Natural product biosynthesis: What's next? An introduction to the JBC Reviews Thematic Series

Abstract

The diversity of natural products not only fascinates us intellectually, but also provides an armamentarium against the microbes that threaten our health. The increased prevalence of pathogens that are resistant to one or more classes of available medicines continues to be a growing global threat. As drug-resistant pathogens erode the effectiveness of the current reserve of antibiotics and antifungals, methodological advances open additional avenues for discovery of new classes of drugs, as well as novel derivatives of existing (and proven) classes of compounds. In this Thematic Review Series, we aim to provide a snapshot of the current state of the art in natural product discovery. The reviews in this series encapsulate convergent approaches toward the identification of different classes of primary and specialized metabolites, including nonribosomal peptides, polyketides, and ribosomally synthesized and post-translationally modified peptides, from all kingdoms of life. Traction in unraveling new and diverse classes of molecules has come largely from the academic sector, which ensures availability of methods and data sets. Such knowledge is needed to thwart serious threats to human health and calls to mind the proverb praemonitus praemunitus (forewarned is forearmed).

Introduction

Nearly all organisms on the planet produce specialized metabolites that are not directly involved in growth or development and are not necessary for survival under normal conditions (1). Instead, these compounds help the producing organism compete when resources are limited, facilitate interactions between species, and provide interspecies defense. Most specialized metabolites are classified according to how they are made (i.e. their biosynthetic origin), and enzymes that carry out their synthesis often use chemistries that resemble processes involved in primary metabolism. Specialized metabolites are chemically diverse compounds with value as pharmaceuticals, but also as flavors, fragrances, fuels, biopolymers, and nutritional molecules (2–4).

During the latter half of the 20th century, natural product discovery was based largely on phenotypic screening. Specifically, materials from microbes and plants would be tested for biological activity followed by purification of the active metabolite (5). As more and more natural products were identified through such arduous means, rediscovery of known scaffolds began to plague investigators. With identification contingent only on phenotype, it became impossible to avoid spending significant effort only to find yet another derivative of an “ineffective” drug like penicillin. More recently, inexpensive sequencing methods and the vast array of resultant genome data led to dramatic inversion of the discovery process toward one based on a priori identification of biosynthetic genes (6).

With any collection of large data sets, the most important issue is one of prioritization. Specifically, how can one dive through all of this digital information to come up with a roadmap to move forward? In this review series, Ben Shen and colleagues (7) detail how advances in genome sequencing can be coupled with new bioinformatics platforms to offer new opportunities for prioritizing drug discovery. They highlight two approaches: the first is based on the anticipated knowledge of the chemical scaffold, and the second uses prediction of likely function of biosynthetic genes. This review showcases how a microbial strain collection, like that at the Scripps Research Institute, can be harnessed for the discovery of new drugs with novel activities as well as to identify strains that can make known drugs, but at greater production levels than previously known.

One of the challenges of “genome-centric” efforts is that many biosynthetic clusters identified through such means do not produce any compounds under laboratory conditions. Several approaches have been pursued to overcome this limitation, including expression of biosynthetic genes in heterologous hosts, genetic manipulation of protein expression levels, and increasing levels of necessary starter molecules; however, these synthetic biology methods focus on natural products from microbes where the co-occurrence of biosynthetic genes and decades of prior efforts on heterologous expression have accelerated efforts and are not applicable to all organisms. The review by Hiroshi Maeda (8) discusses how synthetic biology efforts may be expanded to plants to allow for reconstruction of natural product pathways that cannot be produced in single-celled organisms. Strategies discussed include optimizing primary metabolism, which may also improve production of many plant-sourced medicines in heterologous systems.

Much of natural product research has mined microbes and plants as sources of useful molecules. This is in large part because these systems represent “low-hanging fruit” that can be exploited using known methods to achieve deliverables. The review by Torres and Schmidt (9) discusses a largely overlooked source of natural product—the animal kingdom. As more animal genomes become accessible, it is becoming evident that several encode new specialized biosynthetic pathways. The authors conclude that there is likely an untapped diversity of natural products (and their biosynthetic enzymes) of animal origins.

The last three reviews in the series focus on specific classes of natural products, namely polyketides, glycopeptides, and ribosomally synthesized and post-translationally modified peptides (10). Morita et al. (11) discuss enzymes called type III polyketide synthases that use acetyl-CoA to build complex carbon skeletons. Although these enzymes share a common three-dimensional fold, type III polyketide synthases catalyze reactions that lead to remarkable chemical diversity. This review summarizes the structural and biochemical studies of plant and microbial type III polyketide synthases that reveal the mechanistic details of how these “simple” enzymes assemble complex chemical scaffolds and how these enzymes can be manipulated to produce molecules not found in nature.

Keeping in theme, the review from Marschall et al. (12) focuses on glycopeptides, a class of bacterial and fungal natural products that are assembled by large “assembly line”–like proteins called nonribosomal peptide synthetases and then further decorated with sugars and other functional groups to produce bioactive compounds. These modifications are critical for activity, focusing research directed at assembling similar peptide scaffolds with new-to-nature modifications. This review presents a detailed analysis of the synthetic chemical, genetic, and chemoenzymatic approaches that have been developed to afford new glycopeptides in the hopes of finding ones with improved or new biological activities.

Last, Li and Rebuffat (13) focus on post-translationally modified peptides, a class of natural products for which several are shown to demonstrate antimicrobial activity, but the exact roles of these compounds in the context of their microbial ecosystems is not yet fully understood. This review suggests that one possible role of these modified peptide natural products is in mediating interspecies and interkingdom interactions.

Thematically, these six reviews highlight recent developments, new approaches, and unexplored sources for understanding natural product biosynthesis and mining its chemical diversity.