Targeting and extending the eukaryotic druggable genome with natural products

All natural products are bioactive. Organisms expend great effort and energy to produce these “expensive” genetically encoded compounds, or specialized metabolites, for good reasons – survival and competitive advantage. It is our challenge and responsibility as natural products scientists to translate the ecological functions of natural products into biomedical benefit to humanity, which may be viewed as “repurposing” as we change the original intent. In fact, most drugs on the market are natural product-derived or inspired by the molecular architecture of often complex natural products.¹ Other natural products have proven to be important chemical tools to probe biological processes and to decipher enigmatic biology.^2,3 Either way, the translation of natural products into drugs or tools requires the identification of the functionally-relevant biological targets, including binding sites, and the detailed determination of the mechanisms of action and even compound-specific pleiotropic effects. Then these natural products can serve as starting points for medicinal chemistry campaigns and development efforts that have better chances of success. In many cases, natural products have been templates that then led to derivatives or analogues with enhanced selectivity and therapeutic efficacy against classical druggable targets most commonly modulated by marketed drugs, including GPCRs, kinases, ion channels, proteases, and other proteins with enzymatic functions.^1,4 However, the druggable space is evolving, and “undruggable” would be more suitably termed “yet-to-be-drugged”.^5,6 Natural products play a key role in this regard, targeting and extending the druggable genome, as also illustrated in this themed collection, including the articles highlighted below.

Even among proven druggable targets, there is a large unexploited space. Singling out ion channels, of which only a few are targeted by current drugs, tremendous opportunities still exist through targeting other channels that are increasingly linked to different diseases (Chandy et al., DOI: 10.1039/C9NP00056A). Cryo-electron microscopy will become an important tool, particularly for ion channels, to discover and visualize ligand interactions. Natural products with great structural diversity and of diverse origin from animals, plants and cyanobacteria have evolved to interact with ion channels, and new discoveries are always just around the corner (Chandy et al., DOI: 10.1039/C9NP00056A). Usually natural products were the first known ligands for a specific receptor or target protein, which then inspired the synthesis of natural product-like compounds that borrowed the pharmacophore or topological features of a natural product, such as for classically druggable proteases (Al-Awadhi and Luesch, DOI: 10.1039/C9NP00060G).¹ At the same time, these first-in-class pharmacological agents have been used to validate new targets or protein–protein interactions for drug discovery and have led to the discovery of novel mechanisms of action. The exploding field of epigenetics was driven by natural products that modulate the acetylation status of histones at the level of chromatin reorganization, which has led to therapeutics but also illuminated the role of dietary natural products in the delay of disease onset, particularly inflammation, which is a precursor to many diseases (Ferguson et al., DOI: 10.1039/C9NP00057G). With respect to inflammation, natural products modulate the process also by targeting specific transcription factor signaling, particularly Nrf2, for which many natural product modulators exist; activation (to combat inflammation) and inhibition (e.g. cancer) can both be beneficial in a context-dependent fashion, increasing the complexity of pharmacological intervention (Chapman and Zhang, DOI: 10.1039/C9NP00061E). In turn, natural products assisted in elucidating this transcription factor’s role (Chapman and Zhang, DOI: 10.1039/C9NP00061E).

Natural products are trailblazers in showing us the druggability of previously considered undruggable targets, or complexes and processes that have previously not even been remotely considered by humans for drug discovery. In general, the targets of bioactive molecules can be proteinous or non-proteinous. For the latter they act at the level of nucleic acids (DNA, RNA) or metabolites, such as glycans or lipids; however, the majority of natural products target proteins.

Targeting the synthesis of proteins has shown therapeutic benefit in the cancer space. General protein synthesis is inhibited at various stages by natural products, including at the levels of initiation, elongation and termination (Pelletier and Shen, DOI: 10.1039/C9NP00052F; Brönstrup and Sasse, DOI: 10.1039/D0NP00011F). For example, translation initiation is inhibited by rocaglates and pateamine A by targeting eukaryotic initiation factor (eIF) 4A, yet they interfere with this helicase’s RNA-binding activity in a distinct manner (Pelletier and Shen, DOI: 10.1039/C9NP00052F). These compounds exemplify how natural products can modulate RNA–protein interactions. At the level of elongation, there is a vast array of structurally diverse natural products, with cycloheximide being the classical inhibitor, targeting eEF2-mediated translocation (Brönstrup and Sasse, DOI: 10.1039/D0NP00011F). Elucidating the precise function of other natural products acting at the elongation phase has paid off, even for compounds that seem to have almost been given up on years ago. For example, didemnin B was shown to inhibit protein elongation at the level of eukaryotic initiation factor eEF1A, and more recently to have a secondary protein target, indicating polypharmacology that in some cases is beneficial or can serve as a predictive pharmacogenomic response marker (Brönstrup and Sasse, DOI: 10.1039/D0NP00011F).⁷ In general, “off-target” activities always have to be considered and in some cases translate into therapeutic benefit, particularly in cancer, where single targeting might be compensated for by the cancer cell or more readily acquired mutational resistance. Synthetic lethality is a complementary concept that should be more widely explored to take advantage of additional vulnerabilities in disease systems,^8–10 especially for privileged structures like natural products where multiple targets might exist, or to resurrect natural products that have not been applied in the optimal (genetic) setting. In the case of didemnin B, a closely related analogue, plitidepsin, was recently approved in Australia for multiple myeloma (Brönstrup and Sasse, DOI: 10.1039/D0NP00011F).

Beyond protein synthesis, pathways for protein export are also increasingly targeted for drug discovery, beyond classical natural products like brefeldin A and tunicamycin (Luesch and Paavilainen, DOI: 10.1039/C9NP00066F). Using examples from the secretory pathway, brefeldin A, is the first known inducer of a protein–protein interaction. Cotransins and apratoxins target an emerging druggable target, translocon component Sec61, and at different sites, resulting in different pharmacological fingerprints, enabling distinct applications where secretion plays a role (Luesch and Paavilainen, DOI: 10.1039/C9NP00066F).

Beyond proteins, recent chemical genomic methods coupled with biophysical methods have identified and characterized new classes of natural products targeting membrane lipids (Nishimura and Matsumori, DOI: 10.1039/C9NP00059C). The druggability of membrane lipids is proven: lipids are promising drug targets not just for bacteria but also for eukaryotes, especially as antifungal targets but also in mammalian cells. Detailed interrogations have revealed different specificities of natural products and distinct modes of interaction (Nishimura and Matsumori, DOI: 10.1039/C9NP00059C).

Many natural products have been shown to target cytoskeletal proteins that are classical drug targets, especially in the case of microtubules (Risinger and Du, DOI: 10.1039/C9NP00053D). In that biological context, natural products have also shown that downstream pharmacological effects differ depending on the distinct binding sites, providing several potent anticancer drugs. Some of them serve as payloads in antibody–drug conjugates.^11,12 It is increasingly clear that their anticancer efficacy is not exclusively due to antimitotic effects, demonstrating that a lot remains to be learned about seemingly established targets and the importance of elucidating binding sites and not merely targets (Risinger and Du, DOI: 10.1039/C9NP00053D). New natural products against the same target are not necessarily “me-too” compounds, as pointed out for eIF4A inhibitors and Sec61 modulators (Pelletier and Shen, DOI: 10.1039/C9NP00052F; Luesch and Paavilainen, DOI: 10.1039/C9NP00066F). In the case of microtubule targeting agents with differing binding sites, they also continue to add in a complementary manner to the current arsenal of anticancer agents, but possibly also against Alzheimer’s disease, where microtubules play an important role, providing opportunities for repurposing. The cytoskeletal target actin might also have a shot at a comeback with distinct compound-specific pharmacology being deciphered, and additional underexplored cytoskeletal targets are slowly moving out of the shadow of tubulin and actin.

In many cases, natural products are also most-potent-in-class, a paradigm that is particularly emerging for natural products from marine organisms. While terrestrial natural products have traditionally served as lead compounds for drug discovery, there is an apparent shift towards marine sources, concomitant with the improvement of analytical techniques and particularly the ability to define molecular targets and mechanisms of action with the small quantities of material generally available for marine natural products (Andersen and Williams, DOI: 10.1039/C9NP00054B).¹³ Coupling novel discoveries from genetically diverse novel sources with chemical synthesis and medicinal chemistry is a powerful combination that can trigger the onset of a new wave of drugs. Again, the underlying basis is the functional annotation of natural products to give them the best possible shot for drug development. Target identification and mechanism of action studies remain a bottleneck in drug discovery because of the lack of standard recipes, which simultaneously continues to drive innovation in the field. It is imperative to study the pharmacological properties of natural products in depth, which adds tremendous value to them. In fact, without function, any isolation effort remains a purely academic exercise and only adds to the laundry list of “orphan” natural products (as structurally beautiful as they might be in the eye of the beholder). There should not be any orphans, given that all natural products have a receptor in nature. The natural product discovery community needs to commit to fully exploring the biological function of the molecules that are isolated. Assigning the functions of natural products, however, is nontrivial but can be extremely rewarding, as shown by many studies that have attempted to illuminate the molecular basis of a compound’s action beyond descriptive biology. Natural products are destined to expand the druggable genome or therapeutic space, in part also because they are usually larger than classical small molecules and have more surface area to effectively modulate protein–protein/RNA interactions.

In general, starting with a promising disease-modulating phenotype induced by a natural product at the screening or discovery stage, rigorous mechanistic characterization will enable us to extend the druggable genome and validate previously unknown or undruggable targets or target complexes, turning them druggable. Natural products with intrinsic functions will continue to lead the way towards new target spaces if investigated to the fullest extent. The recent past has shown that chemistry-driven approaches cannot outsmart nature, but only offer complementary solutions at best. Clues from chemical ecology, including the physiological function of natural products in the producer, will enable us to select suitable bioassays and biomedical contexts, as we are limited by the extent of the biology to which we expose these compounds (and our own drive to understand the molecular pharmacology). Chances are that a new target can be discovered through rigorous mechanistic characterization of a natural product, opening new opportunities and therapeutic options.

References

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