Chemical Space Virtual Screening against Hard-to-Drug RNA Methyltransferases DNMT2 and NSUN6

Abstract

Targeting RNA methyltransferases with small molecules as inhibitors or tool compounds is an emerging field of interest in epitranscriptomics and medicinal chemistry. For two challenging RNA methyltransferases that introduce the 5-methylcytosine (m5C) modification in different tRNAs, namely DNMT2 and NSUN6, an ultra-large commercially available chemical space was virtually screened by physicochemical property filtering, molecular docking, and clustering to identify new ligands for those enzymes. Novel chemotypes binding to DNMT2 and NSUN6 with affinities down to KD,app = 37 µM and KD,app = 12 µM, respectively, were identified using a microscale thermophoresis (MST) binding assay. These compounds represent the first molecules with a distinct structure from the cofactor SAM and have the potential to be developed into activity-based probes for these enzymes. Additionally, the challenges and strategies of chemical space docking screens with special emphasis on library focusing and diversification are discussed.

Structure-based virtual screening of unbiased and RNA-focused libraries to identify new ligands for the HCV IRES model system

“…Thus, all molecules selected for testing originate from the unbiased library. We hypothesize that focusing of larger VS libraries or even make-on-demand chemical spaces 65–68 has the potential to result in higher hit rates and numbers. Eventually, the general concept of RNA-focusing might be insufficient.…”

The impact of tRNA modifications on translation in cancer: identifying novel therapeutic avenues

“…Since the discovery of the efficacy of the first inhibitor targeting METTL3, novel drugs aimed at epitranscriptomic targets have been developed to enhance treatments for cancer and various diseases. Notably, recent advancements include the creation of new molecules inhibiting NSUN6, NSUN2 and PUS7, with ongoing efforts in progress ( 97 , 192–194 ). In this era of big data, we now possess the opportunity to analyze physicochemical properties, molecular docking and compound library clustering through virtual screening.…”

“…This approach allows us to identify compounds capable of inhibiting undruggable or challenging targets. Employing chemical space docking screens, NSUN2 and NSUN6 inhibitors have been identified as promising candidates ( 192 , 193 ).…”

“…Another member of the NSUN family is NSUN6, which lacked previously designed inhibitors. However, employing diverse predictive techniques led to the design of initial compounds demonstrating affinities for NSUN6 ( 192 ). These compounds against NSUN family members are in early stages of development and need further efforts by the pharmaceutical industry to advance with the development of epitranscriptomic drugs as a new therapy for cancer treatment.…”