Methyltransferase Inhibitors: Competing with, or Exploiting the Bound Cofactor

Freitas, Renato Ferreira de; Ivanochko, Danton; Schapira, Matthieu

doi:10.3390/molecules24244492

Cited by 45 publications

(40 citation statements)

References 95 publications

(138 reference statements)

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“…In this regard, an inhibitor of DOT1L (pinometostat) has recently entered clinical trials in leukemia [ 91 , 145 ], and it may be possible to see if this agent also inhibits NSUN2. Large consortia such as the Structural Genomics Consortium (SGC) may identify novel agents capable of targeting this RNMT [ 146 ], or indeed, companies targeting RNA epigenetics may develop candidate leads to move forward in the clinic [ 140 ].…”

Section: Resultsmentioning

confidence: 99%

The RNA Methyltransferase NSUN2 and Its Potential Roles in Cancer

Chellamuthu

Gray

2020

Cells

137

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5-methylcytosine is often associated as an epigenetic modifier in DNA. However, it is also found increasingly in a plethora of RNA species, predominantly transfer RNAs, but increasingly found in cytoplasmic and mitochondrial ribosomal RNAs, enhancer RNAs, and a number of long noncoding RNAs. Moreover, this modification can also be found in messenger RNAs and has led to an increasing appreciation that RNA methylation can functionally regulate gene expression and cellular activities. In mammalian cells, the addition of m5C to RNA cytosines is carried out by enzymes of the NOL1/NOP2/SUN domain (NSUN) family as well as the DNA methyltransferase homologue DNMT2. In this regard, NSUN2 is a critical RNA methyltransferase for adding m5C to mRNA. In this review, using non-small cell lung cancer and other cancers as primary examples, we discuss the recent developments in the known functions of this RNA methyltransferase and its potential critical role in cancer.

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Section: Resultsmentioning

confidence: 99%

The RNA Methyltransferase NSUN2 and Its Potential Roles in Cancer

Chellamuthu

Gray

2020

Cells

137

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“…Methyltransferases have been shown to be druggable, 32 with more than 20 potent, selective, and cell-active small molecules (chemical probes) discovered for such enzymes in the last decade. 32 Typically, both SAM 33 and substrate binding sites of methyltransferases can be targeted for drug discovery. 32 The optimized FP-based RNA displacement assay for the nsp10-nsp16 complex is suitable for high-throughput screening to identify RNA competitive inhibitors.…”

Section: Resultsmentioning

confidence: 99%

A High-Throughput RNA Displacement Assay for Screening SARS-CoV-2 nsp10-nsp16 Complex toward Developing Therapeutics for COVID-19

et al. 2021

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SARS-CoV-2, the coronavirus that causes COVID-19, evades the human immune system by capping its RNA. This process protects the viral RNA and is essential for its replication. Multiple viral proteins are involved in this RNA capping process, including the nonstructural protein 16 (nsp16), which is an S-adenosyl-l-methionine (SAM)-dependent 2′- O-methyltransferase. Nsp16 is significantly active when in complex with another nonstructural protein, nsp10, which plays a key role in its stability and activity. Here we report the development of a fluorescence polarization (FP)-based RNA displacement assay for nsp10-nsp16 complex in a 384-well format with a Z′ factor of 0.6, suitable for high-throughput screening. In this process, we purified the nsp10-nsp16 complex to higher than 95% purity and confirmed its binding to the methyl donor SAM, the product of the reaction, S-adenosyl-l-homocysteine (SAH), and a common methyltransferase inhibitor, sinefungin, using isothermal titration calorimetry (ITC). The assay was further validated by screening a library of 1124 drug-like compounds. This assay provides a cost-effective high-throughput method for screening the nsp10-nsp16 complex for RNA competitive inhibitors toward developing COVID-19 therapeutics.

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“…26 Methyltransferases are druggable. 27 In the last decade, a significant number of selective and cell-active small molecules (chemical probes) have been discovered for human methyltransferases 24,28,29 and some are in clinical trials for various cancers. 28,29…”

Section: Discussionmentioning

confidence: 99%

Probing the SAM Binding Site of SARS-CoV-2 nsp14 in vitro Using SAM Competitive Inhibitors Guides Developing Selective bi-substrate Inhibitors

Devkota

Schapira

Perveen

et al. 2021

Preprint

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The COVID-19 pandemic has clearly brought the healthcare systems world-wide to a breaking point along with devastating socioeconomic consequences. The SARS-CoV-2 virus which causes the disease uses RNA capping to evade the human immune system. Non-structural protein (nsp) 14 is one of the 16 nsps in SARS-CoV-2 and catalyzes the methylation of the viral RNA at N7-guanosine in the cap formation process. To discover small molecule inhibitors of nsp14 methyltransferase (MT) activity, we developed and employed a radiometric MT assay to screen a library of 161 in house synthesized S-adenosylmethionine (SAM) competitive methyltransferase inhibitors and SAM analogs. Among seven identified screening hits, SS148 inhibited nsp14 MT activity with an IC50 value of 70 ± 6 nM and was selective against 20 human protein lysine methyltransferases indicating significant differences in SAM binding sites. Interestingly, DS0464 with IC50 value of 1.1 ± 0.2 μM showed a bi-substrate competitive inhibitor mechanism of action. Modeling the binding of this compound to nsp14 suggests that the terminal phenyl group extends into the RNA binding site. DS0464 was also selective against 28 out of 33 RNA, DNA, and protein methyltransferases. The structure-activity relationship provided by these compounds should guide the optimization of selective bi-substrate nsp14 inhibitors and may provide a path towards a novel class of antivirals against COVID-19, and possibly other coronaviruses.

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Methyltransferase Inhibitors: Competing with, or Exploiting the Bound Cofactor

Cited by 45 publications

References 95 publications

The RNA Methyltransferase NSUN2 and Its Potential Roles in Cancer

The RNA Methyltransferase NSUN2 and Its Potential Roles in Cancer

A High-Throughput RNA Displacement Assay for Screening SARS-CoV-2 nsp10-nsp16 Complex toward Developing Therapeutics for COVID-19

Probing the SAM Binding Site of SARS-CoV-2 nsp14 in vitro Using SAM Competitive Inhibitors Guides Developing Selective bi-substrate Inhibitors

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