Ligand-based virtual screening and biological evaluation of inhibitors of Mycobacterium tuberculosis H37Rv.

Novel antimycobacterial compounds are needed to expand the existing toolbox of therapeutic agents, which sometimes fail to be effective. In our study we extracted, filtered, and aggregated the diverse data on antimycobacterial activity of chemical compounds from the ChEMBL database version 24.1. These training sets were used to create the classification and regression models with PASS and GUSAR software. The IOC chemical library consisting of approximately 200,000 chemical compounds was screened using these (Q)SAR models to select novel compounds potentially having antimycobacterial activity. The QikProp tool (Schrödinger) was used to predict ADME properties and find compounds with acceptable ADME profiles. As a result, 20 chemical compounds were selected for further biological evaluation, of which 13 were the Schiff bases of isoniazid. To diversify the set of selected compounds we applied substructure filtering and selected an additional 10 compounds, none of which were Schiff bases of isoniazid. Thirty compounds selected using virtual screening were biologically evaluated in a REMA assay against the M. tuberculosis strain H37Rv. Twelve compounds demonstrated MIC below 20 µM (ranging from 2.17 to 16.67 µM) and 18 compounds demonstrated substantially higher MIC values. The discovered antimycobacterial agents represent different chemical classes.

Role of Small Noncoding RNAs in Bacterial Metabolism.

The study of prokaryotic small RNAs is one of the most important directions in modern molecular biology. In the last decade, multiple short regulatory transcripts have been found in prokaryotes, and for some of them functional roles have been elucidated. Bacterial small RNAs are implicated in the regulation of transcription and translation, and they affect mRNA stability and gene expression via different mechanisms, including changes in mRNA conformation and interaction with proteins. Most small RNAs are expressed in response to external factors, and they help bacteria to adapt to changing environmental conditions. Bacterial infections of various origins remain a serious medical problem, despite significant progress in fighting them. Discovery of mechanisms that bacteria employ to survive in infected organisms and ways to block these mechanisms is promising for finding new treatments for bacterial infections. Regulation of pathogenesis with small RNAs is an attractive example of such mechanisms. This review considers the role of bacterial small RNAs in adaptation to stress conditions. We pay special attention to the role of small RNAs in Mycobacterium tuberculosis infection, in particular during establishment and maintenance of latent infection.

Biochemical and morphological changes in dormant ("Nonculturable") Mycobacterium smegmatis cells.

Biochemical and morphological changes have been studied during transition of Mycobacterium smegmatis cells into their dormant ("nonculturable") state. A significant fraction of the population of irreversibly "nonculturable" (NC) cells has a thicker cell wall, condensed cytoplasm, and a decreased number of ribosomes. The lipid contents in the NC cells are lower than in the metabolically active cells, with a relatively decreased amount of phospholipid and neutral lipid. Free mycolic acids, which are abundant in metabolically active cells, were not found in the NC cells. The NC forms are also characterized by decreased respiratory activity on endogenous substrates; however, the respiratory chain enzymes retain their activities in the isolated membranes. Activities of the Krebs cycle and glyoxylate cycle enzymes are markedly decreased. Despite a significant decrease in metabolic activity, NC cells possess membrane potential that seems to provide for reversibility of the NC state of mycobacteria, i.e. their capability of reactivating.

M. tuberculosis Gene Expression during Transition to the "Non-Culturable" State.

We analyzed the gene expression profile under specific conditions during reversible transition of M. tuberculosis cells to the "non-culturable" (NC) state in a prolonged stationary phase. More than 500 genes were differentially regulated, while 238 genes were upregulated over all time points during NC cell formation. Approximately a quarter of these upregulated genes belong to insertion and phage sequences indicating a possible high intensity of genome modification processes taking place under transition to the NC state. Besides the high proportion of hypothetical/conserved hypothetical genes in the cohort of upregulated genes, there was a significant number of genes belonging to intermediary metabolism, respiration, information pathways, cell wall and cell processes, and genes encoding regulatory proteins. We conclude that NC cell formation is an active process involved in the regulation of many genes of different pathways. A more detailed analysis of the experimental data will help to understand the precise molecular mechanisms of dormancy/latency/persistence of M. tuberculosis in the future. The list of upregulated genes obtained in this study includes many genes found to be upregulated in other models of M. tuberculosis persistence. Thirteen upregulated genes, which are common for different models, can be considered as potential targets for the development of new anti-tuberculosis drugs directed mainly against latent tuberculosis.

[The role of 2-C-methylerythritol-2,4-cyclopyrophosphate in the resuscitation of the "nonculturable" forms of Mycobacterium smegmatis].

2-C-Methyl-D-erythritol-2,4-cyclopyrophosphate (MEC), an intermediate of the biosynthesis of isoprenoid compounds in bacteria, was found to be capable of exerting a resuscitating effect on resting Mycobacterium smegmatis cells. The introduction of an additional copy of the ispE gene encoding cytidyl-methylerythritol kinase, an enzyme involved in MEC synthesis in M. smegmatis, resulted in the emergence of a capacity for spontaneous reactivation of "nonculturable" M. smegmatis cells, which is not characteristic of the wild-type cells of this species. The involvement of MEC in the transition from the "nonculturable" state to the state of active growth is indicative of a previously unknown function of MEC, assumed to consist in regulation of the bacterial genome activity.

[The effect of liposomes on the growth and sensitivity of Mycobacterium smegmatis to isoniazide].

The effects of the liposome form of isoniazide (IN) and liposomes without IN on the growth of Mycobacterium smegmatis were studied. Fluorescent assay demonstrated that the fraction of liposomes that interacted with M. smegmatis amounted to 1-3%. It was shown that the IN efficiency in a liposomal form decreased depending on the liposome composition and concentration as compared with the IN in water solution. A preincubation of mycobacteria with liposomes led to a decrease in their sensitivity to IN. An analogous effect was observed when incubating M. smegmatis with oleic acid. It was postulated that the relative resistance of M. smegmatis to the antibiotic when using lipids as a carbon substrate appeared due to a change in the agent's metabolism and should be taken into account when testing in vitro the liposomal forms of antibiotics.

[Role of carbon substrates of culture media on Mycobacterium smegmatis susceptibility to antitubercular agents].

Influence of medium composition on Mycobacterium smegmatis growth and susceptibility to antituberculosis drugs (ATD)--isoniazid and rifabutin--was studied. It was shown that addition of phospholipids (PL) in form of liposomes to meat peptone broth resulted in activation of M. smegmatis growth and decrease of its susceptibility to ATD. Growth characteristics of M. smegmatis and its susceptibility to ATD were studied using variants of modified on source of carbon synthetic medium Sauton as growth substrate. It was revealed that presence of acetate or PL in growth medium results in significant decrease of M. smegmatis susceptibility to isoniazid and rifabutin. It was suggested that this phenomenon is determined by activation of glyoxylate cycle by PL and fatty acids, which, in its turn, can stimulate expression of a number of proteins, including cell membrane pumps excreting antibiotics out of microbial cell.

[Cell-cell interactions during formation and reactivation of "nonculturable" mycobacteria].

To date, the possible existence of "nonculturable" (NC) but potentially viable forms has been shown for some bacteria. NC mycobacteria have attracted particular interest due to the assumption that the latent form of tuberculosis is associated with the conversion of its causative agent, Mycobacterium tuberculosis, into the NC state. A number of approaches have been developed to obtain NC forms of mycobacteria, but the mechanisms of transition into or from this state have been insufficiently studied. This review considers cell-cell communications involved in the formation and reactivation of NC forms of the bacteria M. smegmatis and M. tuberculosis. Special attention has been paid to the secreted Rpf family proteins, which belong to peptidoglycan hydrolases and participate in the resuscitation of NC mycobacteria.

Proteins of the Rpf (resuscitation promoting factor) family are peptidoglycan hydrolases.

The secreted Micrococcus luteus protein, Rpf, is required for successful resuscitation of dormant "non-culturable" M. luteus cells and for growth stimulation in poor media. The biochemical mechanism of Rpf action remained unknown. Theoretical predictions of Rpf domain architecture and organization, together with a recent NMR analysis of the protein structure, indicate that the conserved Rpf domain has a lysozyme-like fold. In the present study, we found that both the secreted native protein and the recombinant protein lyse crude preparations of M. luteus cell walls. They also hydrolyze 4-methylumbelliferyl-beta-D-N,N',N''-triacetylchitotrioside, a synthetic substrate for peptidoglycan muramidases, with optimum activity at pH 6. The Rpf protein also has weak proteolytic activity against N-CBZ-Gly-Gly-Arg-beta-naphthylamide, a substrate for trypsin-like enzymes. Rpf activity towards 4-methylumbelliferyl-beta-D-N,N',N''-triacetylchitotrioside was reduced when the glutamate residue at position 54, invariant for all Rpf family proteins and presumably involved in catalysis, was altered. The same amino acid substitution resulted in impaired resuscitation activity of Rpf. The data indicate that Rpf is a peptidoglycan-hydrolyzing enzyme, and strongly suggest that this specific activity is responsible for its growth promotion and resuscitation activity. A possible mechanism of Rpf-mediated resuscitation is discussed.