Identification of consensus hairpin loop structure among the negative sense subgenomic RNAs of SARS-CoV-2.

Background: SARS-CoV-2 is the causative agent of worldwide pandemic disease coronavirus disease 19. SARS-CoV-2 bears positive sense RNA genome that has organized and complex pattern of replication/transcription process including the generation of subgenomic RNAs. Transcription regulatory sequences have important role in the pausing of replication/transcription and generation of subgenomic RNAs. Results: In the present bioinformatics analysis, a consensus secondary structure was identified among negative sense subgenomic RNAs of SARS-CoV-2. This consensus region is present at the adjacent of initiation codon. Conclusions: This study proposed that consensus structured domain could involve in mediating the long pausing of replication/transcription complex and responsible for subgenomic RNA production. Supplementary Information: The online version contains supplementary material available at 10.1186/s42269-023-01002-3.

Regulation of polyphosphate glucokinase gene expression through cotranscriptional processing in Mycobacterium tuberculosis H37Rv.

Transcription is a molecular process that involves the synthesis of RNA chain into the 5'-3' direction, and simultaneously nascent RNA chain tends to form geometric structures, known as cotranscriptional folding. This folding determines the functional properties of RNA molecules and possibly has a critical role during the synthesis. This functioning includes the characterized properties of riboswitches and ribozymes, which are significant when the transcription rate is comparable to the cellular environment. This study reports a novel noncoding region important in the genetic expression of polyphosphate glucokinase (ppgk) in Mycobacterium tuberculosis. This noncoding element of ppgk gene undergoes cleavage activity during the transcriptional process in M.tuberculosis. We revealed that cleavage occurs within the nascent RNA, and the resultant cleaved 3'RNA fragment carries the Shine-Dalgarno (SD) sequence and expression platform. We concluded cotranscriptional processing at the noncoding region as the required mechanism for ppgk expression that remains constitutive within the bacterial environment. This study defines the molecular mechanism dependent on the transient but highly active structural features of the nascent RNA.

Screening of antitubercular compound library identifies novel ATP synthase inhibitors of Mycobacterium tuberculosis.

A limited number of anti-tuberculosis drug candidates with novel mode of action have entered clinical trials in recent years. ATP synthase is one such validated drug target which has yielded a drug recently. The aim of this study was to identify the novel chemical scaffolds targeting the Mycobacterium tuberculosis (M. tuberculosis) ATP synthase. In this study, inverted membrane vesicles of Mycobacterium smegmatis were prepared to establish luciferin based ATP estimation assay. This assay was used to screen 700 compounds which were earlier found to be active on the whole cell of M. tuberculosis. Antibacterial activity of hits against various susceptible and drug-resistant strains of M. tuberculosis was evaluated using the microplate alamar blue assay and their cytotoxicity was also determined to select the safe compounds for further study. Screening of 700 compounds resulted in the identification of two compounds (5228485 and 5220632) exhibiting an IC50 of 0.32 and 4.0 µg/ml respectively. Both compounds showed excellent anti-TB activity (MIC of 0.5-2.0 µg/ml against Mtb H37Rv) and low cytotoxicity in human cell line and sub-mitochondrial particles. The three-dimensional structure of M. tuberculosis ATPase was predicted using in-silico approach and docking studies were performed with the active compounds. The interaction between compounds and bacterial ATP synthase was confirmed by molecular docking analysis. In conclusion screening of compound library has resulted in the identification of two novel chemical scaffolds targeting mycobacterial ATP synthase.

Physicochemical, pharmacokinetic, efficacy and toxicity profiling of a potential nitrofuranyl methyl piperazine derivative IIIM-MCD-211 for oral tuberculosis therapy via in-silico-in-vitro-in-vivo approach.

Recent tuberculosis (TB) drug discovery programme involve continuous pursuit for new chemical entity (NCE) which can be not only effective against both susceptible and resistant strains of Mycobacterium tuberculosis (Mtb) but also safe and faster acting with the target, thereby shortening the prolonged TB treatments. We have identified a potential nitrofuranyl methyl piperazine derivative, IIIM-MCD-211 as new antitubercular agent with minimum inhibitory concentration (MIC) value of 0.0072 µM against H37Rv strain. Objective of the present study is to investigate physicochemical, pharmacokinetic, efficacy and toxicity profile using in-silico, in-vitro and in-vivo model in comprehensive manner to assess the likelihood of developing IIIM-MCD-211 as a clinical candidate. Results of computational prediction reveal that compound does not violate Lipinski's, Veber's and Jorgensen's rule linked with drug like properties and oral bioavailability. Experimentally, IIIM-MCD-211 exhibits excellent lipophilicity that is optimal for oral administration. IIIM-MCD-211 displays evidence of P-glycoprotein (P-gp) induction but no inhibition ability in rhodamine cell exclusion assay. IIIM-MCD-211 shows high permeability and plasma protein binding based on parallel artificial membrane permeability assay (PAMPA) and rapid equilibrium dialysis (RED) assay model, respectively. IIIM-MCD-211 has adequate metabolic stability in rat liver microsomes (RLM) and favourable pharmacokinetics with admirable correlation during dose escalation study in Swiss mice. IIIM-MCD-211 has capability to appear into highly perfusable tissues. IIIM-MCD-211 is able to actively prevent progression of TB infection in chronic infection mice model. IIIM-MCD-211 shows no substantial cytotoxicity in HepG2 cell line. In acute toxicity study, significant increase of total white blood cell (WBC) count in treatment group as compared to control group is observed. Overall, amenable preclinical data make IIIM-MCD-211 ideal candidate for further development of oral anti-TB agent.

Hearing molecules, mechanism and transportation: modeled in Drosophila melanogaster.

Mechanosensory transduction underlies the perception of touch, sound and acceleration. The mechanical signals exist in the environment are resensed by the specialized mechanosensory cells, which convert the external forces into the electrical signals. Hearing is a magnificent example that relies on the mechanotransduction mediated by the auditory cells, for example the inner-ear hair cells in vertebrates and the Johnston's organ (JO) in fly. Previous studies have shown the fundamental physiological processes in the fly and vertebrate auditory organs are similar, suggesting that there might be a set of similar molecules underlying these processes. The molecular studies of the fly JO have been shown to be remarkably successful in discovering the developmental and functional genes that provided further implications in vertebrates. Several evolutionarily conserved molecules and signaling pathways have been shown to govern the development of the auditory organs in both vertebrates and invertebrates. The current review describes the similarities and differences between the vertebrate and fly auditory organs at developmental, structural, molecular, and transportation levels.