LongeCityNews Last Updated: 05 December 2025 - 06:53 AM

PKMYT1 (Membrane-associated Tyrosine/Threonine Protein Kinase 1) is a serine/threonine protein kinase that plays a pivotal role in cell cycle regulation. Previous studies have shown that inhibiting PKMYT1 through a synthetic lethality approach allows for the selective elimination of cancer cells bearing specific genetic mutations, such as CCNE1 amplification or mutations in FBXW7 and PPP2R1A, while sparing normal healthy cells and minimizing adverse effects. It makes PKMYT1 a promising therapeutic target for biomarker-defined patient populations.

However, existing PKMYT1 inhibitors face significant limitations, including insufficient molecular diversity and poor selectivity, which can lead to off-target effects and dose-limiting toxicity in clinical trials. Additionally, concerns about acquired resistance arising from mutations in cancer cells further complicate inhibitors’ efficacy. Research also indicates that PKMYT1 has important non-catalytic functions, such as stabilizing β-catenin and activating Wnt signaling, which are not addressed by conventional inhibitors. These challenges underscore the need for new therapeutic strategies that can more effectively and safely target PKMYT1 in cancer.

In a recent pioneering study, researchers at Insilico Medicine (“Insilico”), a generative artificial intelligence (AI)-driven clinical-stage biotechnology company, harnessed its AI-driven generative chemistry platform, Chemistry42, to design a novel, first-in-class PROTAC targeting PKMYT1, D16-M1P2, which employs a dual mechanism of action—inducing PKMYT1 degradation while directly inhibiting its kinase activity. This innovative strategy holds promises for overcoming limitations of existing inhibitors, such as poor selectivity and acquired resistance, and to effectively target both the catalytic and non-catalytic functions of PKMYT1. As a result, the PROTAC demonstrates the potential for a more selective, potent, and durable therapeutic effect.

Published in Nature Communications, this work highlights the powerful capabilities of Insilico’s AI-driven generative chemistry and serves as a compelling example of its ability to guide complex, multi-component drug design.

The process of discovery began with the design of PKMYT1 inhibitors. Researchers at Insilico utilized the Chemistry42 AI platform to design a novel PKMYT1 inhibitor by integrating the pharmacophore features of two established kinase inhibitors. Guided by over 40 AI models within Chemistry42, they generated 2,023 novel molecules. A thorough filtering process—assessing novelty, binding interactions, and drug-like properties—identified the most promising candidate, which was subsequently synthesized as compound 1.

Subsequently, the team systematically optimized compound 1 through structure-based design and medicinal chemistry. This iterative process enhanced its potency and pharmacokinetic properties, ultimately yielding compound 4—an inhibitor with excellent kinase selectivity that provided an ideal attachment point for PROTAC development.

After obtaining the optimized inhibitor, the team constructed a 3D virtual model of the PKMYT1–PROTAC–CRBN ternary complex to determine optimal linker parameters. Leveraging the Chemistry42 AI platform, they generated novel linkers to connect compound 4 to the E3 ligase, ultimately synthesizing the first-generation PROTAC, D1. Through subsequent evaluation and modification, the PROTACs were further optimized for solubility, clearance, and oral exposure, leading to the development of D16-M1P2 as the final lead candidate.

The lead PROTAC, named D16-M1P2, demonstrated promising performance in preclinical studies.It exhibited remarkable selectivity, inhibiting only 4 out of 403 kinases tested, which resulted in potent anti-tumor activity in xenograft models as well as favorable oral bioavailability across multiple preclinical species. Compared to traditional PKMYT1 inhibitors, D16-M1P2 induces more durable and sustained effects by targeting PKMYT1 for complete degradation through the ubiquitin-proteasome system, with activity maintained for at least 24 hours after drug removal. Additionally, D16-M1P2 offers a dual mechanism of action: it primarily degrades PKMYT1 but also directly inhibits residual kinase activity at higher concentrations, ensuring comprehensive pathway suppression.

“The dual-mechanism of D16-M1P2, combining potent degradation with kinase inhibition, offers a multi-pronged attack on a critical cell cycle regulator in cancer,” said Feng Ren, PhD, co-CEO and Chief Scientific Officer of Insilico Medicine. “Its high selectivity and sustained pharmacodynamic effects observed in preclinical studies suggest it could overcome the safety and efficacy limitations of previous PKMYT1 inhibitors. This molecule serves as both a powerful chemical probe to study PKMYT1 biology and a promising new therapeutic candidate.”

The research team has now advanced D16-M1P2 to the Pre-Candidate (Pre-PCC) validation stage. Previously, Insilico published the design and optimization process of the PKMYT1 inhibitor series from this program in the JMC in February 2025. Building on this foundation, the new research upgrades the modality from small molecules to PROTACs, achieving further improvements in selectivity, safety, and efficacy. This study also exemplifies how AI tools can adeptly navigate the complexities of PROTAC design—spanning inhibitor design to linker optimization —pioneering new directions in AI-driven drug discovery.

“This paper is a clear demonstration of our AI platform’s ability to innovate beyond conventional small molecules and tackle next-generation therapeutic modalities like PROTACs,” said Alex Zhavoronkov, PhD, founder and co-CEO of Insilico Medicine. “By generating both the novel warhead and the optimal linker, we have shown that AI can be an invaluable partner in designing highly specific, multi-functional drugs for challenging cancer targets.”

Since its inception, Insilico has published over 200 peer-reviewed papers. This marks the sixth publication by the company in Nature Portfolio journals since 2024. Leveraging sustained scientific breakthroughs at the intersection of biotechnology, artificial intelligence, and automation, Insilico ranked Top 100 global corporate institutions in Nature Index‘s “2025 Research Leaders: global corporate institutions for biological sciences and natural sciences publications”.

Harnessing state-of-the-art AI and automation technologies, Insilico has significantly improved the efficiency of preclinical drug development, setting a benchmark for AI-driven drug R&D. While traditional early-stage drug discovery typically requires 2.5 to 4 years, Insilico has nominated 20 preclinical candidates with an average timeline—from project initiation to preclinical candidate (PCC) nomination—of just 12 to 18 months per program, with only 60 to 200 molecules synthesized and tested in each program.

About Insilico Medicine

Insilico Medicine, a leading and global AI-driven biotech company, utilizes its proprietary Pharma.AI platform and cutting-stage automated laboratory to accelerate drug discovery and advance innovations in life sciences research. By integrating AI and automation technologies and deep in-house drug discovery capabilities, Insilico is delivering innovative drug solutions for unmet needs including fibrosis, oncology, immunology, pain, and obesity and metabolic disorders. Additionally, Insilico extends the reach of Pharma.AI across diverse industries, such as advanced materials, agriculture, nutritional products and veterinary medicine. For more information, please visit www.insilico.com.

One of the most interesting areas of research into aging at the moment is the question of whether detrimental epigenetic changes that occur in cells throughout the body with age, altering cell behavior for the worse, are caused by the operation of DNA repair processes in response to stochastic damage to nuclear DNA. The concept and animal study evidence are recent enough that it should be considered speculative, and any of the details published to date subject to revision.

If true, however, this relationship in which DNA repair causes epigenetic aging would neatly resolve a range of challenges in the understanding of the role of nuclear DNA damage in aging. For example that mutational damage to nuclear DNA doesn't appear to cause enough harm to cell function to explain the major changes that occur with age. Most nuclear DNA damage occurs in somatic cells with few cell divisions remaining, limiting the spread of the mutation, and occurs in gene sequences that don't much matter or are not even used.

Somatic mosiacism, the spread of mutations over time from stem cell populations out into the tissues they support via the vector of daughter somatic cells, can somewhat salvage this situation by amplifying a tiny number of mutations into widespread existence. However, present investigations of the role of clonal hematopoiesis of indeterminate potential, the name given to somatic mosaicism in hematopoietic cells and the immune system, suggest that it isn't harmful enough to explain very much of aging. It raises risks, it isn't driving degeneration.

Today's open access paper is a recent exploration of epigenetic change induced by DNA damage, employing a mouse model generated a few years ago. Here, this model is crossbred with an Alzheimer's disease model in order to look at relevance to that condition. Cynically, one should assume that this choice of direction in research is driven as much by the funding incentives as the reasonable scientific rationale for the relevance of a mechanism of aging to any specific age-related condition, as work on Alzheimer's disease represents a sizable fraction of all public funding for aging research. Still, all significant new work on this issue of DNA repair and epigenetic change is welcome.

DNA Break-Induced Epigenetic Alterations Promote Plaque Formation and Behavioral Deficits in an Alzheimer's Disease Mouse Model

The dramatic increase in human longevity over recent decades has contributed to a rising prevalence of age-related diseases, including neurodegenerative disorders such as Alzheimer's disease (AD). While accumulating evidence implicates DNA damage and epigenetic alterations in the pathogenesis of AD, their precise mechanistic role remains unclear. To address this, we developed a novel mouse model, DICE (Dementia from Inducible Changes to the Epigenome), by crossing the APP/PSEN1 (APP/PS1) transgenic AD model with the ICE (Inducible Changes to the Epigenome) model, which allows for the controlled induction of double-strand DNA breaks (DSBs) to stimulate aging-related epigenetic drift.

We hypothesized that DNA damage induced epigenetic alterations could influence the onset and progression of AD pathology. After experiencing DNA damage for four weeks, DICE mice, together with control, ICE, and APP/PS1 mice, were allowed to recover for six weeks before undergoing a battery of behavioral assessments including the open-field test, light/dark preference test, elevated plus maze, Y-maze, Barnes maze, social interaction, acoustic startle, and pre-pulse inhibition (PPI). Molecular and histological analyses were then performed to assess amyloid-β pathology and neuroinflammatory markers.

Our findings reveal that DNA damage-induced epigenetic changes significantly affect cognitive behavior and alters amyloid-β plaque morphology and neuroinflammation as early as six months of age. These results provide the first direct evidence that DNA damage can modulate amyloid pathology in a genetically susceptible AD model. Future studies will be aimed at investigating DNA damage-induced epigenetic remodeling across additional models of AD and neurodegeneration to further elucidate its role in brain aging and disease progression.

In Nature Aging, researchers have published their finding that targeting urokinase plasminogen activator receptor (uPAR), a senescence-associated protein, restores gut function in mice.

One way the gut lining ages

Of all the tissues in the human body, the intestinal epithelium, which lines the gut, replaces its cells most quickly [1]. This self-renewal diminishes with aging [2], leading to leaky gut and an overall decline in function [3]. While there has been substantial previous research in this area, leading to multiple potential treatments, these researchers note that the safety and efficacy of such approaches remain unproven in human beings.

They point out two main hallmarks of aging that are of interest in this context: the chronic, age-related inflammation known as inflammaging and the increasing numbers of senescent cells. Their previous work has revealed that senescent cells that express uPAR are harmful in excess and that CAR T cells programmed to attack this receptor may be useful in dealing with them [4]. Other researchers have concurred, finding that using CAR T cells against uPAR-expressing cells fights liver fibrosis in a mouse model [5].

That previous work was on other tissues, and this is the first study that specifically uses CAR T cells to target uPAR cells in the intestinal epithelium.

Removing uPAR cells restores gut function

To begin their study, the researchers analyzed cells from the small intestines of 3-month-old and 20-month-old mice. Unsurprisingly, the older mice had more uPAR-expressing cells, and these cells were also very likely to express the senescence biomarker SA-β-gal and have other presentations of senescence, such as a lack of proliferation. A gene expression analysis found that these uPAR cells had upregulated DNA repair and immune response. Of all the cells identified as senescent by SenMayo analysis [6], roughly three-fifths expressed uPAR.

Similar results were found in cells derived from human beings; using samples taken from 25- to 30-year-olds and 65- to 70-year-olds, the researchers found that, like mice, older people have more uPAR-expressing cells and that these cells have similar gene expression profiles and a similar relationship to senescence.

The researchers then introduced their CAR T cells into the bloodstreams of 3-month-old and 18- to 20-month-old mice. In the small intestines of the older animals, this cell population rapidly expanded, dramatically reducing the numbers of cells that expressed uPAR and SA-β-gal, while restoring intestinal integrity as measured by FITC-Dextran.

The numbers of stem cells and proliferating cells were also restored, with the stem cells of treated mice more readily able to form organoids. There was also a decrease in inflammation and dysbiosis, with the treated animals having gut flora that more strongly resembled that of younger animals. Further work found that these results were due to the CAR T cells’ effects on intestinal tissues rather than on immune cells.

The study also took a look at the well-known senolytic combination of dasitnib and quercetin. The results were similar to CAR T cells, with this combination also reducing senescent cell levels and restoring stem cells in the small intestine.

Long-term benefits

Amazingly, one treatment with anti-uPAR CAR T cells in 3-month-old mice persisted throughout the lifespans of these animals, despite having negligible effects during youth. The mice so treated had detectable uPAR-fighting cells 15 months later, with a signfiicant decline in cellular senescence along with improvements in stem cell numbers, intestinal integrity, and gut health.

In total, the researchers hold that “uPAR+ epithelial cells are key drivers of intestinal aging and associated inflammation and dysfunction.” While regeneration-promoting approaches have been previously linked to cancer, the researchers note that none of the mice that received CAR T cells developed intestinal cancer as a result. Clinical trials are needed to determine if this approach is safe and effective in humans.

Literature

[1] Barker, N. (2014). Adult intestinal stem cells: critical drivers of epithelial homeostasis and regeneration. Nature reviews Molecular cell biology, 15(1), 19-33.

[2] Brunet, A., Goodell, M. A., & Rando, T. A. (2023). Ageing and rejuvenation of tissue stem cells and their niches. Nature Reviews Molecular Cell Biology, 24(1), 45-62.

[3] Dumic, I., Nordin, T., Jecmenica, M., Stojkovic Lalosevic, M., Milosavljevic, T., & Milovanovic, T. (2019). Gastrointestinal tract disorders in older age. Canadian Journal of Gastroenterology and Hepatology, 2019(1), 6757524.

[4] Amor, C., Feucht, J., Leibold, J., Ho, Y. J., Zhu, C., Alonso-Curbelo, D., … & Lowe, S. W. (2020). Senolytic CAR T cells reverse senescence-associated pathologies. Nature, 583(7814), 127-132.

[5] Dai, H., Zhu, C., Huai, Q., Xu, W., Zhu, J., Zhang, X., … & Wang, H. (2024). Chimeric antigen receptor-modified macrophages ameliorate liver fibrosis in preclinical models. Journal of hepatology, 80(6), 913-927.

[6] Saul, D., Kosinsky, R. L., Atkinson, E. J., Doolittle, M. L., Zhang, X., LeBrasseur, N. K., … & Khosla, S. (2022). A new gene set identifies senescent cells and predicts senescence-associated pathways across tissues. Nature communications, 13(1), 4827.

Butyrate is one of the better known metabolites generated by microbial populations within the gut microbiome, a product of the fermentation of dietary fiber. Butyrate has been shown to produce beneficial effects in a range of tissues, such as via increased BDNF signaling to improve brain and muscle health. Production of butyrate declines with age, a consequence of harmful shifts in the composition of the gut microbiome that take place with age. Here, researchers show that butyrate is senomorphic, in that is reduces the number of cells entering a senescent state. This sort of effect is thought to be beneficial over time, as it allows the normal mechanisms of senescent cell clearance, impaired with age but still operating, to catch up and reduce the age-related burden of senescence.

Advancing age is accompanied by an accumulation of senescent T cells that secrete pro-inflammatory senescence-associated secretory phenotype (SASP) molecules. Gut-microbiota-derived signals are increasingly recognised as immunomodulators. In the current study, we demonstrated that ageing and the accumulation of senescent T cells are accompanied by a reduction in microbial-derived short-chain fatty acids (SCFAs).

Culturing aged T cells in the presence of butyrate suppresses the induction of a senescence phenotype and inhibits the secretion of pro-inflammatory SASP factors, such as IL6 and IL8. Administration of faecal supernatants from young mice rich in butyrate prevented in vivo accumulation of senescent spleen cells in aged mice. The molecular pathways governing butyrate's senomorphic potential include a reduced expression of DNA damage markers, lower mitochondrial reactive oxygen species (ROS) accumulation, and downregulation of mTOR activation, which negatively regulates the transcription factor NFκB.

Our findings establish butyrate as a potent senomorphic agent and provide the evidence base for future microbiome restitution intervention trials using butyrate supplements for combating T cell senescence, ultimately reducing inflammation and combating age-related pathologies to extend lifelong health.

Link: https://doi.org/10.1111/acel.70257