Peptide Deformylase Inhibitors Research Articles

Toward More Selective Antibiotic Inhibitors: A Structural View of the Complexed Binding Pocket of E. coli Peptide Deformylase.

Peptide deformylase (PDF) is involved in bacterial protein maturation processes. Originating from the interest in a new antibiotic, tremendous effort was put into the refinement of PDF inhibitors (PDFIs) and their selectivity. We obtained a full NMR backbone assignment the emergent additional protein backbone resonances of ecPDF 1-147 in complex with 2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide (2), a potential new structural scaffold for more selective PDFIs. We also determined the complex crystal structures of E. coli PDF (ecPDF fl) and 2. Our structure suggests an alternative ligand conformation within the protein, a possible starting point for further selectivity optimization. The orientation of the second ligand conformation in the crystal structure points toward a small region of the S1' pocket, which differs between bacterial PDFs and human PDF. Moreover, we analyzed the binding mode of 2 via NMR TITAN line shape analysis, revealing an induced fit mechanism.

Discovery of novel peptide deformylase inhibitors: Ensemble complex-based pharmacophore modeling, docking and binding affinity studies

Pseudomonas aeruginosa infections are quickly increasing in association with a variety of illnesses, necessitating the development of novel medications. This study employed an in silico technique to find PDF inhibitors against P. aeruginosa Peptide deformylase (PaPDF). PaPDF's structure is comparable to that of other PDFs; however, binding site studies found that PaPDF has a smaller pocket than Staphylococcus aureus, covering the S1 and S2 sub pockets, and maintains a conserved hydrophobic nature. The Zn metal binding site of modified PaPDFs was examined using molecular dynamics, and the results revealed that Cys92Ala differed from His134Ala and His138Ala, respectively. Complex-based pharmacophore investigation revealed three significant pharmacophoric characteristics within the pocket: two hydrophobic and one H-bond acceptor. This allows us to perform virtual screening using the ChemBride database to uncover a variety of potential hits with specific inhibitory characteristics. Several restrictions, including docking and molecular mechanics/general born-volume integral implicit solvent (MM/GBVI), were applied, and the top-ranked ligands were tested for inhibitory characteristics against key residues in the active site. Furthermore, the bioavailability and toxicity prediction identified seven potential leads and suggested future research into the design and synthesis of a unique class of PaPDF inhibitors.

A new inhibitor of human peptide deformylase suppresses cell proliferation and induces cell apoptosis and autophagy in cancers.

Human peptide deformylase (hsPDF) has been found overexpressed in many cancer cells and its inhibitors exhibit antitumor activity. Studies were performed to validate that hsPDF is a good antitumor target. The inhibitory effect of PDF64 on hsPDF enzymatic activity was measured and confirmed by computation analysis. Antiproliferation activity was determined and in-vivo antitumor activity were analyzed in HCT116 and HL60 nude mice xenografts. Mitochondrial membrane potential (MMP), cell apoptosis, and autophagic cell death were analyzed by flow cytometry. ATP level was quantified using an ATP assay kit. Protein expression and kinase phosphorylation were determined by western blotting. A new hsPDF inhibitor PDF64 was identified. It showed evident antiproliferation activity in 10 cancer cells and significantly suppressed tumor growth in HCT116 and HL60 xenografts. It induced an obvious decrease in MMP and caused apparent cell apoptosis and autophagy in HCT116 and Jurkat cells. PDF64 treatment also led to an evident decrease in cellular ATP levels in these cells. Moreover, PDF64 downregulated c-Myc expression and had some effects on extracellular regulated protein kinases (ERK) and protein kinase B (Akt)/ mammalian target of rapamycin (mTOR) pathways. PDF64 exhibited good antitumor effects both in vivo and in vitro . It caused cell apoptosis and autophagic death in HCT116 and Jurkat cells. The effects may be mediated by inhibiting c-Myc expression and ERK or PI3K-Akt-mTOR pathway. Therefore, PDF64 may be a promising reagent for antitumor drug development, which further supports that hsPDF is a good antitumor drug target.

Acarbose Potentially Binds to the Type I Peptide Deformylase Catalytic Site and Inhibits Bacterial Growth: An In Silico and In Vitro Study.

In bacteria, peptide deformylase (PDF), a metalloenzyme, removes N-formyl methionine from a nascent protein, which is a critical step in the protein maturation process. The enzyme is ubiquitously present in bacteria and possesses therapeutic target potential. Acarbose, an FDA-approved antidiabetic drug, is an alpha-glucosidase inhibitor of microbial origin. Clinical studies indicate that acarbose administration in humans can alter gut microbiota. As per the best of our knowledge, the antibacterial potential of acarbose has not been reported. The present study aimed to check the binding ability of acarbose to the catalytic site of E. coli PDF and assess its in vitro antibacterial activity. Molecular docking, molecular dynamic (MD) simulation, and MM-PBSA experiments were performed to study the binding potential of the catalytic site, and a disc diffusion assay was also employed to assess the antibacterial potential of acarbose. Acarbose was found to form a hydrogen bond and interact with the metal ion present at the catalytic site. The test compound showed a better docking score in comparison to the standard inhibitor of PDF. MD simulation results showed energetically stable acarbose-PDF complex formation in terms of RMSD, RMSF, Rg, SASA, and hydrogen bond formation throughout the simulation period compared to the actinonin-PDF complex. Furthermore, MM-PBSA calculations showed better binding free energy (ΔG) of acarbose PDF than the actinonin-PDF complex. Moreover, acarbose showed in vitro antibacterial activity. Acarbose forms conformational and thermodynamically stable interaction with the E. coli peptide deformylase catalytic site. Results of the present work necessitate in-depth antimicrobial potential studies on the effect of acarbose on drug resistance and nonresistant bacteria.

DMAP-catalysed synthesis, antibacterial activity evaluation, cytotoxicity and docking studies of some heterocyclic molecules bearing sulfonamide moiety

DMAP has been shown to be a highly efficient nucleophilic catalyst when compared to triethylamine and pyridine using acetonitrile as solvent for the synthesis of a series of novel N - heterocyclic sulfonamide derivatives. The influence of the reaction parameters, like choice of solvent, catalyst, amount of catalyst and reaction time on product yield has been studied. Antibacterial screening involving a range of sulfonamide analogues as new peptide deformylase (PDF) inhibitors have been focused. The molecules show significant antibacterial activity (MIC value 6.2 − 3.1 µg/mL) against B. subtilis , S. pyrogenes , P. vulgaris and P. mirabilis . Potential in silico docking studies have been in conjugation with in vitro antibacterial results. Molecular docking of all compounds with PDF enzyme (PDB code: 1G2A) explain how certain moieties play significant roles in increasing the binding interactions and stabilizing the protein-ligand complexes. The compounds also have confirmed low extent of cytotoxicity when tested on HEL and HeLa cell lines.

Regioselectivity in inhibition of peptide deformylase from Haemophilus influenzae by 4- vs 5-azaindole hydroxamic acid derivatives: Biochemical, structural and antimicrobial studies

Ribosome assisted protein synthesis in all prokaryotes begins with a formylated methionine. Deformylation and demethionylation of these newly synthesized proteins are critical co-translational events carried out by peptide deformylase (PDF) and methionine aminopeptidase (MetAP) in all living cells. Since the mechanism of N-terminal modification is common between the infectious microbes and the host human cells, it is a challenge to identify selective inhibitors. Given that both MetAP and PDF are metalloenzymes, and have strong affinity for hydroxamic acids, we reasoned that the azaindole-based hydroxamic acids could inhibit the PDF enzymes. In the present study we describe the screening of a 17-compound library with 4- and 5- substituted azaindole hydroxamic acid derivatives against PDF enzyme from H. influenzae (HiPDF), M. tuberculosis (MtPDF) and human PDF (HsPDF). Several of these molecules showed nanomolar inhibition against HiPDF enzyme, best at 21 nM (15). On the other hand, none of these compounds inhibited the human enzyme while only two molecules showed moderate inhibition against Mtb enzyme. Surprisingly only 5-substituted azaindole derivatives inhibited the PDF enzymes. Some of the 5-substituted azaindole compounds inhibited the growth of different microbes indicating their potential application in antimicrobial therapy. Crystallographic and modeling studies provided the mechanistic view of regioselective inhibition.

Therapeutic potential of human serum albumin nanoparticles encapsulated actinonin in murine model of lung adenocarcinoma

Non-small cell lung cancer comprises 85% of the global lung cancer cases. Conventional chemotherapeutics possess certain limitations like systemic toxicity and drug resistance that requires the development of new therapeutic agents for successful treatment of lung cancer. Actinonin, a human peptide deformylase inhibitor, has demonstrated anti-cancerous properties in various leukemias and solid cancer types. However, it has limited therapeutic application because of its low bioavailability and systemic toxicity if administered in free form. This limitation can be overcome by using nano-delivery systems that will increase the therapeutic efficacy of actinonin. In the present study, human serum albumin actinonin nanoparticles were prepared using a desolvation technique and folic acid was conjugated to lysine residues of albumin for effective delivery to the lung. The lung adenocarcinoma model was established 24 weeks after intraperitoneal administration of urethane and chemotherapeutic efficacy of free as well as nanoencapsulated actinonin was evaluated. This study demonstrated anti-proliferative potential of folic acid conjugated human serum albumin nanoparticles encapsulating actinonin. The intraperitoneally administered nanoformulation exhibited sustain release profile of actinonin with longer half-life and mean retention time. The reduced dose frequency resulted in therapeutic efficacy comparable to free drug in vivo in terms of 100% survival and reduced tumor burden along with downregulation of epidermal growth factor receptor, folate receptor α and peptide deformylase expression in lung adenocarcinoma mice model. Therefore, actinonin encapsulated albumin nanoparticles-based therapy holds great potential as an alternative strategy to improve its anti-cancerous activity against lung adenocarcinoma.

System-wide analyses reveal essential roles of N-terminal protein modification in bacterial membrane integrity

SummaryThe removal of the N-terminal formyl group on nascent proteins by peptide deformylase (PDF) is the most prevalent protein modification in bacteria. PDF is a critical target of antibiotic development; however, its role in bacterial physiology remains a long-standing question. This work used the time-resolved analyses of the Escherichia coli translatome and proteome to investigate the consequences of PDF inhibition. Loss of PDF activity rapidly induces cellular stress responses, especially those associated with protein misfolding and membrane defects, followed by a global down-regulation of metabolic pathways. Rapid membrane hyperpolarization and impaired membrane integrity were observed shortly after PDF inhibition, suggesting that the plasma membrane disruption is the most immediate and primary consequence of formyl group retention on nascent proteins. This work resolves the physiological function of a ubiquitous protein modification and uncovers its crucial role in maintaining the structure and function of the bacterial membrane.

Prediction of Pharmacokinetics of IDP-73152 in Humans Using Physiologically-Based Pharmacokinetics.

IDP-73152, a novel peptide deformylase inhibitor with an antibacterial effect against Gram-positive bacteria, is in phase I development. The objective of this study was to develop a physiologically-based pharmacokinetic model (PBPK) for IDP-73152 in animals, and to extend the model to humans. Biopharmaceutical properties of IDP-73152 are determined using in vitro/in vivo experimentations for the PBPK model. A transit model consisting of gastrointestinal segments is applied for an estimation of the intestinal absorption kinetics. The PBPK model of IDP-73152 in rats is able to appropriately predict the plasma concentration–time profiles after the administration of IDP-73152 at different doses and by different routes (combined absolute average fold error (cAAFE), 1.77). The model is also found to be adequate in predicting the plasma concentration–time profiles of IDP-73152 in mice (cAAFE 1.59) and dogs (cAAFE 1.42). Assuming the oral administration of IDP-73152 to humans at doses of 640 and 1280 mg, the model is able to reproduce the concentration–time profiles obtained in humans (cAAFE 1.38); therefore, these observations indicate that the PBPK model used for IDP-73152 is applicable to animal species and humans. This model may be useful in predicting efficacious doses of IDP-73152 for the management of infectious disease in humans.

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.

Ferulic Hydroxamic Acid Triazole Hybrids as Peptide Deformylase Inhibitors: Synthesis, Molecular Modelling and Biological Evaluation

AbstractDesign and development of peptide deformylase (PDF) inhibitors has gained attention as it is a highly conserved and specific enzyme for bacterial protein synthesis. This makes it a specific and attractive drug target. Therefore, based on the targeted drug‐discovery approach, a series of ferulic acid‐based nonpeptidic hydroxamic acid‐triazole hybrids was synthesized. All the semi‐synthetic compounds (8 a–p) were evaluated against a panel of Gram‐positive and Gram‐negative bacterial strains. Most of the compounds showed antibacterial activities against S. pneumoniae while few were active against E. coli. Among all, the compound 8 j showed strong potency against S. pneumoniae with IC50 value 34.57 μg/mL whereas for E. coli the observed IC50 was 66.20 μg/mL. Growth kinetics study showed the bacteriostatic nature of compound 8 j against S. pneumoniae. Interestingly, in the studied concentration range, no significant hemolysis or cytotoxicity was observed towards human cells, suggesting the non‐toxic nature of compound 8 j. Molecular docking studies showed that compound 8 j occupies the same active site where actinonin (a known inhibitor of PDF) binds and it also mimics the mode of interactions by offering significant interactions with the corresponding amino acid residues of PDF. The outcome of this study suggested the potential implications of the present scaffold for the development of antibacterial molecules targeting PDF.

Moving away from traditional antibiotic treatment: can macrocyclic lactones from marine macroalga-associated heterotroph be the alternatives?

Intertidal red algae Hypnea valentiae associated Bacillus amyloliquefaciens MTCC 12716 revealed potential inhibitory effects on the growth of drug-resistant pathogens. In the genome of B. amyloliquefaciens MTCC 12716, biosynthetic gene clusters encoding antibacterial metabolites were predicted, which might be expressed and contributed to the broad-spectrum anti-infective activity. Three homologue members of the 24-membered macrocyclic lactone family, named as bacvalactones 1-3 bearing 13-O-ethyl (1); 15-O-furanyl-13-O-isobutyl-7-O-propyl-propanoate (2); and 15-O-furanyl-13-O-isobutyl-7-O-propyl-propanoate-7,24-dimethyl (3) functionalities, were acquired through bioactivity-guided purification. The macrocyclic lactones displayed bactericidal activity against opportunistic pathogens causing nosocomial infections, for instance, methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecalis (VREfs), and multidrug-resistant strains of Pseudomonas aeruginosa and Klebsiella pneumonia with MIC ≤ 3.0μg/mL, whereas standard antibiotics ampicillin and chloramphenicol were active only at concentrations of ≥ 6.25mg/mL. The biosynthetic pathway of macrocyclic lactones that are generated by trans-AT polyketide synthases through stepwise extension of an acetyl starter unit by eleven sequential Claisen condensations with malonyl-CoA was established, and the structures were correlated with the gene organization of the mln operon, which encompasses nine genes mln A-I (approximately 47kb in size). The best binding poses for each compounds (1-3) with Staphylococcus aureus peptide deformylase (SaPDF) unveiled docking scores (≥ 9.70kcal/mol) greater than that of natural peptide deformylase inhibitors, macrolactin N and actinonin (9.14 and 6.96kcal/mol, respectively), which supported their potential in vitro bioactivities. Thus, the present work demonstrated the potential of macrocyclic lactone for biotechnological and pharmaceutical applications against emerging multidrug-resistant pathogens. Key Points •Three antibacterial bacvalactones were identified from the symbiotic bacterium. •The symbiotic bacterial genome was explored to identify the biosynthetic gene clusters. •Trans-AT pks-assisted mln biosynthetic pathway of the macrocyclic lactone was proposed. •In silicomolecular interactions of the bacvalactones with S. aureus PDF were analyzed.

The search for peptide deformylase inhibitor from Indonesian Medicinal Plant Database: an in-silico investigation

The peptide deformylase protein (PDF) has emerged as a promising target for the discovery of novel antibiotics with a novel mechanism of action. The current investigation was aimed at identifying potential inhibitor of PDF by using structure-based pharmacophore modelling. The pharmacophore hypothesis consisted of one hydrophobic, one negative ionizable, and one hydrogen bond donor features which were built using the structure of cognate ligand of PDF (BB2). Further, the pharmacophore model was validated and used to screen hit molecule against Indonesian Medicinal Plant Database and retrieved 32 hit molecules. All hit molecules were docked to PDF and four best molecules were subjected for 50-ns molecular dynamics (MD) simulation. MD simulation confirmed the docked poses of ligand as indicated by the RMSD and RMSF values. Prediction of affinities employing Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) method revealed that quercetin 3-(6''-malonylneohesperidoside) had a comparable affinity with that of BB2, which indicated its potential as a novel herbal-based PDF inhibitor.

Oxygenated elansolid-type of polyketide spanned macrolides from a marine heterotrophic Bacillus as prospective antimicrobial agents against multidrug-resistant pathogens

Three homologous oxygenated elansolid-type of polyketide spanned macrolides were isolated from a heterotrophic marine bacterium, Bacillus amyloliquefaciens MTCC 12716, associated with an intertidal red alga Hypnea valentiae. The complete genome of the bacterium was sequenced and all detectable natural product gene clusters were analysed. The B. amyloliquefaciens MTCC 12716 genome features polyketide synthase (pks) systems of every known formally classified family, nonribosomal peptide synthetases and hybrid clusters. Comprehensive spectroscopic studies revealed the compounds to possess isobenzofuranyl benzoate and 1H-furopyrano[2,3-c]oxacyclononadecine-6-carboxylate moieties. The identified compounds displayed broad-spectrum bactericidal activity against methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecalis, and drug-resistant strains of Pseudomonas aeruginosa and Klebsiella pneumoniae with minimum inhibitory concentrations (MICs) of ≤1.0 µg/mL, whereas the standard antibiotics ampicillin and chloramphenicol were active only at concentrations of ≥6.25 µg/mL. The plausible mechanism of elansolid-type macrolide biosynthesis by trans-AT polyketide synthases through the pks starter unit para-hydroxybenzoic acid was hypothesised, and the structures were correlated with the gene organisation, with the predicted gene cluster comprising 16 genes (~81 kb in size). The best binding poses for each compound with the peptide deformylase (PDF) protein of S. aureus revealed docking scores (>11.30 kcal/mol) greater than actinonin (6.96 kcal/mol), a natural PDF inhibitor. The higher electronic values along with optimum lipophilic parameters support the potential anti-infective properties of the studied macrolides. These antibacterial elansolid-type of polyketide spanned macrolides in marine symbiotic B. amyloliquefaciens could be potential leads for biotechnological and pharmaceutical applications against emerging multidrug-resistant pathogens.

Synthesis and characterisation of Co(iii) complexes of N-formyl hydroxylamines and antibacterial activity of a Co(iii) peptide deformylase inhibitor complex.

The X-ray crystal structure and pKa values of GSK322, a well-known and effective peptide deformylase inhibitor and antibacterial drug candidate, are reported. The first examples of Co(iii) complexes of N-formyl hydroxylamines are reported. Reaction of N-hydroxy-N-phenylformamide (HFA) with [Co(tren)Cl2]Cl and [Co(tpa)Cl2]Cl (where tren = tris(2-aminoethyl)amine, tpa = tris(2-pyridylmethyl)amine) with one equivalent of NaOH in H2O afforded [Co(tren)(HFA-1H)](PF6)1.5Cl0.5 (1) and [Co(tpa)(HFA-1H)]Cl2 (2), respectively. X-ray crystal structures of both complexes revealed that the N-formyl hydroxylamine group acts as a bidentate ligand, coordinating the Co(iii) centres via the carbonyl oxygen and deprotonated hydroxy group (O,O'), a coordination mode typically observed for closely related mono-deprotonated hydroxamic acids. Reaction of the N-formyl hydroxylamine-based GSK322 with [Co(tpa)Cl2]Cl afforded the corresponding Co(iii) chaperone complex of the peptide deformylase inhibitor, [Co(tpa)(GSK322-1H)](PF6)2. GSK322 and [Co(tpa)(GSK322-1H)](PF6)2 exhibited better Gram-positive activity than Gram-negative, where low MICs (1.56-6.25 μM) were determined for S. aureus strains, independent of their antibiotic susceptibility.

Inhibitors of Selected Bacterial Metalloenzymes.

The utilization of bacterial metalloenzymes, especially ones not having mammalian (human) counterparts, has drawn attention to develop novel antibacterial agents to overcome drug resistance and especially multidrug resistance. In this review, we focus on the recent achievements on the development of inhibitors of bacterial enzymes peptide deformylase (PDF), metallo-β-lactamase (MBL), methionine aminopeptidase (MetAP) and UDP-3-O-acyl- N-acetylglucosamine deacetylase (LpxC). The state of the art of the design and investigation of inhibitors of bacterial metalloenzymes is presented, and challenges are outlined and discussed.

Pharmacokinetics and tolerability of IDP-73152 mesylate after a single oral administration under fasted and fed conditions in healthy volunteers.

Background and objectiveIDP-73152 mesylate is a peptide deformylase inhibitor under investigation for the treatment of complicated skin and respiratory tract infections. The objective of this study was to investigate the pharmacokinetic (PK) profile and tolerability of IDP-73152 and the effect of food after a single oral administration.MethodsA dose block-randomized, double-blind, placebo-controlled, dose-escalation study was conducted. A total of 56 healthy volunteers received IDP-73152 mesylate in a single oral dose of 40, 80, 160, 320, 640, or 1280 mg in the fasted and fed (640 mg only) states. Blood and urine samples for PK analysis were collected up to 48 h post dose.ResultsThe area under the plasma concentration-time curve (AUC0-t) of IDP-73152 increased in a dose-proportional manner in the range of 40–320 mg. The mean terminal half-life decreased from 10.7 to 6.2 hrs as the dose increased. The fraction excreted unchanged in the urine ranged from 0.05 to 0.12. In the 640-mg dose group, food delayed the median time to peak concentration (tmax) from 0.9 to 3.5 hrs. Furthermore, the maximum plasma concentration (Cmax) were decreased by 36.2%; however, AUC0-t was not generally affected. No serious adverse event or clinically significant findings were observed.ConclusionsThe systemic exposure of IDP-73152 proportionally increased as the dose increased up to 320 mg. The rate of absorption and extent of exposure were reduced by food intake. IDP-73152 was well tolerated without clinically significant adverse effects after a single oral administration.

In Silico Study to Assess Antibacterial Activity from Cladophora Sp. on Peptide Deformylase: Molecular Docking Approach

Increasing antibiotic-resistant pathogenic bacteria is a severe problem in the world. Therefore, there is a need to identify new drugs from natural products and also new drug targets. Cladophora sp. is a marine organism which is known to have bioactive compounds and a potential antibacterial. On the other hand, Peptide Deformylase (PDf) may prove to be a novel drug target since it is crucial for native peptide functioning in most pathogenic bacteria. This study screens for PDf inhibition activity of compounds from Cladophora sp. using molecular docking approach and screening the binding affinity of bioactive compounds against the peptide receptor PDf using Pyrex Autodock Vina software. Docking results were stored and visualized using Biovia Discovery Studio and PyMOL ligand. Ligands were obtained from previous literature in PubChem, and receptor peptide PDf from pathogenic bacteria: Pseudomonas aeruginosa (PDB ID:1N5N), Escherichia coli (PDB ID:1BSK), Enterococcus faecium (PDB ID:3G6N) and Staphylococcus aureus (PDB ID:1LQW), was obtained from the peptide data bank. The results of this screening show with ligand the highest binding affinity against PDf of P. aeruginosa, E. coli, E. faecium, and S. aureus is stearic acid (-5.9 kcal/mol), eicosapentaenoic acid (-6.6 kcal/mol), stearic acid (-5.8 kcal/mol), and stearic acid (-6.2 kcal/mol) respectively. The binding of natural compounds from Cladophora sp. with PDf models may provide a new drug with a different drug target for antibacterial potential.

Discovery of piperazic acid peptide deformylase inhibitors with in vivo activity for respiratory tract and skin infections

The discovery of a novel series of peptide deformylase inhibitors incorporating a piperazic acid amino acid found in nature is described. These compounds demonstrated potent in vitro enzymatic potency and antimicrobial activity. Crystal structure analysis revealed the piperazic acid optimized a key contact with the PDF protein that accounted for the increased enzymatic potency of these compounds. We describe lead optimization of the P3' region of the series that resulted in a compound with good potency against three target organisms. One molecule showed in vivo efficacy in a rat respiratory infection model but ultimately did not meet candidate progression criteria.

Total synthesis of (±)-fumimycin and analogues for biological evaluation as peptide deformylase inhibitors

A concise 7-step total synthesis of (±)-fumimycin in 11.6% overall yield is reported. An acid-catalyzed intramolecular aza-Friedel–Crafts cyclization was developed to construct the benzofuranone skeleton of the natural product bearing an α,α-disubstituted amino acid moiety in a single step. Regioselective chlorination followed by a Suzuki–Miyaura cross-coupling rapidly enabled the preparation of a library of analogues which were evaluated against peptide deformylase for antibacterial activity.