Description of the technology
Classic acrylamide:
- irreversible
- lower selectivity
- limited synthetic elaboration
Reversible acrylamide:
- increased reactivity
- lower selectivity
- limited synthetic elaboration
Nature inspired warheads:
- 3D structure
- increased reactivity
- resilience against off-targets
- simpler synthetic elaboration
Tunable JNK-IN-8 analogs:
- improved JNK selectivity
- resilience against off-target thiols
- JNK isoform selectivity available
- reactivity and binding affinity comparable or superior
- fine-tuning residence time
Protenic Kft designs and synthesizes nature inspired cyclic warheads for selective targeting nucleophiles on protein surfaces. Classic acrylamide based warheads make irreversible covalent bonds with cysteines. Although modified versions of this warhead (e.g., cynoacrylamide) may form a reversible covalent bond but their simple acyclic structure is fundamentally different from cyclic warhead designs. With double-activated cyclopentenone/cyclohexenone based compounds there is a great deal of steric congestion in the protein adduct at the beta-carbon in the α,β-unsaturated ketone motif. This gives new properties to the Michael acceptor electrophile regarding its interaction with nucleophiles such as cysteine or histidine.
Many biologically active natural products contain electrophilic Michael acceptor fragments. For example, curcumin and 4-hydroxyderricin contain an acyclic α,β-unsaturated ketone that alkylates cysteines. Other antitumor or anti-inflammatory herbal compounds such as Withaferin A or zerumbone contain cyclic α,β-unsaturated ketones and react with nucleophilic residues of proteins. These observations contributed to a paradigm shift in drug design and development in the last two decades: various drugs have been developed and approved containing a covalent warhead. Despite the apparent importance and success of covalent warheads in current drug design and developments, the applied warheads display a rather limited structural variance and complexity which automatically limits the attainable chemical space. Furthermore, to minimize possible side-reactions during the synthesis of drugs, the applied warheads are added appendages in the late-stage of the synthetic route, thus a warhead scaffold that can be synthetically easily varied using orthogonal chemistry and used as a tunable covalent warhead is still missing. Such a structurally more complex scaffold would be much more like the warheads of the natural products and is expected to be more selective in targeting nucleophiles found on proteins. Moreover, owing to a larger contact surface, it might be more suitable for targeting shallow protein surfaces involved in protein-protein interactions.
Normally drugs work by binding to proteins in surface pockets without engaging a strong chemical bond: these binding events are referred to as secondary interactions whose nature is hydrophobic, electrostatic or may involve a weak “hydrogen-bond”. Proteins are built up by chemical building blocks (amino acids) and some of them is chemically reactive, hence they can form a strong covalent bond. Plants produce a great variety of chemically reactive compounds for their own use but many natural products from plants are also often used in traditional medicine and are recognized to contain compounds effective against cancer or inflammatory diseases. These molecules contain a chemically interesting signature motif through which they form covalent bonds to certain amino acids on specific proteins. To put it simply: active natural compounds may “attack” proteins via a covalent bond and thus achieve high-affinity binding. A covalent bond however may be dangerous, it is normally irreversible, and if it forms on the wrong target protein it causes unwanted side-effects. Protenic’s research was inspired by the “soft” covalent bonds that some plant-based natural product make with protein surface amino acids. We developed compounds that form a high-energy covalent bond which is reversible and thus it may be better suited to make more complex covalent drugs, since the “power” of a specific covalent bond is normally an order of magnitude stronger compared to secondary interaction.