Drug Discovery Targeting Bacterial and Viral non-coding RNA: pH Modulation of RNAStability and RNA-RNA Interactions
| Autor: | Hossain, Md Ismail |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2022 |
| Předmět: |
Biochemistry
Biology Genetics Non-coding RNA T-box Riboswitch Stem-Loop II Motif RNA thermometer ompA shuT shuA Drug Discovery SARS-CoV-2 tRNA-mRNA interaction In vitro transcription Fluorescence Anisotropy EMSA Thermal denaturation pH RNA stability and conformation RNA structure probing Thermal hysteresis 16S rRNA Nucleic acid research |
| Druh dokumentu: | Text |
| Popis: | Antibiotic resistance is a global threat beside the ongoing pandemic by SARS-CoV-2.The number of deaths due to antibiotic-resistant infections is increasing at an alarmingrate. The COVID-19 pandemic has already claimed millions of deaths worldwide.Fighting against antibiotic-resistant superbugs and the SARS-CoV-2 has become achallenge. A significant amount of research is going on to develop the vaccine and smallmolecule antiviral and antibacterial therapeutics targeting proteins. Fortunately, novelnon-coding regulatory RNA targets have been identified for developing new antibacterialand antiviral drugs such as bacterial T-box riboswitch, RNA thermometers, and viralstem-loop II motif. T-box riboswitch can control the transcription or translation of aminoacid-related genes in bacteria by forming unique interactions between tRNA and mRNA.RNA thermometers (RNATs) are temperature-responsive riboswitches that control thetranslation based on temperature sensing thus controlling the interaction with the mRNAand 16S rRNA. In Shigella dysenteriae, three RNATs, i.e., ompA, shuT, and shuA, havebeen discovered. ompA RNAT controls the translation of outer membrane protein A.shuT, and shuA RNAT controls the translation of two proteins that are crucial to thebacterial heme utilization system. The Stem-loop II motif (S2M) is a highly conservedRNA element found in most coronaviruses, astroviruses, and picornaviruses that plays apotential role in viral replication and invasion. The RNA structure plays a significant rolein its regulatory function for all of these potential therapeutic targets. Consequently, it isessential to examine the factors that affect the RNA structure and RNA-RNA interaction.Despite having limited building blocks, RNA has diverse functions in the cells. Baseprotonation and protonated base pairs often occur in RNA when interacting with otherbiomolecules, thus could play a critical role in vital biological processes. Differentbiophysical assays, including UV use in monitoring thermal denaturation, FRET,fluorescence polarization, chemical and enzymatic probing, EMSA, and In vitrotranscription assay were used to probe the RNA structures, stability, conformation, andpotential function. These assays were also used to investigate the effect of potentialligands targeting these non-coding regulatory RNAs. Our study showed that pH affectsthe stability and conformations, including antiterminator model RNAs, RNATs, stemloopII motif, and the RNA-RNA interaction between the tRNA and antiterminator andRNAT and 16S rRNA mimic. Using the drug discovery screening assays, we identifiedseveral quinoline compounds that affected the riboswitch function and alteredconformation of the stem-loop II motif of SARS-CoV-2 and antiterminator element of Tboxriboswitch. Several 4,5-disubstituted oxazolidinones were also identified as weakinhibitors of T-box riboswitch function. |
| Databáze: | Networked Digital Library of Theses & Dissertations |
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