Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets

Abstract

Antibiotic resistance (AR) is an acute problem that results in prolonged and debilitating illnesses. AR mortality worldwide is growing and causes a pressing need to research novel mechanisms of action and untested target molecules. This article presents in silico analyses of eight bacterial riboswitches for their suitability for antibacterial drug targets. Most bacterial riboswitches are located in the 5′-untranslated region of messenger RNAs, act as allosteric cis-acting gene control elements, and have not been found in humans before. Sensing metabolites, the riboswitches regulate the synthesis of vital cellular metabolites in various pathogenic bacteria. The analyses performed in this article represent a complete and informative genome-wide bioinformatics analysis of the adequacy of eight riboswitches as antibacterial drug targets in different pathogenic bacteria based on four criteria. Due to the ability of the riboswitch to control biosynthetic pathways and transport proteins of essential metabolites and the presence/absence of alternative biosynthetic pathways, we classified them into four groups based on their suitability for use as antibacterial drug targets guided by our in silico analyses. We concluded that some of them are promising targets for antibacterial drug discovery, such as the PreQ1, MoCo RNA, cyclic-di-GMP I, and cyclic-di-GMP II riboswitches.

Targeting SAM-I Riboswitch Using Antisense Oligonucleotide Technology for Inhibiting the Growth of Staphylococcus aureus and Listeria monocytogenes

“…Designer pVEC-ASOs targeting FMN [ 7 ], TPP [ 8 ], and SAM-I riboswitches have MIC80 around 700 nM and exhibit a bacteriostatic effect. All designer pVEC-ASOs worked as expected, proving the high fidelity of our rational approach for drug design, including drug-target evaluation [ 4 , 5 ]. FMN, TPP, and SAM-I are essential co-factors for many enzymes in the cell, and it takes 3 to 5 h after stopping their syntheses till the inhibition of bacterial growth.…”

“…This ASO-based riboswitch targeting technology is already proven and published for glmS 6a and FMN riboswitches 6b . Our approach combines bioinformatics analyses [ 5 , 11 ] for the suitability of riboswitches to be antibacterial drug targets with the rational design of chimeric ASOs. We can claim that we have achieved 100% efficiency in inhibiting the growth in vitro of various human pathogenic bacteria by targeting all selected riboswitches.…”

“…Our research in this paper is focused on developing new efficient strategies for antibacterial drug discovery that may lead to a shorter development time and a higher success rate of drug candidate discovery. Our approach combines synthetic biology methods, bioinformatics [ 4 , 5 ], and rational drug design of antisense oligonucleotides (ASOs) [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 ]. Herein, we employ ASO that binds explicitly with the complementary sequence of the S-adenosyl methionine (SAM-I) riboswitch located in the 5′-untranslated region (UTR) of mRNAs and inhibits the growth of pathogenic human bacteria, such as S. aureus and Listeria (L.) monocytogenes [ 15 ].…”

Multidimensional Applications and Challenges of Riboswitches in Biosensing and Biotherapy

“…Moreover, riboswitches are highly selective and unlikely to harm probiotics. [230] Lastly, riboswitches are a highly conserved part of the developmental system, responding to common necessary metabolites and second messengers, and performing key physiological functions. [231] Before we can effectively design riboswitches as novel antibacterial drug targets, we must first properly study their distribution, structure, conformational folding conditions, and regulatory mechanism.…”

Targeting TPP Riboswitches Using Chimeric Antisense Oligonucleotide Technology for Antibacterial Drug Development

“…We employ the thiamine pyrophosphate (TPP) riboswitch as a new target to develop new antibacterial drug candidates . Our approach combines bioinformatics and the rational design of antisense oligonucleotides . We use antisense oligonucleotides (ASOs) engineered to specifically hybridize to the sequence of the TPP aptamer located in the 5′-untranslated region (UTR) of mRNAs in Listeria monocytogenes and also found in Bacillus subtilis.…”