Conserved G-Quadruplex Motifs in Gene Promoter Region Reveals a Novel Therapeutic Approach to Target Multi-Drug Resistance Klebsiella pneumoniae

Abstract

An opportunistic pathogen, Klebsiella pneumoniae is known to cause life-threating nosocomial infection with a high rate of morbidity and mortality. Evolutions of multi-drug-resistant and hyper-virulent strains of K. pneumoniae make the situation worse. Currently, there is no incisive drug molecule available for drug-resistant hyper-virulent K. pneumoniae infection that emphasizes the need for identification of novel and more promising drug targets in K. pneumoniae . Recently, various non-canonical structures of nucleic acids especially G-quadruplex (G4) motifs have been identified as potential therapeutic targets against several human pathogenic bacteria and viruses including Mycobacterium tuberculosis , Streptococcus pneumoniae , human immunodeficiency virus (HIV), Ebola, and Nipah. Therefore, in present study we screened the K. pneumoniae genomes for identification of evolutionary conserved G4 structure-forming motifs as promising anti-bacterial drug targets. Bioinformatics analysis revealed the presence of six highly conserved G4 motifs in the promoter region of five essential genes that play a critical role in nutrient transport and metabolism. Biophysical studies showed the formation of G4 structure by these conserved motifs. Circular Dichroism melting analysis showed the stabilization of these G4 motifs by a well-known G4-stabilizing agent, BRACO-19. The stabilization of these motifs by BRACO-19 was also able to stop the primer extension process, which is an essential phenomenon for expression of the G4-harboring gene. The addition of G4-specific ligand at low micromolar range was observed to be lethal for the growth of this bacteria and negatively controlled the expression of the G4-harboring genes via G4 structure stabilization. These observations strengthen the formation of G4 structures by the predicted G4 motif in vivo , which can be stabilized by G4 ligands like BRACO-19. This stabilization of G4 structures can attenuate the expression of G4-harboring essential genes and thus play a critical role in the regulation of gene expression. Thus, taking all given result in consideration, for the first time, this study showed the new therapeutic avenue for combating K. pneumoniae infection by characterizing the conserved G4 motifs as promising therapeutic targets.

G-quadruplex stabilization in the ions and maltose transporters gene inhibit Salmonella enterica growth and virulence

“…Pyridostatin is also observed to stabilize the G-quadruplex structure formed in the mRNA of the nuclear antigen 1 protein of EBV, leading to its translation suppression [ 39 ]. Recently, BRACO-19 has shown an inhibitory effect on Mycobacterium tuberculosis, and Klebsiella pneumoniae, while Quarfloxin inhibited Plasmodium falciparum, by stabilizing G-quadruplexes present in various regions of their genome [ 25 , 40 , 41 ]. Previously, 9-Aminoacridine and its derivatives have been observed for their anti-proliferative properties in cancer cells [ 42 ] by binding to the telomeric region [ 43 ], the c-Myc gene [ 44 ] and c-Kit promoter [ 45 ].…”

Exploring Computational and Biophysical Tools to Study the Presence of G-Quadruplex Structures: A Promising Therapeutic Solution for Drug-Resistant Vibrio cholerae

“…G-quadruplex motifs, depending upon its location, regulates the expression of the genes. PGQ motifs at the upstream/promoter region of the gene are reported to regulate the transcription of the harboring genes and are widely used as therapeutic targets against various pathogenic viruses, bacteria, protozoa, and other human diseases including cancer and neurological disorders (Balasubramanian et al, 2011;Kota et al, 2015;Tosoni et al, 2015;Perrone et al, 2017a;Shankar et al, 2020). Stabilization of PGQ motifs in the open reading frame of a gene has been reported to suppress their expression (Endoh et al, 2013b).…”

“…Interestingly, three highly conserved GQ forming motifs were recognized in the hsdS, recD, and pmrA genes which could act as potential drug targets against pathogenic Streptococcus pneumoniae (Mishra et al, 2019a). A recent analysis revealed the presence of GQ motifs in various genes of Klebsiella pneumoniae that influenced the gene expression (Shankar et al, 2020). Likewise, several human infecting viruses including Zika (Fleming et al, 2016), Nipah (Majee et al, 2020a), Herpes Simplex virus (Biswas et al, 2016), Human Papillomavirus (Tlučková et al, 2013), and Human Adenovirus (Majee et al, 2020b) are reported to possess potential GQ forming sequences.…”

Evolution of Diverse Strategies for Promoter Regulation

“…For example, the presence of potential G quadruplex sequences has been mapped to promoter regions of Mycobacterium tuberculosis [55] and direct regulation of transcription due to G-quadruplex stabilization was shown in the soil bacterium Paracoccus denitrificans [56]. Furthermore, G-quadruplexes in promoter regions have been suggested as a novel therapeutic approach for multidrug-resistant Klebsiella pneumoniae [57].…”