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

Abstract

Nowadays, the emergence and the transmission of multidrug-resistant pathogenic bacteria are a severe menace mounting a lot of pressure on the healthcare systems worldwide. Many severe outbreaks of bacterial infections have been reported worldwide in recent years. Thus, there is an immediate demand to develop antibiotics. Some riboswitches are potential targets for overcoming bacterial resistance. This paper demonstrates the bacteriostatic effect of an antisense oligonucleotide (ASO) engineered to suppress the growth of pathogenic bacteria such as Listeria monocytogenes by targeting the Thiamine Pyrophosphate (TPP) riboswitch. It does not inhibit the growth of the conditional pathogenic bacteria Escherichia coli, as it lacks the TPP riboswitch, showing the specificity of action of our ASO. It is covalently bonded with the cell-penetrating protein pVEC. We did bioinformatics analyses of the thiamine pyrophosphate riboswitch regarding its role in synthesizing the metabolite thiamine pyrophosphate, which is essential for bacteria. L. monocytogenes is intrinsically resistant to cephalosporins and usually is treated with ampicillin. A dosage of ASO has been established that inhibits 80% of bacterial growth at 700 nM (4.5 μg/mL). Thus, the TPP riboswitch is a valuable antibacterial target.

Exploring the structure, function of thiamine pyrophosphate riboswitch, and designing small molecules for antibacterial activity

“…Recently, a new approach has been developed where the TPP riboswitch is targeted by the engineered antisense oligonucleotide (ASO) to suppress the growth of pathogenic bacteria (Traykovska et al, 2022). Listeria monocytogenes is resistant to the cephalosporin class of antibiotics, and ASO has shown inhibition of 80% bacterial growth at 700 nM dosage.…”

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 ].…”

“…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 ].…”

Investigating the Frontiers of Genetic Regulation and Unlocking the Secrets of Gene Expression: The Power of RNA-based Therapeutics

“…Treatments: Antisense radiopharmaceuticals and oligonucleotides can be applied to various brain disorders, autoimmune disorders, and other diseases [113,114] This technology has also enabled the production of stress-tolerant crop varieties, such as beta-carotene in potatoes, reduced glutenin producing wheat varieties, and decaffeinated coffee varieties. However, Antisense Technology has its own limitations as well.…”