Showing papers by "Jon Clardy published in 2006"

New antibiotics from bacterial natural products.

Abstract: For the past five decades, the need for new antibiotics has been met largely by semisynthetic tailoring of natural product scaffolds discovered in the middle of the 20(th) century. More recently, however, advances in technology have sparked a resurgence in the discovery of natural product antibiotics from bacterial sources. In particular, efforts have refocused on finding new antibiotics from old sources (for example, streptomycetes) and new sources (for example, other actinomycetes, cyanobacteria and uncultured bacteria). This has resulted in several newly discovered antibiotics with unique scaffolds and/or novel mechanisms of action, with the potential to form a basis for new antibiotic classes addressing bacterial targets that are currently underexploited.

A biosynthetic gene cluster for the acetyl-CoA carboxylase inhibitor andrimid.

Abstract: Increasing bacterial resistance to antibiotics with conventional targets has focused attention on antibiotics with unconventional targets One promising candidate, the acetyl-CoA carboxylase (ACC) inhibitor andrimid, is a potent, broad-spectrum antibiotic with high selectivity for prokaryotic ACC Here, we report the use of a DNA-based approach to clone the andrimid biosynthetic gene cluster from Pantoea agglomerans, yielding a cosmid that confers robust andrimid production on Escherichia coli This gene cluster encodes a hybrid nonribosomal peptide/polyketide (NRP/PK) synthase with several unusual features, including three enzymes that form and insert beta-phenylalanine, two transglutaminase-like enzymes that likely serve as condensation catalysts, and four densely hybrid modules that form the succinimide precursor Unlike most type I NRPSs and PKSs, the andrimid gene cluster is a dissociated system comprised of small proteins Therefore, future efforts can exploit the genetic manipulability of E coli to engineer the andrimid synthase with the goal of producing a diverse set of andrimid analogues for clinical evaluation

Structure of Plasmodium falciparum dihydroorotate dehydrogenase with a bound inhibitor.

Abstract: Membrane-associated dihydroorotate dehydrogenase (DHODH) is an antimalarial therapeutic target without an effective inhibitor. Studies on human DHODH (HsDHODH) led to a structural mechanistic model in which respiratory quinones bind in a tunnel formed by the highly variable N-­terminus that leads to the flavin mononucleotide-binding site. The therapeutic agents leflunomide (Arava) and brequinar sodium inhibit HsDHODH by binding in this tunnel. Plasmodium falciparum DHODH (PfDHODH) and HsDHODH have markedly different sensitivities to the two drugs. To understand the structural basis of this differential sensitivity and begin a structure-based drug-design cycle for PfDHODH inhibitors, the three-dimensional structure (2.4 A, R = 20.1%) of PfDHODH bound to the active metabolite of leflunomide was determined by X-ray crystallography. Comparison of the structures of HsDHODH and PfDHODH reveals a completely different binding mode for the same inhibitor in these two catalytically identical enzymes and explains the previously observed species-specific preferential binding. Because no effective inhibitors have been described for PfDHODH, this structure provides critical insight for the design of potential antimalarials.

A chemical study of cyclic depsipeptides produced by a sponge-derived fungus.

Abstract: Two novel cyclic depsipeptides, guangomides A (1) and B (2), together with a new destruxin derivative (3) were isolated from the cytotoxic extract obtained from the saltwater culture of an unidentifiable sponge-derived fungus. The new structures were elucidated on the basis of analysis of extensive 1D and 2D NMR data sets, and the absolute configurations of 2S, 9S, 13S, 19S, 24R, 28R of 1 were determined on the basis of the combined X-ray and Marfey's method structure analysis. Identical absolute configurations were assumed for 2. The cytotoxicity of the extract was found to be due to brefeldin A, while 1 and 2 showed weak antibacterial activity against Staphylococcus epidermidis and Enterococcus durans.

Stopping trouble before it starts.

Abstract: A recent publication revealing that the cytotoxic marine natural product pateamine A targets eukaryotic initiation factor eIF4A continues a story with lessons for both chemists and biologists, that is, the significance of natural products, the importance of synthetic organic chemistry, the small molecule regulation of eukaryotic translation machinery, and possibly a new approach to cancer chemotherapy.

The Biosynthetic genes of pantocin A and pantocin B of Pantoea agglomerans Eh318

Abstract: Pantocin A and pantocin B are low-molecular weight, peptide-based antibiotics that are produced in minimal media by the biocontrol agent Pantoea agglomerans, which are inhibitory to the fire blight pathogen, Erwinia amylovora. Pantocin A and pantocin B are members of a family of antibiotics whose toxicity is inhibited by certain amino acids. They inhibit enzymes in pathways for histidine and arginine biosynthesis, respectively. The biosynthetic gene cluster for pantocin A was sequenced, and it is 2.84 kb in size. It contains a small gene (paaP) that encodes a thirty-amino acid precursor peptide and three genes, paaA, paaB and paaC that encode the enzymes necessary to process the precursor into pantocin A. PaaC is proposed to be responsible for resistance to pantocin A. The determinants for pantocin B biosynthesis are encoded in a cluster of 13 open reading frames (PabA through pabM within a 17.5 kb region. Functions are proposed for the individual gene products, based on DNA sequence homology and on the chemical structure of pantocin B. PabA is similar to multidrug resistance proteins (like YqjV of Bacmus subtilis) and is likely responsible for pantocin B resistance. However, pabB, pabC and pabD may also encode resistance determinants. The products of the pabJKLM operon are believed to be involved in the addition of the methyl sulfonyl moiety of pantocin B. Cryptic transposase genes are found within and outside of the biosynthetic region, and the G+C ratio is lower inside than outside of the cluster. Thus, the pantocin B biosynthetic region may be a genomic island whose DNA originated from other organisms and was generated through two separate transposition events.