Current Topics in Medicinal Chemistry - Volume 12, Issue 7, 2012

Tuberculosis (TB) remains the second leading cause of infectious disease mortality superseded only by HIV. The etiological agent of TB is Mycobacterium tuberculosis (Mtb), a slow-growing bacillus, which can switch its metabolism to a latent nonreplicating state. The recommended therapy for treatment of TB involves four drugs taken for at least 6 months, referred to as “first-line” drugs due to their high efficacy and relatively low toxicity. These drugs are comprised of isoniazid (first reported in 1951), pyrazinamide (1952), ethambutol (1961), and rifampin (1966). The development of multidrug resistant strains, coupled with the lack of any new antitubercular agents in over four decades, demands the development of new treatment strategies to combat drug resistant TB and to reduce the treatment regimen of susceptible TB strains. In order to put current drug discovery efforts into historical perspective, it should be noted that all of the first-line agents were discovered through phenotypic (i.e. random) screening and subsequent medicinal chemistry optimization. Isoniazid and pyrazinamide are analogs of nicotinamide (vitamin B3) while rifampin is a semisynthetic derivative of the rifamycin polyketide natural products. Ethambutol is a totally synthetic compound based on an ethylenediamine scaffold. The original SAR studies that led to the identification of pyrazinamide and ethambutol were guided solely by efficacy in TB-infected animals, studies that would not be possible now with the increased animal regulations. Surprisingly, the mechanism of action of each of these compounds have only recently been elucidated through advances in molecular genetic techniques of mycobacteria. The genome sequence of M. tuberculosis was published in 1998 providing the first glimpse into the metabolic capacity of this organism. Subsequent studies identified approximately 600 essential genes (at least under the growth conditions evaluated) among the more than 4000 open reading frames. Structural genomic and biochemical efforts have now provided the three dimensional structures and detailed functional characterization of many of these so-called essential gene products. Collectively, these data provide a wealth of information for target-based approaches using rational drug design. Despite the intellectual attractiveness of target-based rational-design, not a single new antibacterial agent has yet been discovered by this approach. Thus classical methods to TB drug discovery, namely phenotypic screening and optimization of known scaffolds, whose mechanism of action may or may not be known, remains a viable approach to discovery of new anti-TB drugs.....

The bacterial type II fatty acid biosynthesis (FASII) pathway is an essential but unexploited target for drug discovery. In this review we summarize SAR studies on inhibitors of InhA, the enoyl-ACP reductase from the FASII pathway in M. tuberculosis. Inhibitor scaffolds that are described include the diaryl ethers, pyrrolidine carboxamides, piperazine indoleformamides, pyrazoles, arylamides, fatty acids and imidazopiperidines, all of which form ternary complexes with InhA and the NAD cofactor, as well as isoniazid and the diazaborines which covalently modify the cofactor. Analysis of the structural data has enabled the development of a common binding mode for the ternary complex inhibitors, which includes a hydrogen bond network, a large hydrophobic pocket and a third ‘ size-limited’ binding area comprised of both polar and non-polar groups. A critical factor in InhA inhibition involves ordering of the substrate binding loop, located close to the active site, and a direct link is proposed between loop ordering and slow onset enzyme inhibition. Slow onset inhibitors have long residence times on the enzyme target, a property that is of critical importance for in vivo activity.

Antiviral chemotherapy often relies on nucleoside analogues, which, once phophorylated by intracellular kinases, target viral polymerases impeding DNA synthesis. In contrast, nucleoside analogues are much less explored as antibacterial drugs. Thymidine monophosphate kinase from Mycobacterium tuberculosis (TMPKmt), which is essential to DNA replication, was selected as a promising target for the design of new inhibitors. This review describes stepwise modifications of the TMPKmt substrate, guided by the feedback of enzyme assays and crystallographic analysis to afford potent enzyme inhibitors some of which also exhibited antitubercular activity. More importantly, several of the reported thymidine analogues provided a deeper understanding of the structure and catalytic mechanism of this intriguing enzyme.

Isoprene biosynthesis is an essential component of metabolism. Two pathways are known for the production of five-carbon (isoprene) intermediates: the mevalonate and nonmevalonate pathways. As many pathogenic organisms rely exclusively on the nonmevalonate pathway (NMP) for isoprenoids and humans do not, the enzymes of this route have been recently explored as new therapeutic targets. The second and first-committed step in the NMP is catalyzed by 1-deoxy-Dxylulose- 5-phosphate reductoisomerase (Dxr) and has received significant attention as a novel drug target. This review describes the biochemistry and crystal structures of Dxr and the synthesis and biological activity of inhibitors to date, with a focus on compounds targeting E. coli, Plasmodium, and M. tuberculosis enzymes and intact cells. Most inhibitors for Dxr use natural products fosmidomycin and FR900098 as starting points. The review discusses several families of fosmidomycinrelated analogs including α-substituted, ‘reverse’ and modified hydroxamate, spacer-modified, and hydroxy-amide analogs. Also discussed are non-fosmidomycin-like inhibitors, the aryl phosphonates, and lipophilic prodrugs of fosmidomycin and FR900098 designed to increase cell penetration. A comprehensive SAR of inhibitors is presented.

New antituberculosis (anti-TB) drugs are urgently needed to battle drug-resistant Mycobacterium tuberculosis (Mtb) strains and to shorten the long treatment regimen. A series of isoxazole-based compounds, bearing a carboxy moiety at the C3 position, are highly potent and versatile anti-TB agents. Several members of this compound class exhibit submicromolar in vitro activity against replicating Mtb (R-TB) and thus comparable activity to the current first-line anti-TB drugs. Remarkably, certain compounds also show low micromolar activity in a model for nonreplicating Mtb (NRP-TB) phenotype, which is considered a key to shortening the current long treatment protocol. The series shows excellent selectivity towards Mtb and, in general, shows no cytotoxicity on Vero cells (IC50's > 128 μM). Selected compounds retain their activity against isoniazid (INH), rifampin (RMP), and streptomycin (SM) resistant Mtb strains. The foregoing facts make derivatives of 3- isoxazolecarboxylic acid esters a promising anti-TB chemotype, and as such present attractive lead compounds for TB drug development.

New therapeutics are urgently needed to combat the immense disease burden of tuberculosis and related mycobacterial diseases worldwide. Natural products continue to provide leads for the development of novel drugs to treat the rapidly growing numbers of patients with multi- and extensively-drug resistant tuberculosis. This review presents natural products and synthesized analogues with anti-mycobacterial activity published between 2006 through 2009. Structure activity relationships, synthetic analogues and newly reported activities of known compounds reported during this period are also included.

Adenylation or adenylate-forming enzymes (AEs) are widely found in nature and are responsible for the activation of carboxylic acids to intermediate acyladenylates, which are mixed anhydrides of AMP. In a second reaction, AEs catalyze the transfer of the acyl group of the acyladenylate onto a nucleophilic amino, alcohol, or thiol group of an acceptor molecule leading to amide, ester, and thioester products, respectively. Mycobacterium tuberculosis encodes for more than 60 adenylating enzymes, many of which represent potential drug targets due to their confirmed essentiality or requirement for virulence. Several strategies have been used to develop potent and selective AE inhibitors including highthroughput screening, fragment-based screening, and the rationale design of bisubstrate inhibitors that mimic the acyladenylate. In this review, a comprehensive analysis of the mycobacterial adenylating enzymes will be presented with a focus on the identification of small molecule inhibitors. Specifically, this review will cover the aminoacyl tRNAsynthetases (aaRSs), MenE required for menaquinone synthesis, the FadD family of enzymes including the fatty acyl- AMP ligases (FAAL) and the fatty acyl-CoA ligases (FACLs) involved in lipid metabolism, and the nonribosomal peptide synthetase adenylation enzyme MbtA that is necessary for mycobactin synthesis. Additionally, the enzymes NadE, GuaA, PanC, and MshC involved in the respective synthesis of NAD, guanine, pantothenate, and mycothiol will be discussed as well as BirA that is responsible for biotinylation of the acyl CoA-carboxylases.

Manuel A. de Pablo Martinez was born in Jaén (Spain) in 1967. He obtained his first University degree in 1991 at the University of Granada (Spain), and his Ph.D. in Biology at the University of Jaen in 1995 where he received a special doctorate award with his thesis, “The effect of an olive oil rich diet on the immune system”. His work became the origin of new research at the University of Jaen. Dr. de Pablo was assistant Professor of Microbiology from 1995 to 2000, and Lecturer in the Faculty of Experimental Sciences, Department of Microbiology from 2000 until his death. In 1998 he was visiting Professor at the Centre National de la Recherche Scientifique (CNRS, Villejuif, Paris, France), working with Dr. Guido Kroemer researching the role that mitochondria play in the molecular mechanism of apoptosis. Dr. de Pablo published more than forty articles in international scientific journals. His main research field was focused on the role of dietary lipids on the immune system and resistance to infection. Other research areas in his scientific career were the role of peptides and natural antioxidants on apoptosis mechanisms, and the action of lactic acid bacteria on immune system and resistance to infection. Manuel was co-author of several books and book chapters, and took part in numerous scientific conferences related to Nutrition, Immunology and Microbiology. He was a reviewer for several international journals in Microbiology, Immunology and Nutrition and was Associate Editor of Nutritional Therapy and Metabolism (Official Journal of the Italian Society of Parenteral and Enteral Nutrition)....