Abstract
Anti-infection drugs target vital functions of infectious agents, including their ribosome and other essential non-coding RNAs. One of the reasons infectious agents become resistant to drugs is due to mutations that eliminate drug-binding affinity while maintaining vital elements. Identifying these elements is based on the determination of viable and lethal mutants and associated structures. However, determining the structure of enough mutants at high resolution is not always possible. Here, we introduce a new computational method, MC-3DQSAR, to determine the vital elements of target RNA structure from mutagenesis and available high-resolution data. We applied the method to further characterize the structural determinants of the bacterial 23S ribosomal RNA sarcin–ricin loop (SRL), as well as those of the lead-activated and hammerhead ribozymes. The method was accurate in confirming experimentally determined essential structural elements and predicting the viability of new SRL variants, which were either observed in bacteria or validated in bacterial growth assays. Our results indicate that MC-3DQSAR could be used systematically to evaluate the drug-target potentials of any RNA sites using current high-resolution structural data.
Highlights
Across the world, people are dying from bacterial infections, which formerly we were able to manage with antibiotics
Mutagenesis experiments produce invaluable information by providing positive, and negative, examples, which combined with high-resolution structures have been shown crucial to identify nucleotides interactions and chemical groups involved in vital functions of bacterial ribosomal RNA
The ␣-sarcin catalyzes the hydrolysis of the phosphodiester linkage between the R and A nucleotides of the sarcin–ricin loop (SRL) GNRA tetraloop [43], while the ricin favors the depurination of the N [44]
Summary
People are dying from bacterial infections, which formerly we were able to manage with antibiotics. The structures of several prokaryotic and eukaryotic ribosomes free and bound to antibiotics have been determined at high resolution [2,3]. These structures revealed important molecular details about how some antibiotics bind and affect ribosome function, how mutations can lead to antibiotic resistance and offer new insights into designing new antibiotics [4,5]. Mutagenesis experiments produce invaluable information by providing positive, and negative, examples, which combined with high-resolution structures have been shown crucial to identify nucleotides interactions and chemical groups involved in vital functions of bacterial ribosomal RNA (rRNA). The comparison of crystal structures of viable and lethal sequence variants in Escherichia coli provided further insights into structural elements of the 23S rRNA involved in the recognition and binding to the elongation factor G (EF-G) [6,7,8]
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call