STARFISH DNA

You will find here news and information regarding STARFISH DNA in a "go with the flow" manner:

STARFISH DNA's goals achieved!

[Dec. 13, 2019] That’s done! Just before the end of her MSCA fellowship, Katerina succeeded in achieving the originally defined goal of the STARFISH DNA project, that is, to show that i- three-way DNA junctions (TWJs) can be targeted by small-molecules to create DNA damage with ultimately leads to cancer cell death, and ii- this effect can be potentiated by DNA repair inhibitors in an approach referred to as chemically induced synthetic lethality. With the help of Anton Granzhan (Institut Curie, Orsay FR), who synthesized exquisite molecular tools to target TWJs, and Sébastien Britton (IPBS, Toulouse FR) who designed the drug cocktails to synergistically kill cancer cells, we have been able to provide the community with new targets for anticancer strategy, fully validated small-molecules to target them in cells, and an innovative combination of drugs to optimize the chemotherapeutic response. These results have now been accepted for publication in the JACS: congrats to all!

-> The manuscript can be downloaded at the publisher's website here

-> A personnal, unformatted copy of this manuscript can be found here

Our STARFISH DNAs' results summed up in a review

[Aug. 21, 2019] We are really happy that the first results we collected in the framework of this ERC fellowship are now summed up in a review published in EurJOC. Part of these results indeed belong to a global strategy we follow for several years now, aiming at diversifying the use of poly-aza-macrocycles (PAM, or macrocyclic polyamines, MPA) beyond their classical roles of molecular cages for metals. This was the case for the biomimetic quadruplex ligands TASQ but also here for one of our best prototypes of DNA junction ligand TACN-Q. Delighted to write this 100% ICMUB review with Katerina along with Pauline, Claire, Ibai and Tony. Hope you will enjoy reading it as much as we enjoyed writing it!

-> The manuscript can be downloaded at the publisher's website here

-> An open access, unformatted copy of this manuscript can be found here

A step further: screening 1200 compounds for identifying hits

[Apr. 3, 2019] Compared to normal cells, cancer cells harbor a flawed repertoire of DNA damages signaling and repair capabilities. This aspect thus provides a window of therapeutic opportunities for compounds that trigger DNA damage. In the framework of the STARFISH DNA project, we focus on small-molecules that stabilize three-way DNA junctions (TWJ), given that these higher-order DNA structures represent topological hindrances to polymerase that can hamper proper DNA transactions (replication, transcription). The TWJ-ligands could thus represent a novel and promising class of crisis-inducing agents. To demonstrate this, we have, over the past months, invested massive efforts to identify promising TWJ-ligands (affinity, selectivity), on the basis of the previously reported TWJ-screen assay. We have screened >1200 compounds (from 3 different libraries) and identified 15 candidates on stringent criteria. Next, we have designed and implemented a new in vitro workflow comprising 6 different assays, that is, TWJ-screen, PAGE, FRET-melting, ESI-MS, dialysis and SRB assays, which allowed for to refine our pool of candidates to 3 (1,5-BisNP-O, 2,7-BisAO and 3,3'-TrisBP). With these molecules in hands, we finally provided the first evidences that TWJ-ligands indeed trigger DNA damage, through immunodetection studies using labeled antibody against gamma-H2AX.

These resultas have now been published in J. Med. Chem. Congrats to Katerina for this huge, multidisciplinary work, and to our collaborators that helped us in this endeavor, chief among them Sébastien Britton (IPBS Toulouse) and Dominique Delmas' team (LNC Dijon), along with our regular collaborators Anton & Marie-Paule (Institut Curie Orsay, FR), Murielle (CEA Grenoble, FR), Charles (ICMUB, Dijon) and Bruno (Neuchâtel, CH).

-> The manuscript can be downloaded at the publisher's website here

-> An open access, unformatted copy of this manuscript can be found here

A beautiful start for our ERC grantee Katerina!

[Feb. 16, 2018] Katerina Duskova, our proud ERC MSCA fellow, started the STARFISH DNA project in Oct. 2017, and.. what a start! No sooner had she arrived that she developed and optimized a reliable in vitro high-throughput screening (HTS) assay for facilitating the quest of chemicals displaying promising TWJ-interacting properties. Indeed, for cell-based investigations to be reliably performed and interpreted, specific molecular tools must be uncovered that display both exquisite affinity and selectivity for their DNA targets. To date, the rational design of TWJ interacting compounds (or TWJ ligands) has proven efficient but has offered a limited diversity of ligands; to tackle this issue, high-throughput screens of unbiased chemical libraries provide unique opportunities to discover unexpected chemical scaffolds.We have thus invested massive efforts in the development of an HTS assay on the basis of what has been done and reported over the past years in various nucleic acids fields, to allow for the identification of TWJ interacting agents on highly stringent criteria in terms of efficiency and selectivity. This assay named TWJ-Screen provides information about the capacity of a ligand to interact with TWJ that folds from separated DNA single strands (to mimic DNA strand separation that occurs during replication) in a competitive context (that is, in presence of mixture of nucleic acids). This in vitro HTS assay named TWJ-Screen provides a ligands selection in i- a practically convenient manner since it is neither technically demanding (mix-and-measure approach) nor time-consuming (1h at 37°C), and ii- a highly reliable manner, as illustrated by the numerous controls (up to 5) performed during each ligand evaluation. This makes TWJ-Screen assay a robust and versatile HTS.

This assay has now been published in Nucleic Acids Res. (Methods section), an authoritative, gold open access journal from Oxford University Press.

-> The manuscript can be downloaded free of charge at the publisher's website here

STARFISH DNA: let's go!

[Oct. 1, 2017] Cancer continues to claim the lives of millions of patients (more than 8.8 million deaths in 2015, see the NIH cancer statistics and WHO cancer statistics), despite the recent advances in cancer therapeutics. The 5-year survival rates are now over 90% for patients who are diagnosed with prostate and skin cancers for instance, but patients suffering from pancreatic, liver and lung cancers have far lower survival rates (circa 20%). The situation is even more complicated for certain type of cancers with good prognosis (e.g., breast cancer) nevertheless displaying very low 5-year survival rates for some subtypes of tumors. This highlights the urgent need of new therapeutic strategies, either deviating from classical anticancer drug regiments or exploiting them in an alternative manner.

Most of the anticancer drugs currently under clinical use trigger irreversible DNA damages and thus, promote replicative stress. Replicative stress (RS) is a generic term that encompasses all putative impediments to DNA replication able to stall or collapse replication fork. It thus creates DNA damages that trigger unsustainable genetic instabilities, which eventually leads to cell death. Current chemotherapeutic interventions aim at bolstering RS as a way to inflict severe genetic injuries to cancer cells to cause proliferation machinery stoppages. The specificity (cancer versus healthy cells) of the treatment is relying on the poor ability of cancer cells to deal with DNA damages properly. DNA-damaging drugs, including oxidizing and alkylating agents as well as inhibitors of DNA-related enzymes, trigger irreversible DNA damages, therefore representing a golden way to provoke RS.

Over the past years, the non-covalent stabilization of unusual, non-B-DNA structures (i.e., all DNA structures that deviate from the canonical duplex-DNA) has emerged as an alternative and very promising way to create DNA damages. Indeed, DNA replication favors the rise of non-canonical DNA structures both upstream and downstream the replication forks due to positive and negative DNA supercoiling, respectively, along with strand separation. If not processed efficiently by specific cellular machineries, these non-canonical DNA structures represent another class of topological hindrances to replication fork progression that equally threaten genetic integrity. One of such non-B-DNA structures of particular interest for us is the three-way DNA junction (TWJ): our hypothesis is that the stabilization of TWJ by specific small molecules (so called TWJ ligands) might represent robust roadblocks to replication fork, thus providing a highly promising way to trigger RS and promote cell death of malignant cells.

The main goal of the project "Stalling the Replication Fork via the Impedimental Stabilization of Higher-order DNAs" (STARFISH DNA) is thus to identify compounds capable of fostering RS creating DNA damages through an original mechanism, i.e., blocking the progression of the replication fork via the small molecule-mediated stabilization of alternative DNA structures. This multidisciplinary research program encompasses all key fields of chemical biology, from the synthetic chemistry (ligands, fluorescent probes) biophysics, cell-biology and genomics to preclinical evaluations of best candidates. STARFISH DNA also aims at improving the efficacy of drugs currently under clinical uses (synergy, synthetic lethality, targeted therapies) to improve the patient treatment and well-being, therefore being in line with the most important societal issues and top priorities of H2020 programs.