Novel chemotherapeutics for treating multidrug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) are required to combat the spread of tuberculosis, a disease that kills more than 2 million people annually. Using structure-based drug design, we have developed a series of alkyl diphenyl ethers that are uncompetitive inhibitors of InhA, the enoyl reductase enzyme in the MTB fatty acid biosynthesis pathway. The most potent compound has a Ki' value of 1 nM for InhA and MIC99 values of 2-3 microg mL(-1) (6-10 microM) for both drug-sensitive and drug-resistant strains of MTB. Overexpression of InhA in MTB results in a 9-12-fold increase in MIC99, consistent with the belief that these compounds target InhA within the cell. In addition, transcriptional response studies reveal that the alkyl diphenyl ethers fail to upregulate a putative efflux pump and aromatic dioxygenase, detoxification mechanisms that are triggered by the lead compound triclosan. These diphenyl ether-based InhA inhibitors do not require activation by the mycobacterial KatG enzyme, thereby circumventing the normal mechanism of resistance to the front line drug isoniazid (INH) and thus accounting for their activity against INH-resistant strains of MTB.

Acyl carrier proteins play a central role in metabolism by transporting substrates in a wide variety of pathways including the biosynthesis of fatty acids and polyketides. However, despite their importance, there is a paucity of direct structural information concerning the interaction of ACPs with enzymes in these pathways. Here we report the structure of an acyl-ACP substrate bound to the Escherichia coli fatty acid biosynthesis enoyl reductase enzyme (FabI), based on a combination of x-ray crystallography and molecular dynamics simulation. The structural data are in agreement with kinetic studies on wild-type and mutant FabIs, and reveal that the complex is primarily stabilized by interactions between acidic residues in the ACP helix ␣2 and a patch of basic residues adjacent to the FabI substrate-binding loop. Unexpectedly, the acyl-pantetheine thioester carbonyl is not hydrogen-bonded to Tyr 156 , a conserved component of the short chain alcohol dehydrogenase/reductase superfamily active site triad. FabI is a proven target for drug discovery and the present structure provides insight into the molecular determinants that regulate the interaction of ACPs with target proteins. Acyl carrier proteins (ACPs)7 play an essential role in a diverse array of metabolic pathways including the biosynthesis of fatty acids (1, 2), polyketides (3), membrane-derived oligosaccharides (4), lipopolysaccharides (5, 6), and phospholipids (7). In each case the growing substrate is attached via a thioester to the ACP phosphopantetheine group. ACPs must therefore be able to recognize and interact, in an acyl group-dependent manner, with a wide variety of enzymes. In eukaryotic type I fatty acid synthesis (FASI) and in polyketide biosynthesis, the ACP occurs as part of a larger polypeptide that is also associated with other catalytic activities. In contrast, in bacterial type II fatty acid biosynthesis (FASII), each of the enzyme activities as well as the ACP are encoded by separate polypeptide chains (2). ACPs that function in FASII-mediated biosynthesis are small, highly soluble, acidic proteins that vary in molecular mass from 7.5 kDa (Escherichia coli) to 13 kDa (Mycobacterium tuberculosis) (1, 8 -11).Despite the central role that ACPs play in metabolism, structural details of their interaction with target proteins are sparse. Whereas the structures of ACPs from a variety of different species have been determined by x-ray crystallography (12) and NMR spectroscopy (see for example, Refs. 13 and 14), only one structure has been determined of ACP in complex with another protein, the holo-ACP synthase (AcpS) (15), and no structural information is available for the interaction between ACP and enzymes of the fatty acid biosynthesis pathway. AcpS attaches the phosphopantetheine to the ACP serine and thus, although valuable, the complex of AcpS and ACP differs fundamentally from other ACP-protein complexes and does not provide insight into the delivery of substrate by ACP.The NMR studies reveal that ACPs are highly flexible, a structural f...

Despite the recent decline of natural product discovery programs in the pharmaceutical industry, approximately half of all new drug approvals still trace their structural origins to a natural product. Herein, we use principal component analysis to compare the structural and physicochemical features of drugs from natural product-based versus completely synthetic origins that were approved between 1981–2010. Drugs based on natural product structures display greater chemical diversity and occupy larger regions of chemical space than drugs from completely synthetic origins. Notably, synthetic drugs based on natural product pharmacophores also exhibit lower hydrophobicity and greater stereochemical content than drugs from completely synthetic origins. These results illustrate that structural features found in natural products can be successfully incorporated into synthetic drugs, thereby increasing the chemical diversity available for small-molecule drug discovery.

Macrocycles are key structural elements in numerous bioactive small molecules and are attractive targets in the diversity-oriented synthesis of natural product-based libraries. However, efficient and systematic access to diverse collections of macrocycles has proven difficult using classical macrocyclization reactions. To address this problem, we have developed a concise, modular approach to the diversity-oriented synthesis of macrolactones and macrolactams involving oxidative cleavage of a bridging double bond in polycyclic enol ethers and enamines. These substrates are assembled in only 4–5 synthetic steps and undergo ring expansion to afford highly functionalized macrocycles bearing handles for further diversification. In contrast to macrocyclization reactions of corresponding seco-acids, the ring expansion reactions are efficient and insensitive to ring size and stereochemistry, overcoming key limitations of conventional approaches to systematic macrocycle synthesis. Cheminformatic analysis indicates that these macrocycles access regions of chemical space that overlap with natural products, distinct from currently-targeted synthetic drugs.