New class of orthopoxvirus antiviral drugs that block viral maturation

By using a homology-based bioinformatics approach, a structural model of the vaccinia virus (VV) I7L proteinase was developed. A unique chemical library of approximately 51,000 compounds was computationally queried to identify potential active site inhibitors. The resulting biased subset of compounds was assayed for both toxicity and the ability to inhibit the growth of VV in tissue culture cells. A family of chemotypically related compounds was found which exhibits selective activity against orthopoxviruses, inhibiting VV with 50% inhibitory concentrations of 3 to 12 microM. These compounds exhibited no significant cytotoxicity in the four cell lines tested and did not inhibit the growth of other organisms such as Saccharomyces cerevisiae, Pseudomonas aeruginosa, adenovirus, or encephalomyocarditis virus. Phenotypic analyses of virus-infected cells were conducted in the presence of active compounds to verify that the correct biochemical step (I7L-mediated core protein processing) was being inhibited. Electron microscopy of compound-treated VV-infected cells indicated a block in morphogenesis. Compound-resistant viruses were generated and resistance was mapped to the I7L open reading frame. Transient expression with the mutant I7L gene rescued the ability of wild-type virus to replicate in the presence of compound, indicating that this is the only gene necessary for resistance. This novel class of inhibitors has potential for development as an efficient antiviral drug against pathogenic orthopoxviruses, including smallpox.     

Computation of non-covalent interactions in TNF proteins and interleukins

The roles played by the non-covalent interactions have been investigated for a set of six TNF proteins and nine Interleukins. The stabilizing residues have been identified by a consensus approach using the concepts of available surface area, medium and long-range interactions and conservation of amino acid residues. The cation-pi interactions have been computed based on a geometric approach such as distance and energy criteria. We identified an average of 1 energetically significant cation-pi interactions in every 94 residues in TNF proteins and 1 in every 62 residues in Interleukins. In TNF proteins, the cationic groups Lys preferred to be in helix while Arg preferred to be in strand regions while in Interleukins the Arg residues preferred to be in helix and Lys preferred to be in strand regions. From the available surface area calculations, we found that, almost all the cation and pi residues in TNF proteins and Interleukins were either in buried or partially buried regions and none of them in the exposed regions. Medium and long-range interactions were predominant in both TNF proteins and Interleukins. It was observed that the percentage of stabilizing centers were more in TNF proteins as compared to the Interleukins, while the percentage of conserved residues were more in Interleukins than in TNF proteins. In the stabilizing residues Lys was observed to be a stabilizing residue in both TNF proteins and Interleukins. Among the aromatic group, Phe was seen to be a stabilizing residue in both TNF and Interleukins. We suggest that this study on the computation of cation-pi interactions in TNF proteins and Interleukins would be very helpful in further understanding the structure, stability and functional similarity of these proteins.     

New clerodane diterpenoids from the aerial parts of Pulicaria wightiana

Two new ent-clerodane-type diterpenoids, compounds 1 and 2, were isolated from the aerial parts of Pulicaria wightiana, together with three known constituents. Their structures were established based on spectroscopic data, and their antibacterial activities were evaluated (Table 2).     

Do N-glycoproteins have preference for specific sequons?

Protein N-glycosylation requires the presence of asparagine (N) in the consensus tri-peptide NXS/T (where X is any amino acid, S is serine and T is threonine). Several factors affect the glycosylation potential of NXS/T sequons and one such factor is the type of amino acid at position X. While proline was shown to negatively affect N-glycosylation, the nature of other amino acids at this position is not clear. Using Markov chain analysis of tri-peptide NXS/T from viral, archaeal and eukaryotic proteins as well as experimentally confirmed N-glycosylated sequons from eukaryotic proteins, we show here that the occurrence of most sequon types differ significantly from the expected probability. Sequon types with F, G, I, S, T and V amino acids are consistently preferred while those with P and charged amino acids are under-represented in all four groups. Further, proteins contained far fewer number of possible sequon types (maximum 20 types for NXS or NXT taken separately) for any given number of sequons, which may be explained based on random sampling. Consistent with the present finding, majority of the over-represented sequons found in two important viral envelope glycoproteins (hemagglutinin of influenza A H3N2 and glycoprotein120 of HIV-1) are indeed preferred sequon types, which may provide a selective advantage. Accordingly, although there seems to be some preference for sequons, this preference may not be unique to N-glycosylation.     

A PAS Domain Binds Asparagine in the Chemotaxis Receptor McpB in Bacillus subtilis

During chemotaxis toward asparagine by Bacillus subtilis, the ligand is thought to bind to the chemoreceptor McpB on the exterior of the cell and induce a conformational change. This change affects the degree of phosphorylation of the CheA kinase bound to the cytoplasmic region of the receptor. Until recently, the sensing domains of the B. subtilis receptors were thought to be structurally similar to the well studied Escherichia coli four-helical bundle. However, sequence analysis has shown the sensing domains of receptors from these two organisms to be vastly different. Homology modeling of the sensing domain of the B. subtilis asparagine receptor McpB revealed two tandem PAS domains. McpB mutants having alanine substitutions in key arginine and tyrosine residues of the upper PAS domain but not in any residues of the lower PAS domain exhibited a chemotactic defect in both swarm plates and capillary assays. Thus, binding does not appear to occur across any dimeric surface but within a monomer. A modified capillary assay designed to determine the concentration of attractant where chemotaxis is most sensitive showed that when Arg-111, Tyr-121, or Tyr-133 is mutated to an alanine, much more asparagine is required to obtain an active chemoreceptor. Isothermal titration calorimetry experiments on the purified sensing domain showed a K_D to asparagine of 14 μm, with the three mutations leading to less efficient binding. Taken together, these results reveal not only a novel chemoreceptor sensing domain architecture but also, possibly, a different mechanism for chemoreceptor activation.     

Cyclin D1 Is a Bona Fide Target Gene of NFATc1 and Is Sufficient in the Mediation of Injury-induced Vascular Wall Remodeling

Platelet-derived growth factor BB induced cyclin D1 expression in a time- and nuclear factor of activated T cells (NFAT)-dependent manner in human aortic smooth muscle cells (HASMCs), and blockade of NFATs prevented HASMC DNA synthesis and their cell cycle progression from G₁ to S phase. Selective inhibition of NFATc1 by its small interfering RNA also blocked HASMC proliferation and migration. Characterization of the cyclin D1 promoter revealed the presence of several NFAT binding sites, and the site at nucleotide −1333 was found to be sufficient in mediating platelet-derived growth factor BB-induced cyclin D1 promoter-luciferase reporter gene activity. In addition to its role in cell cycle progression, cyclin D1 mediated HASMC migration in an NFATc1-dependent manner. Balloon injury-induced cyclin D1-CDK4 activity requires NFAT activation, and adenovirus-mediated transduction of cyclin D1 was found to be sufficient to overcome the blockade effect of NFATs by VIVIT on balloon injury-induced vascular wall remodeling events, including smooth muscle cell migration from the medial to luminal region, their proliferation in the intimal region, and neointima formation. Together, these results provide more mechanistic evidence for the role of NFATs, particularly NFATc1, in the regulation of HASMC proliferation and migration as well as vascular wall remodeling. NFATc1 could be a potential therapeutic target against the renarrowing of artery after angioplasty.     

Redundant Function of cmaA2 and mmaA2 in Mycobacterium tuberculosis cis Cyclopropanation of Oxygenated Mycolates

The Mycobacterium tuberculosis cell envelope contains a wide variety of lipids and glycolipids, including mycolic acids, long-chain branched fatty acids that are decorated by cyclopropane rings. Genetic analysis of the mycolate methyltransferase family has been a powerful approach to assign functions to each of these enzymes but has failed to reveal the origin of cis cyclopropanation of the oxygenated mycolates. Here we examine potential redundancy between mycolic acid methyltransferases by generating and analyzing M. tuberculosis strains lacking mmaA2 and cmaA2, mmaA2 and cmaA1, or mmaA1 alone. M. tuberculosis lacking both cmaA2 and mmaA2 cannot cis cyclopropanate methoxymycolates or ketomycolates, phenotypes not shared by the mmaA2 and cmaA2 single mutants. In contrast, a combined loss of cmaA1 and mmaA2 had no effect on mycolic acid modification compared to results with a loss of mmaA2 alone. Deletion of mmaA1 from M. tuberculosis abolishes trans cyclopropanation without accumulation of trans-unsaturated oxygenated mycolates, placing MmaA1 in the biosynthetic pathway for trans-cyclopropanated oxygenated mycolates before CmaA2. These results define new functions for the mycolic acid methyltransferases of M. tuberculosis and indicate a substantial redundancy of function for MmaA2 and CmaA2, the latter of which can function as both a cis and trans cyclopropane synthase for the oxygenated mycolates.Mycobacterium tuberculosis infection is an ongoing global health crisis. Alleviation of this crisis will require a multidisciplinary approach that must include new antibiotics active against M. tuberculosis. A growing body of literature implicates cell envelope lipids in the pathogenesis of M. tuberculosis infection (5-10, 14-15, 20). The enzymatic pathways that synthesize M. tuberculosis cell envelope lipids are the target of presently available antituberculosis antimicrobials and may be candidates for future antibiotic development.The mycolic acids of M. tuberculosis are alpha-alkyl, beta-hydroxy fatty acids which are 75 to 85 carbons in length (3). There are three classes of major mycolic acids: alpha-, methoxy-, and ketomycolates (Fig. ​(Fig.1).1). Whereas all mycobacteria synthesize mycolic acids, only pathogenic mycobacteria (for example, M. tuberculosis, M. leprae, M. avium, and M. bovis) produce significant quantities of mycolic acids with cyclopropane rings, three-member carbon rings which are added to the meromycolate chain (3). Alpha-mycolates have two cis cyclopropane rings, while methoxy- and ketomycolates have either a cis or trans cyclopropane ring at the proximal position, the latter with a distal methyl branch (Fig. ​(Fig.1).1). In contrast to the case with Escherichia coli, which encodes a single cyclopropane fatty acid synthase (CFAS) (16-17), the M. tuberculosis genome encodes a family of S-adenosyl methionine-dependent methyltransferases that modify cell envelope mycolic acids with methyl branches and cyclopropane rings. Despite substantial amino acid identity, systematic characterization of M. tuberculosis null mutants in each of these methyltransferases has revealed highly specific functions which were not revealed when the enzymes were overexpressed in M. smegmatis (12, 26, 28). Deletion of pcaA greatly reduces synthesis of the proximal cyclopropane ring of the alpha-mycolates (15), whereas deletion of mmaA2 greatly reduces the distal cyclopropane of the same lipid (13). Loss of mmaA2 also causes a mild impairment of methoxymycolate, but not ketomycolate, cis cyclopropanation (13). Similar genetic approaches established cmaA2 as the only trans cyclopropane synthase of oxygenated mycolates (14), while loss of mmaA3 abolishes methoxymycolates, a spontaneous mutation found in many M. bovis BCG strains (4, 11). Finally, deletion of mmaA4 abolishes synthesis of both methoxy- and ketomycolates (10). Recent chemical-genetic analysis of this enzyme family indicates that combined inhibition of their function is lethal to M. tuberculosis, strongly supporting an approach targeting this enzyme family for antimicrobial development (2, 8-19, 25).Open in a separate windowFIG. 1.Chemical structures of the major mycolic acids of M. tuberculosis. Cyclopropane rings and methyl branches are shown and annotated with the methyltransferase responsible for their synthesis.In addition to this essential role in combination, recent evidence implicates individual cyclopropane modifications as important determinants of M. tuberculosis host-pathogen interactions. Inactivation of pcaA causes attenuation of M. tuberculosis in the mouse model of infection while stimulating less-severe granulomatous pathology (15, 23). In contrast, deletion of cmaA2 has no effect on bacterial loads during mouse infection but causes hypervirulence while inducing more-severe granulomatous pathology (24). Inactivation of mmaA4, which leads to an absence of methoxy- and ketomycolates, causes a severe growth defect during the first 3 weeks of infection (10). All of these studies implicate the fine structure of mycolic acids in the pathogenesis of M. tuberculosis infection. One mechanism by which cyclopropanation mediates pathogenesis is through altered inflammatory activity of trehalose dimycolate (TDM), an inflammatory glycolipid. The cyclopropane content of TDM is a major determinant of its inflammatory activity, and this altered TDM is responsible for the virulence phenotypes of cyclopropane-deficient M. tuberculosis strains (9, 23-24).Despite major advances in our understanding of the biosynthesis and pathogenetic function of cyclopropanated mycolic acids through genetic approaches, the methyltransferase(s) that synthesizes the cis cyclopropane ring on the methoxy- and ketomycolates is unknown. In addition, the function of the MmaA1 methyltransferase has not been explored through construction of a null mutant. Prior experiments found that overexpression of mmaA1 in M. tuberculosis resulted in accumulation of trans-unsaturated and -cyclopropanated oxygenated mycolates (27). These data suggested that MmaA1 acts in the biosynthesis of trans-cyclopropanated oxygenated mycolates either by adding the methyl branch distal to the cyclopropane ring or as a cis-trans isomerase or both. In addition, although there was a defect in cis cyclopropanation of methoxymycolates in the ΔmmaA2 strain, this defect was mild, suggesting redundancy with another unidentified enzyme. In this article, we define novel functions for three cyclopropane synthases using a new selectable marker to construct M. tuberculosis strains deficient in multiple mycolic acid methyltransferases. Through this approach, we show that CmaA2 and MmaA2 are redundant for cis cyclopropanation of the proximal position of the methoxymycolates and ketomycolates and that MmaA1 is upstream of CmaA2 in trans cyclopropanation.     

CREMOFAC--a database of chromatin remodeling factors

MOTIVATION: Chromatin-remodeling is an important event in the eukaryotic nucleus rendering nucleosomal DNA accessible for various transaction processes. Remodeling Factors facilitate the dynamic nature of chromatin through participation of the collective action of (i) ATP and (ii) Non-ATP dependent factors. Considering the importance of these factors in eukaryotes, we have developed, CREMOFAC, a dedicated and frequently updated web-database for chromatin-remodeling factors. RESULTS: The database harbors factors from 49 different organisms reported in literature and facilitates a comprehensive search for them. In addition, it also provides in-depth information for the factors reported in the three widely studied mammals namely, human, mouse and rat. Further, information on literature, pathways and phylogenetic relationships has also been covered. The development of CREMOFAC as a central repository for chromatin-remodeling factors and the absence of such a pre-existing database heighten its utility thus making its presence indispensable. AVAILABILITY: http://www.jncasr.ac.in/cremofac/