In this Phase I project Metheor Therapeutics is proposing a unique approach to developing novel DNA methyltransferase (DNMT) inhibitors, testing the concept of a substrate trap designed to capture and deplete the enzyme. Inhibition of DNMT activity is a validated therapeutic approach for Myelodysplastic Syndrome and Acute Myeloid Leukemia. Two nucleoside analogs, Vidaza and Dacogen are marketed for these indications but dose-limiting toxicities due to incorporation in the genome limit their applicationin these indications as well as for other cancers or diseases. The development of novel inhibitors that function without incorporation in the genome has the potential to significantly broaden the clinical use of DNMT inhibitors. In our approach, we merged advances in oligonucleotide chemistry driven by the development of therapeutic RNAi compounds, with the growing understanding of DNMT interaction with oligonucleotide substrates to produce DNMT Trapping Oligonucleotides (DTOs). In preliminary studies, Metheor has identified DTOs with single nM IC50 that re-activate gene expression in cell lines. The objective of this project is to optimize te DTOs and further characterize their activity in cancer cell lines with a view to in vivo studies in Phase II research.
The Specific Aims of the project are:
Aim 1 : To test improved DTOs in a biochemical assay for inhibition of DNMT activity. Active DTOs with a phosphorothioate (PS) backbone will be further improved by inserting 2'OMe-modified nucleotides into the sequence and the inhibition of the new DTOs will be evaluated against the lead in biochemical assays. Extensive optimization is beyond the scope of Phase I program but basic features such as hairpin vs. double stranded vs. single stranded, length and nature of the sequence, and CpG content are additional examples of characteristics that can be explored.
Aim 2 : To evaluate the biologic effect of the DTOs identified in Specific Aim 1 on DNA methylation and gene transcription in human cell lines (T-24 and HepG2). We anticipate 1) Identifying DTOs that effectively inhibit DNMT1 in biochemical assays and cell culture;2) Providing evidence that DTOs effectively inhibit DNMTs in different cellular environments;3) Selecting a panel of modified DTOs, that effectively inactivate DNMT1 in cells and are expected to have favorable PK/PD properties in vivo in animal models of HCC. The results of this work will inform the design of the Phase II study which will lead to selection of a pre-clinical drug candidate.

Public Health Relevance

Inhibitors of DNA Methyltransferases have both research and clinical relevance. Compounds with potent inhibitory activity coupled with improved toxicity profiles could displace existing inhibitors used in the treatment of Myelodysplastic syndrome, and find broader application for other cancers and other diseases. In this project we develop a new approach to DNMT inhibition, using DNMT trapping oligonucleotides. This approach avoids incorporation of modified nucleosides into newly synthesized DNA reducing or eliminating the main cause of dose-limiting toxicities of existing drugs.

National Institute of Health (NIH)
Small Business Innovation Research Grants (SBIR) - Phase I (R43)
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Special Emphasis Panel (ZRG1)
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Fabian, Miles
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Metheor Therapeutics Corporation
United States
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