Structure of microcin J25, a peptide inhibitor of bacterial RNA polymerase, is a lassoed tail

Microcin J25 (MccJ25) is a 21-amino acid peptide inhibitor active against the DNA-dependent RNA polymerase of Gram negative bacteria. Previously, the structure of MccJ25 was reported to be a head-to-tail circle, cyclo(-G(1)GAGHVPEYF(10)VGIGTPISFY(20)G-). On the basis of biochemical studies, mass spectrometry, and NMR, we show that this structure is incorrect, and that the peptide has an extraordinary structural fold. MccJ25 contains an internal lactam linkage between the alpha-amino group of Gly1 and the gamma-carboxyl of Glu8. The tail (Tyr9-Gly21) passes through the ring (Gly1-Glu8), with Phe19 and Tyr20 straddling each side of the ring, sterically trapping the tail in a noncovalent interaction we call a lassoed tail.     

Synthesis of de novo designed small-molecule inhibitors of bacterial RNA polymerase

The de novo molecular design program SPROUT has been used in conjunction with the X-ray crystal structure of RNA polymerase (RNAP) from Thermus aquaticus to produce a novel enzyme inhibitor scaffold. A short and efficient synthesis of molecules corresponding to this scaffold has been developed and in keeping with the design predictions, the resulting inhibitors displayed useful levels of inhibition of Escherichia coli RNAP.     

Stereochemical determination and complex biosynthetic assembly of etnangien, a highly potent RNA polymerase inhibitor from the myxobacterium Sorangium cellulosum

A potent novel analogue of the natural macrolide antibiotic etnangien, a structurally unique RNA polymerase inhibitor from myxobacteria, is reported. It may be readily obtained from fermentation broths of Sorangium cellulosum and shows high antibiotic activity, comparable to that of etnangien. However, it is much more readily available than the notoriously labile authentic natural product itself. Importantly, it is stable under neutral conditions, allowing for elaborate NMR measurements for assignment of the 12 hydroxyl- and methyl-bearing stereogenic centers. The full absolute and relative stereochemistries of these complex polyketides were determined by a combination of extensive high-field NMR studies, including J-based configuration analysis, molecular modeling, and synthetic derivatization in combination with an innovative method based on biosynthetic studies of this polyketide which is also presented here. A first look into the solution conformation and 3D structure of these promising macrolide antibiotics is reported. Finally, the complete biosynthetic gene cluster was analyzed in detail, revealing a highly unusual and complex trans-AT type polyketide biosynthesis, which does not follow colinearity rules, most likely performs programmed iteration as well as module skipping, and exhibits HMG-CoA box-directed methylation.     

Synthesis of taurospongin A: a potent inhibitor of DNA polymerase and HIV reverse transcriptase,using pi-allyltricarbonyliron lactone complexes

The synthesis of taurospongin A has been achieved using, as a key step, a pi-allyltricarbonyliron lactone complex to control a highly stereoselective addition of a methyl group to a carbonyl unit located in the side chain of the complex.     

Practical synthesis of a potent hepatitis C virus RNA replication inhibitor

A practical, efficient synthesis of 1, a hepatitis C virus RNA replication inhibitor, is described. Starting with the inexpensive diacetone glucose, the 12-step synthesis features a novel stereoselective rearrangement to prepare the key crystalline furanose diol intermediate. This is followed by a highly selective glycosidation to couple the C-2 branched furanose epoxide with deazapurine.     

(+)-Myristinin A, a naturally occurring DNA polymerase beta inhibitor and potent DNA-damaging agent

The first stereoselective total synthesis of the naturally occurring flavan myristinin A has been accomplished, as well as its biochemical evaluation. This synthesis verified the structural assignment and allowed for the determination of the absolute stereochemistry. Myristinin A exhibits biochemical activity both as a potent DNA-damaging agent and DNA polymerase beta inhibitor. Relaxation of supercoiled plasmid DNA was observed at picomolar concentrations, in addition to inhibition of polymerase beta at low micromolar concentrations.     

Synthesis of SMP-797: a new potent ACAT inhibitor

A potent ACAT (acyl-CoA: cholesterol acyltransferase) inhibitor SMP-797 was effectively synthesized by the urea formation of 3-amino-4-aryl-1,8-naphthyridin-2(1H)-one and 4-amino-2,6-diisopropylamine. The synthesis of the former compound involved the Suzuki coupling reaction as a key step, and the latter was prepared by the 4-selective nitration of 2,6-diisopropylaniline using 2,3,5,6-tetrabromo-4-methyl-4-nitro-2,5-cyclohexadienone.     

Synthesis of a potent and selective inhibitor of p90 Rsk

[reaction: see text] The synthesis of the naturally occurring kaempferol glycoside SL0101 has been accomplished, as has its biochemical evaluation. SL0101 exhibits selective and potent p90 Rsk inhibitory activity at nanomolar concentrations without inhibiting the function of upstream kinases such as MEK, Raf, or PKC. The synthesis verified the structural assignment of the natural product and has provided access to material sufficient for detailed biological evaluation.     

Synthesis and determination of the relative structure of akaterpin, a potent inhibitor of PI-PLC

We describe the first total synthesis and structural determination of akaterpin, an inhibitor of phosphatidylinositol-specific phospholipase C (PI-PLC). The key features of the synthetic strategy include a regio- and stereoselective C-alkylation at the angular C1′ position and an exo-selective intermolecular Diels-Alder reaction. The relative stereochemistry was determined by a comparison of the NMR spectra of synthetic akaterpin with those of natural akaterpin.     

Synthesis of 1,4,6-Trideoxy-1,4-imino-D-mannitol: a potent α-mannosidase inhibitor

The title trihydroxypyrrolidine 4, readily synthesized $\text{in one step}$ from the naturally occurring sugar D-perosamine, is ten times more active than swainsonine as a competitive inhibitor of jackbean α-mannosidase.     

Synthesis and NMR structure of p41icf,a potent inhibitor of human cathepsin L

The total synthesis and structural characterization of the MHCII-associated p41 invariant chain fragment (P41icf) is described. P41icf plays a crucial role in the maturation of MHC class II molecules and antigen processing, acting as a highly selective cathepsin L inhibitor. P41icf synthesis was achieved using a combined solid-phase/solution approach. The entire molecule (65 residues, 7246 Da unprotected) was assembled in solution from fully protected peptides in the size range of 10 residues. After deprotection, oxidative folding in carefully adjusted experimental conditions led to the completely folded and functional P41icf with a disulfide pairing identical to that of native P41icf. CD, NMR, and surface plasmon resonance (SPR) were used for the structural and functional characterization of synthetic P41icf. CD thermal denaturation showed clear cooperative behavior. Tight cathepsin L binding was demonstrated by SPR. (1)H NMR spectroscopy at 800 MHz of unlabeled P41icf was used to solve the three-dimensional structure of the molecule. P41icf behaves as a well-folded protein domain with a topology very close to the crystallographic cathepsin L-bound form.     

Total synthesis of thapsigargin, a potent SERCA pump inhibitor

The enantioselective total synthesis of thapsigargin, a potent, selective inhibitor of the Ca2+ pump SERCA, is described. Starting from ketoalcohol 8, key steps involve regioselective introduction of the internal olefin at C4-C5, judicious protecting group choice to allow chelation-controlled reduction at C3, and chemoselective introduction of the angelate ester function at C3-O. A selective esterification approach completes the total synthesis in a total of 42 steps and 0.61% overall yield (88.6% average yield per step). [reaction: see text].     

Discovery of kibdelomycin, a potent new class of bacterial type II topoisomerase inhibitor by chemical-genetic profiling in Staphylococcus aureus

Bacterial resistance to known therapeutics has led to an urgent need for new chemical classes of antibacterial agents. To address this we have applied?a Staphylococcus aureus fitness test strategy to natural products screening. Here we report the discovery of kibdelomycin, a novel class of antibiotics produced by a new member of the genus Kibdelosporangium. Kibdelomycin exhibits broad-spectrum, gram-positive antibacterial activity and is a potent inhibitor of DNA synthesis. We demonstrate through chemical genetic fitness test profiling and biochemical enzyme assays that kibdelomycin is a structurally new class of bacterial type II topoisomerase inhibitor preferentially inhibiting the ATPase activity of DNA gyrase and topoisomerase IV. Kibdelomycin is thus the first truly novel bacterial type II topoisomerase inhibitor with potent antibacterial activity discovered from natural product sources in more than six decades.     

Total synthesis of spiruchostatin A, a potent histone deacetylase inhibitor

The total synthesis of spiruchostatin A was accomplished, unambiguously confirming its structure. Key steps included the use of the Nagao thiazolidinethione auxiliary for a diastereoselective acetate aldol reaction and as an activated acylating agent for amide formation, and macrolactonization by the Yamaguchi protocol. Spiruchostatin A is shown to have biological activity similar to that of FK228, a potent histone deacetylase (HDAC) inhibitor in clinical trials. The spiruchostatin A analogue, epimeric at the beta-hydroxy acid, is inactive, highlighting the importance of stereochemistry at this position for interactions with HDACs.     

Synthesis of alpha-galactosyl ceramide,a potent immunostimulatory agent

Alpha-galactosyl ceramide has been identified to be a potent stimulatory agent for a novel immunological process, mediated by CD1 molecules. This paper describes a short and efficient synthesis of alpha-galactosyl ceramide. Starting from commercially available 2-deoxy galactose, a suitable sphingosine derivative was obtained in nine steps and 36% overall yield, which was subsequently glycosylated to give the target molecule. This flexible route will provide various glycolipids for further exploration of this interesting biological process.     

5-Demethoxyfumagillol, a potent angiogenesis inhibitor isolated from Aspergillus fumigatus

A novel angiogenesis inhibitor, 5-demethoxyfumagillol (1), was obtained by isolation, purification and saponification of cultured broth of Aspergillus fumigatus. The structure was assigned as (3R,4R,6R)-4-[(2R,3R)-2-methyl-3-(3-methyl-but-2-enyl)-oxiranyl]-1-oxa-spiro[2,5]octan-6-ol (1) by spectroscopic analysis and confirmed by independent synthesis from fumagillol (3). In addition, 6-O-(chloroacetylcarbamoyl)-5-demethoxyfumagillol (7) showed a potential anti-angiogenic activity in CAPE cells in vitro.