How can the use of small molecules and supramolecular assemblies lead to new therapeutics? This question is addressed in the interview of Dr. Sofia Barluenga from the NCCR lab of Nicolas Winssinger at the University of Geneva. The identification of specific promising lead compounds with therapeutic activity is presented together with the state-of-the-art technology behind this achievement. Some aspects on the translation of new drug targets are also discussed.

In which areas of research is the Winssinger group involved in?

Our lab is involved in the design of innovative methodologies for the discovery of novel small molecules that are biologically interesting because they are designed to probe dynamic processes in biological systems. One of these strategies is the diversity-oriented synthesis based on active natural product scaffolds which have been selected by evolution for specific function.

Do some of your discoveries carry a potential societal impact?

Yes, that is the case. Our research brought us results leading to the development of a drug for cancer treatment. Other projects are still at a more basic research level as we first need to identify the target of the newly identified molecules. We always need to first understand the mode of action of a small molecule, to eventually evaluate its therapeutic potential.

Can you give us some examples of such promising applications?

We first started working on scaffolds of the resorcylic acid lactones (RAL), a group of naturally occurring oestrogenic compounds, with a variety of biological activities. From this scaffold, we developed a potent inhibitor of the heat shock protein HSP90, a molecule with potential therapeutic benefit in the treatment of various types of malignancies, as well as an orally bioavailable prodrug. This inhibitor has now been licensed and it is being developed against the most aggressive brain cancer form, glioblastoma, and other indications. Another interesting example stemming from the RAL scaffold is hypothemycin and a related RAL compound bearing a cis-enone moiety which react with a cysteine in a subset of kinases. These natural product-inspired molecules have emerged as an alternative pharmacophore inhibiting kinases. They are very different to the classical kinase inhibitors, typically adenine mimics, and are very selective owing to the fact that they can only react with kinases that have a cysteine in the right position. Both these two compounds are irreversible inhibitors in vitro of the signaling molecules, VEGFRs, which are implicated in tumor-dependent angiogenesis, while they inhibit in vivo tumor growth in a model of renal cell carcinoma (RENCA) in mouse with comparable efficacy to Sunitinib, an FDA‐ approved VEGFRs inhibitor. In addition, one of them strongly inhibits lung metastasis whereas Sunitinib does not. A collaboration with the pharmaceutical industry is established to further develop these compounds.

More recently, we have targeted the sesquiterpene lactones scaffold. Traditional medicine has extensively used herbal extracts from many plants containing these compounds. These lactones are rich in α,β-unsaturated functionalities that can react covalently with proteins. We first prepared analogues of deoxyelephantopin, a sesquiterpene lactone with anticancer properties. Using alkyne-tagged cellular probes and quantitative proteomics analysis (in collaboration with the former NCCR lab of A. Adibekian), we identified several cellular targets of deoxyelephantopin. We also demonstrated that deoxyelephantopin antagonizes a major nuclear receptor (PPARγ) activity in situ via covalent reaction of a cysteine residue in the zinc-finger motif. Such receptors play an essential role in the regulation of cellular differentiation, development, metabolism and tumorigenesis.

Any breakthrough foreseen in the near future?

Remi Patouret, a PhD student in our lab, is now working on analogues of goyazensolide, the main active ingredient of Eremanthus goyazensis, a plant of the sunflower family, which decreases cell proliferation of the genetic rare disease neurofibromatosis 2 (NF2) associated Schwannoma and Meningiomas. This natural sesquiterpene lactone, has also three α,β-unsaturated functionalities which inferred a potential covalent interaction with cysteines and it is Remi’s goal to prepare cellular probes to understand the target of this natural product. There are a lot of anecdotal evidences of efficacy in sesquiterpene lactones and we hope the basic research we conduct will bring clarity on its efficacy and might allow us to make a more potent analog.

From a drug development perspective, what is the value of identifying inhibitors that will bind irreversibly to their target?

The pharmaceutical industry has avoided the development of covalent drugs fearing that terminally inactivating the target through irreversible binding may result in unwanted toxicities. Allergies to β-lactams antibiotics (a class of broad-spectrum antibiotics) is a classic case. Covalent inhibitors are re-emerging as pharmacologically interesting entities with several candidates having received recent approval for therapeutic intervention. The terminal inactivation of a target can have important advantages, such as patients not needing a second dose of the drug until their body has made more protein (typically, 24-48 hours), thus not requiring to maintain high effective drug concentration in the bloodstream. Also, terminal inactivation is important if the drug binding is in competition with a more favourable interaction. For example, in the case of kinases which are involved in cancer and other diseases, drugs are in competition with the high energy molecule ATP which is present at mM concentrations. It’s tough competition for a drug that is present at 1000-fold lower concentration!

Can you explain the added-value of your technology? What is unique about your solution?

We provide new screening technologies, a new paradigm for library synthesis and ligand discovery which really empowers biomedical research. One of these new strategies is the Peptide nucleic acid (PNA)-encoded screening technology, to screen for inhibitors and profile enzymatic activity in complex proteomes. PNA stands for Peptide Nucleic Acid, a synthetic polymer, analogous to DNA and RNA, in which the sugar phosphate backbone has been replaced by a unit of N-(2 aminoethyl) glycine. In our group, we have favored the use of PNA, based on the more permissive chemistry of PNA relative to DNA. Library preparation can be done by standard solid phase synthesis and we have prepared libraries of peptides, heterocycles and glycoconjugates.

We have reported different screening formats including selections in solution and microarray that have yielded ligands against diverse target classes including lectins, bromodomains, as well as membrane receptors and chaperons like Hsp70 and P97. This technology has the potential to dramatically accelerate the pace at which we can discover a new drug lead. It also dramatically reduces the cost of discovering a ligand to a new protein which is really important in order to validate whether a new target is druggable. Current drugs only target a fraction of the proteome and we clearly need better technologies to limit the risk and cost entailed in the discovery of new targets.

How easy is it for a laboratory in academia to bring a technology/product into the market?

There have been huge efforts over the past 20 years to facilitate the translation of basic research into products useful for society, be it a technology or a drug. I think that today, it is fairly easy for a laboratory in academia to make a research tool commercially available. A different story is to bring a drug or a diagnostics tool into the market; this is a lot more expensive, well beyond what can be funded with academic grants and represents a huge time investment. You might have heard of the Valley of death which depicts the important gap in public and private funding for the first steps towards translation of novel drugs from basic research. But, more and more academic organizations are developing chemical and drug discovery capabilities and technologies, and a combination of venture capital, grants and industrial collaboration make it possible in the end.

Have you collaborated with a company? How fruitful do you think these academia-company collaborations are?

Yes, we had and have several industrial collaborations. From licensing of the HSP90 heat shock inhibitor, to a collaboration for the development of the VEGFR irreversible inhibitors as well as several collaborations in which we have screened industrial targets with our PNA-encoded technology, amongst others. These collaborations are important to develop compounds or technology beyond basic research.

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Sofia Barluenga is reasearch associate in the Winssinger lab, Department of Organic Chemistry, University of Geneva.