Natural products in drug discovery: advances and opportunities

Abstract

Natural products and their structural analogues have historically made a major contribution to pharmacotherapy, especially for cancer and infectious diseases. Nevertheless, natural products also present challenges for drug discovery, such as technical barriers to screening, isolation, characterization and optimization, which contributed to a decline in their pursuit by the pharmaceutical industry from the 1990s onwards. In recent years, several technological and scientific developments - including improved analytical tools, genome mining and engineering strategies, and microbial culturing advances - are addressing such challenges and opening up new opportunities. Consequently, interest in natural products as drug leads is being revitalized, particularly for tackling antimicrobial resistance. Here, we summarize recent technological developments that are enabling natural product-based drug discovery, highlight selected applications and discuss key opportunities.

Fig. 1. Outline of traditional bioactivity-guided isolation steps in natural product drug discovery.

Steps in the process are shown in purple boxes, with associated key limitations shown in red boxes and advances that are helping to address these limitations in modern natural product (NP)-based drug discovery shown in green boxes. The process begins with extraction of NPs from organisms such as bacteria. The choice of extraction method determines which compound classes will be present in the extract (for example, the use of more polar solvents will result in a higher abundance of polar compounds in the crude extract). To maximize the diversity of the extracted NPs, the biological material can be subjected to extraction with several solvents of different polarity. Following the identification of a crude extract with promising pharmacological activity, the next step is its (often multiple) consecutive bioactivity-guided fractionation until the pure bioactive compounds are isolated. A key limitation for the potential of this approach to identify novel NPs is that many potential source organisms cannot be cultured or stop producing relevant NPs when taken out of their natural habitat. These limitations are being addressed through development of new methods for culturing, for in situ analysis, for NP synthesis induction and for heterologous expression of biosynthetic genes. At the crude extract step, challenges include the presence in the extracts of NPs that are already known, NPs that do not have drug-like properties or insufficient amounts of NPs for characterization. These challenges can be addressed through the development of methods for dereplication, extraction and pre-fractionation of extracts. Finally, at the last stage, when bioactive compounds are identified by phenotypic assays, significant time and effort are typically needed to identify the affected molecular targets. This challenge can be addressed by the development of methods for accelerated elucidation of molecular modes of action, such as the nematic protein organization technique (NPOT), drug affinity responsive target stability (DARTS), stable isotope labelling with amino acids in cell culture and pulse proteolysis (SILAC-PP), the cellular thermal shift assay (CETSA) and an extension known as thermal proteome profiling (TPP), stability of proteins from rates of oxidation (SPROX), the similarity ensemble approach (SEA) and bioinformatics-based analysis of connectivity (connectivity map, CMAP)^,–.

Fig. 2. Applications of advanced analytical technologies empowering modern natural product-based drug discovery.

a | An illustrative example of the application of liquid chromatography–high-resolution mass spectrometry (LC–HRMS) metabolomics in the screening of natural product (NP) extracts is the work of Kurita et al., in which 234 bacterial extracts were subjected to image-based phenotypic bioactivity screening and LC–HRMS metabolomics. Clustering of the resulting data allowed prioritization of promising extracts for further analysis, resulting in the discovery of the new NPs, quinocinnolinomycins A–D. b | Another illustrative example of LC–HRMS screening of NP extracts is the work of Clevenger et al., who obtained novel NP extracts through heterologous expression of fungal artificial chromosomes (FACs) containing uncharacterized biosynthetic gene clusters (BGCs) from diverse fungal species in Aspergillus nidulans. Analysis of the LC–HRMS metabolomics data with a FAC-Score algorithm directed the simultaneous discovery of 15 new NPs and the characterization of their BGCs.

Fig. 3. Strategies for genome mining-driven discovery of natural products and natural product-like compounds.

a | Genome mining-based approaches to explore the biosynthetic capacity of microorganisms rely on DNA extraction, sequencing and bioinformatics analysis. The vast majority of microbes from different environments and microbiota communities have not been cultured, and their capacity to produce natural products (NPs) was largely inaccessible until recently. In the case of unculturable microorganisms, the bioinformatics analysis step can be followed by either targeted heterologous expression of biosynthetic gene clusters (BGCs) prioritized as being likely to yield relevant new NPs or direct chemical synthesis of ‘synthetic–bioinformatic’ NP-like compounds. b,c | These two approaches are exemplified by the recent discoveries of malacidins (panel b) and humimycins (panel c), respectively^,. A major strength of the ‘synthetic–bioinformatic’ approach is that it is entirely independent of microbial culture and gene expression. Its limitations are the accuracy of computational chemical structure predictions and the feasibility of total chemical synthesis. NRPS, nonribosomal peptide synthetase.

Fig. 4. Application of advanced microbial culturing approaches to identify new natural products.

New strategies for isolating previously uncultured microorganisms can enable access to new natural products (NPs) produced by them. a | To recapitulate the effect of complex signals coming from the native environment, microorganisms can be cultivated directly in the environment from which they were isolated. This concept is used with the iChip platform, in which diluted environmental samples are seeded in multiple small chambers separated from the native environment with a semipermeable membrane. The potential of this approach is illustrated by the recent discovery of teixobactin, a new antibiotic with activity against Gram-positive bacteria^,. b | Another important recent development involves obtaining information from environmental samples using omics techniques such as metagenomics to identify and partially characterize microorganisms present in a specific environment before culturing. An approach relying on such preliminary information was recently used to engineer the capture of antibodies based on genetic information, which resulted in the successful cultivation of previously uncultured bacteria from the human mouth. This reverse genomics workflow was validated by the isolation and cultivation of three species of Saccharibacteria (TM7) along with their interacting Actinobacteria hosts, as well as SR1 bacteria that are members of a candidate phylum with no previously cultured representatives.

Fig. 5. Strategies to obtain natural product analogues with superior properties.

Unmodified natural products (NPs) often possess suboptimal properties, and superior analogues need to be obtained in order to yield valuable new drugs. a | NP analogues can be accessed through the development of total chemical synthesis followed by chemical derivatization, through semisynthesis using a NP as a starting point for the introduction of chemical modifications, and through biosynthetic engineering using manipulations of biosynthetic pathways of the producing organism to generate NP analogues. b,c | Tetracyclines are an example of NP-derived antibiotics that have already yielded several generations of successfully marketed semisynthetic and synthetic derivatives. The first generation of tetracyclines (such as chlortetracycline and tetracycline) were unmodified NPs, while the two subsequent generations of analogues with optimized properties were semisynthetic (second-generation, doxycycline, minocycline; third-generation, tigecycline) and the most recently developed fourth-generation analogues (eravacycline) are entirely synthetic, accessed via total synthesis^,. More recent examples of property optimization of other classes of NPs through total chemical synthesis followed by chemical derivatization or through semisynthesis are illustrated by studies focused on analogues of chrysomycin A (panel b) and arylomycins (panel c), respectively. d | The biosynthetic engineering approach has also shown potential; for example, in the generation of analogues of rapamycin, bleomycin (panel d) and nystatin. 6′-deoxy-BLM A2, 6′-deoxy-bleomycin A2; BLM A2, bleomycin A2.