, VIC-104959 (LBM415) and BB-83698, have progressed to Phase I clinical trials. In this review, different PDF inhibitors are compared and their biological activities are discussed. Structure-activity relationships have been established and the implications of this work in the design of future PDF inhibitors are considered.

PDF Inhibitors: An Emerging Class of Antibacterial Drugs

The metalloenzyme peptide deformylase (PDF) represents one of the most promising bacterial targets in the search for novel mode of action antibiotics that lack cross-resistance to existing drugs. Initial research and clinical development has focused on anti-pneumococcal applications. During optimization, peptide analogs were developed containing either a hydroxamate or formyl-hydroxylamine as metal interacting group, yielding inhibitors with in vitro activity against a broad spectrum of organisms. Preclinical studies revealed potent antibacterial activity in vivo that is paired with good pharmacokinetic properties and excellent tolerability in different species. BB-83698, a potent PDF inhibitor with i.v. and oral efficacy in preclinical animal models, represents the first class-representative compound evaluated in man. The inhibitor was administered by i.v. infusion and was shown to exhibit generally dose-proportional pharmacokinetics. It was well tolerated up to doses providing predicted therapeutic exposures. These human results, combined with the preclinical information, clearly support the potential of PDF inhibitors for development as a novel class of antibacterial therapeutics.

Identification of novel potent bicyclic peptide deformylase inhibitors

Screening of our compound collection using Staphylococcus aureus Ni–Peptide deformylase (PDF) afforded a very potent PDF inhibitor with an IC 50 in the low nanomolar range but with poor antibacterial activity (MIC). Three-dimensional structural information obtained from Pseudomonas aeruginosa Ni–PDF complexed with the inhibitor suggested the synthesis of a variety of analogues that would maintain high binding affinity while attempting to improve antibacterial activity. Many of the compounds synthesized proved to be excellent PDF–Ni inhibitors and some showed increased antibacterial activity in selected strains.

Binding affinities and geometries of various metal ligands in peptide deformylase inhibitors

Removal of the N-terminal formyl group from newly synthesized proteins by the enzyme peptide deformylase (PDF) is essential for normal growth of bacteria but not higher organisms. Recently, PDF has been explored as a target for novel antibiotics. Screening a collection of natural products for antimicrobial activity identified actinonin and two matlystatin analogs as potent PDF inhibitors. A number of synthetic analogs of these natural products were prepared and their inhibitory potency determined. Previous work has shown that PDF is an iron metalloproteinase also containing a catalytic glutamic acid residue. Ligation of the ferrous cation is an essential feature of potent inhibitors. The structures of actinonin, a matlystatin analog and a synthetic inhibitor complexed with PDF were determined by crystallography. A quantum mechanics/molecular mechanics (QM/MM) method was used to reproduce the geometry of known complexes, to predict the protonation state in the active site and to predict the geometry of additional complexes. The requirement for protonation of the active site glutamate anion is an important factor in understanding the potency of inhibitors with acidic iron-ligating groups such as hydroxamate and carboxylate. Even though potent inhibitors of PDF have been discovered, their bacteriostatic mechanism of action and the rapid development of resistance in vitro may limit their potential as antibacterial drugs.

Asymmetric synthesis of bb-3497—A potent peptide deformylase inhibitor

By screening a library of metalloenzyme inhibitors, the N-formyl-hydroxylamine derivative BB-3497 was identified as a potent inhibitor of Escherichia coli peptide deformylase with antibacterial activity both in vitro and in vivo. The homochiral synthesis of BB-3497, involving a novel asymmetric Michael addition reaction is described.

2-(2-Oxo-1,4-dihydro-2H-quinazolin-3-yl)- and 2-(2,2-dioxo-1,4-dihydro-2H-2lambda6-benzo[1,2,6]thiadiazin-3-yl)-N-hydroxy-acetamides as potent and selective peptide deformylase inhibitors.

Potent, selective, and structurally new inhibitors of the Fe(II) enzyme Escherichia coli peptide deformylase (PDF) were obtained by rational optimization of the weakly binding screening hit (5-chloro-2-oxo-1,4-dihydro-2H-quinazolin-3-yl)-acetic acid hydrazide (1). Three-dimensional structural information, gathered from Ni-PDF complexed with 1, suggested the preparation of two series of related hydroxamic acid analogues, 2-(2-oxo-1,4-dihydro-2H-quinazolin-3-yl)-N-hydroxy-acetamides (A) and 2-(2,2-dioxo-1,4-dihydro-2H-2lambda(6)-benzo[1,2,6]thiadiazin-3-yl)-N-hydroxy-acetamides (B), among which potent PDF inhibitors (37, 42, and 48) were identified. Moreover, two selected compounds, one from each series, 36 and 41, showed good selectivity for PDF over several endoproteases including matrix metalloproteases. However, these compounds showed only weak antibacterial activity.

Identification of a potent peptide deformylase inhibitor from a rationally designed combinatorial library.

Peptide deformylase catalyzes the removal of the N-terminal formyl group from nascent polypeptides during prokaryotic protein synthesis and maturation and is essential for bacterial survival. Its apparent absence from mammalian organisms makes it an attractive target for designing novel antibacterial agents. Based on the substrate specificity of peptide deformylase from Escherichia coli, a focused library of peptide thiols was synthesized on TentaGel resin using a disulfide linkage. Screening of the library against the purified deformylase was carried out in solution phase after the inhibitors were released from the resin with a reducing agent. A potent deformylase inhibitor was obtained from a 750-member library and was further optimized through rational modification into a low nanomolar inhibitor (KI = 15 nM against E. coli deformylase).

Hydroxamic acid derivatives as potent peptide deformylase inhibitors and antibacterial agents.

Low-molecular-weight beta-sulfonyl- and beta-sulfinylhydroxamic acid derivatives have been synthesized and found to be potent inhibitors of Escherichia coli peptide deformylase (PDF). Most of the compounds synthesized and tested displayed antibacterial activities that cover several pathogens found in respiratory tract infections, including Chlamydia pneumoniae, Mycoplasma pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. The potential of these compounds as antibacterial agents is discussed with respect to selectivity, intracellular concentrations in bacteria, and potential for resistance development.

Actinonin, a naturally occurring antibacterial agent, is a potent deformylase inhibitor.

Peptide deformylase (PDF) is essential in prokaryotes and absent in mammalian cells, thus making it an attractive target for the discovery of novel antibiotics. We have identified actinonin, a naturally occurring antibacterial agent, as a potent PDF inhibitor. The dissociation constant for this compound was 0.3 x 10(-)(9) M against Ni-PDF from Escherichia coli; the PDF from Staphylococcus aureus gave a similar value. Microbiological evaluation revealed that actinonin is a bacteriostatic agent with activity against Gram-positive and fastidious Gram-negative microorganisms. The PDF gene, def, was placed under control of P(BAD) in E. coli tolC, permitting regulation of PDF expression levels in the cell by varying the external arabinose concentration. The susceptibility of this strain to actinonin increases with decreased levels of PDF expression, indicating that actinonin inhibits bacterial growth by targeting this enzyme. Actinonin provides an excellent starting point from which to derive a more potent PDF inhibitor that has a broader spectrum of antibacterial activity.