Joined: Jan. 2006
In response to a request by Arden and a topic "introduced" by FTK I thought I'd bung this up for shits and giggles!
It's taken from a very early version of my PhD thesis (i.e. prior to submission and examination, it was trimmed to shorten an already massive introduction and is quite rusty). I hope I can get the images in and I am happy to elaborate on or explain any part of it.
This is a very very brief overview of a massive bit of chemistry/biochemistry that is only partially relevant to the goals of my PhD work, so if it's a bit waffley and non-technical remember it's come from the "setting the scene" section of my introduction as opposed to the real meat. I've also cut a few bits (mostly synthetic chem that isn't relevant) out so hopefully it makes some sort of coherent sense.
The importance of natural products in organic chemistry, and the scientific endeavour as a whole, cannot be overestimated. Natural products have formed both the backbone of, and the inspiration for, the pursuit of organic chemistry. Human societies have used chemicals derived from a wide variety of natural sources for an equally wide variety of purposes for millennia. From curare, a crude, dried extract of the plant Chrondrodendron tomentosum, prepared by sixteenth century South American Indians and used with lethal efficacy against the invading European colonists. To nutmeg, a humble spice derived from the ground kernel of the fruit from the tree Myristica fragrans, and widely used to obscure the taste of spoiled meat.1
It is however in the field of medicine where natural products have arguably made their greatest impact. Chemicals found in nature have been used as medicines by every human society throughout recorded history, there is even evidence that suggests that non-human primates self medicate with materials found in nature.2
Natural products and their chemistry don’t just have real world practical applications, profound scientific insights into the workings of nature have been derived from the study of natural products chemistry. Take for example the discovery of the effects of penicillin by Fleming in 1929, which aided in the development of modern medicine by demonstrating the potential use of certain chemicals (antibiotics) in fighting bacterial pathogens and was one of the founding discoveries in the germ theory of disease. 3 Perhaps most notable amongst classical discoveries though is the synthesis of urea by Wöhler in 1828, which helped to disprove the widely held belief in vitalism (i.e. that living matter and non-living matter were profoundly different). 4
The contribution made by natural products to medicine has not dwindled since the seminal works of the 19th and early 20th centuries, rather it has flourished. Many molecules isolated from nature are being used to grant us new insights into the workings of some of the most pernicious diseases to afflict humanity, and thus allow us to design treatments. This practice continues today, with some of the most important drugs such as Taxotere™ and Artemisinin being closely derived from natural products. In fact, roughly 61% of the 877 new chemical entities produced in the pharmaceutical industry world wide from 1981 to 2002 can be traced to natural products. 78% of antibacterials and 74% of anticancer compounds from that set of chemical entities are either natural products themselves or inspired by a natural product. 5
2.A Brief Comment About Secondary Metabolite Sources
Many species of microorganism produce structurally complex and highly biologically active secondary metabolites. For example the largest non-biopolymeric secondary metabolite isolated to date, maitotoxin (1), has been isolated from a single celled red tide dinoflagellate, Gambierdiscus toxicus.
While the marine environment remains a very rich source of biologically active materials, the largest antibiotic producing microorganism genus discovered so far is a genus of actinomycete soil bacteria, Streptomyces. The number of antimicrobial compounds reported from the species of this genus per year increased almost exponentially for about two decades, followed by a steady rise to reach a peak in the 1970s, and with a substantial decline in the late 1980s and 1990s.6 This decline appears to be due to a fall off in screening efforts rather than an exhaustion of the potential of this genus. Recent re-screening of actinomycete derived antibiotics has produced some potentially useful antitumour compounds.
3. A Brief Overview of Secondary Metabolite Evolution
Any understanding of natural product biosynthesis must be tempered with some understanding of the origins of natural products and their import in nature. The existence of natural products immediately begs the question: why do these complex, cytotoxic chemical persist in nature? In other words, what does an organism gain by producing natural products? There are several hypotheses regarding the evolutionary significance and origins of natural products, and these have been extensively debated in the literature. 7-15
Most prominent among them are:
1. Natural products are essentially neutral with respect to selection pressure.
2. Natural products provide a reservoir of non-functional variety out of which new functional processes can emerge.
3. Natural products are waste or detoxification products derived from primary metabolism.
4. Natural products are a by-product of the enzymatic processes of primary and secondary metabolism, and it is the processes on which selection acts, as opposed to the natural products.
5. Natural products have had, at some time in the organism’s development, a functional metabolic role.
6. Natural products are a measure of the fitness of an organism. The ability to synthesise an array of natural products which may repel or attract other organisms has evolved as one facet of the organism’s survival strategy.
Whilst each proposal has some basis in the literature, the two proposals that are the most supported by the available data are proposal 6, and a modified version of proposal 2.
The initial problem with proposal 2 is that of teleology, in other words: pre-programmed purpose. Since evolution is not a purposeful process, this rather defeats this proposal.16 However, a re-examination of this proposal in terms of the “Screening Hypothesis” shows that it can be used as a rigourous explanation of the diversity and abundance of natural products.17 The Screening Hypothesis takes note of the fact that the property of molecular bioactivity is rare. It proposes that natural selection would favour organisms that can produce a wide diversity of chemical structures (a “screen”, by analogy to human efforts to create bioactive molecules) because these organisms would be more likely to make a “hit” bioactive molecule.
One of the most compelling pieces of evidence for this proposal is that the organisms that typically produce natural products are “simple” organisms that lack an immune system (with some notable exceptions like poison arrow frogs etc). Many of the antibodies produced by an organism’s immune system are currently redundant, they have evolved for antigens that they will never now encounter. This variety of antibodies is an essential facet of successful immune systems because diversity of antibodies at relatively cheap metabolic cost, allows an organism to safely encounter an equally wide variety of antigens. By analogy, diversity in natural product production provides a similar type of fitness for microorganisms.
However, proposal 2 relies heavily on the fact that the production of natural products is due to functional redundancy and high substrate tolerance in the enzymes of primary metabolism, and low energetic cost of the production of the natural products. In some cases the enzymes responsible for the production of natural products are functionally redundant and substrate tolerant, but this is highly variable across species and natural products.
What is less variable is the energy cost of production of natural products. This is one of the key tenets of proposal 6. The high metabolic cost of producing natural products indicates that they must have some value to the organism producing them. The great structural diversity, generally high concentrations of natural product in some parts of the organism, high biological activity and the nature of that activity, different species often produce the same (or very similar) natural products all serve to demonstrate that it is likely that natural products perform some function beneficial to the organism producing them.
Further evidence for this function comes from soil organisms. It has been estimated that 1 g of surface soil contains the following populations: bacteria (10^6-10^8), actinomycetes (10^6-10^7), protozoa (10^5-10^6), fungi (10^4-10^6), and algae (10^4-5x10^4).9 It has also been shown that it is comparatively easy to establish a population of a new soil organism in a sterilised sample of soil as opposed to a soil sample that has an established indigenous fauna. These facts demonstrate a highly competitive environment. Considering the modes of action of many actinomycete derived natural products (antibacterial, inhibitory of DNA production, or similar direct action on primary metabolism) one can see how soil organism chemical agents may have evolved as part of a “chemical war” between soil organisms.
There is also a wealth of genetic evidence that supports this hypothesis. For example the clustering of genes on the natural product biosynthesis pathway with genes that code for resistance to antibiotics. In this case an organism that produces a cytotoxic, antibiotic natural product would be strongly selected against should it fall victim to its own toxin. Genes that code for antibiotic resistance are also found in nature in species that do not produce antibiotic natural products themselves, but that co-exist with organisms that do.18-22
However, more relevant to medicine, and modern uses of natural products, is the often astonishing potency and specificity of bioactive natural products. This is also a key piece of evidence for the proposal that natural products provide some functional benefit to the organism that produces them. High specificity for a given substrate and biological activity, as mentioned above, are rare molecular traits. As these traits are rare, and as the specificity of interaction is so high, it is unlikely for these natural products to have arisen ex nihilo, add to that the fact that we find a gradual spectrum of natural product activities in nature, and you have a powerful argument in favour of hypothesis 6. An elegant example of this is the complementarity shown between the antibiotic vancomycin’s binding site and the cell wall peptide analogue N-acetyl-D-alanine-D-alanine. A schematic representation of this interaction is shown below in Scheme 3.i. 23-25
As has been mentioned, the chemical substances isolated from earth’s biota are astonishingly varied in structure and activity. Looking at the structures of polyketides shows that even in one biosynthetic class of natural products, the structural diversity is great. However, an examination of the structure of vancomycin, shown below in Scheme 3.i, one can see a mixed peptide/polyketide biosynthesis. Organisms also produce peptide natural products as an outgrowth of peptide synthesis in primary metabolism. These peptide natural products target similar primary metabolic processes to the non-peptide based natural products discussed above.
Scheme 3.i Schematic Representation of the Interaction between Vancomycin and a Bacterial Cell Wall Peptide Model
This is an important point to note, it would appear that organisms have evolved a variety of very different natural products to do a similar series of jobs. This not only provides yet more evidence for the hypothesis that natural products have evolved for specific functions, but it has important implications for medicine, and drug development.
Peptide natural products such as nostacyclamide (2), a potent antimicrobial, telomestatin (3), a telomerase inhibitor and potential anticancer lead, diazonamide, an anticancer target, (4) and the mixed peptide/polyketides ulapualide (5), an antifungal anticancer compound and phorboxazole (6), one of the most potent anticancer cytotoxins yet discovered, show not only some of the wide structural diversity mentioned, but also some of the most useful bioactivity yet found in natural products. This selection of natural products has been chosen to illustrate just some of the structural diversity found in peptide, and mixed polyketide/peptide natural products. The five natural products are derived from very different species, but they achieve roughly the same ends in nature, albeit with different modes of action. They all inhibit cell proliferation either by directly destroying the cell itself (nostacyclamide (2) and ulapualide (5)), or by acting in such a way as to interrupt DNA synthesis in the cell (diazonamide (4), ulapualide (5), and phorboxazole (6)), or by preventing cancer cells from being extremely long lived due to a quirk of their DNA repair mechanisms (telomestatin (3)).
Nostacyclamide (2), Telomestatin (3), Diazonamide (4) Ulapualide (5) and Phorboxazole (6)
Because the biological origins of these natural products, their structure related biological activity and their biosynthesis are so intimately and inextricably linked, understanding how natural products have evolved is a key part of understanding their structure-activity relationship, and thus is a cornerstone of both developing new treatments and our understanding of the natural world. Whilst the precise evolutionary origins and utility of natural products remain reasonably disputed matters, a large body of work has shown precisely how these natural products are synthesised in nature.
1 J. Mann, Magic, Murder and Medicine, Oxford University Press, 2000.
2 J. E. Page, M. A. Huffman, V. Smith, and G. H. N. Towers, Journal of Chemical Ecology, 1997, 23, 2211-2226.
3 A. Fleming. On the Antibacterial Action of Cultures of Penicillium, With Special Reference to Their Use in the Isolation of B. Influenzae. The British Journal of Experimental Pathology 10, 226-236. 1929.
4 F Wöhler. On the Artificial Production of Urea. Annalen der Physik und Chemie 88, 253. 1828.
5 M. S. Lesney. Nature's Pharmaceuticals. Today's Chemists at Work July, 26-32. 2004.
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7 R. D. Firn and C. G. Jones, Natural Product Reports, 2003, 20, 382-391.
8 R. D. Firn and C. G. Jones, Molecular Microbiology, 2000, 37, 989-994.
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11 L. C. Vining, Annual Review of Microbiology, 1990, 44, 395-427.
12 D. H. Williams, M. J. Stone, P. R. Hauck, and S. K. Rahman, Journal of Natural Products, 1989, 52, 1189-1208.
13 G. Cimono and Ghiselin M.T., Marine Natural Products As and Evolutionary Narrative, in Marine Chemical Ecology, CRC, 2001, pp. 115-155.
14 B. B. Jarvis and J. D. Miller, Natural Products, Complexity and Evolution, in Phytochemical Diversity and Redundancy in Ecological Interactions, ed. Romeo et al, Plenum Press, New York, 1996, pp. 265-293.
15 B. B. Jarvis, The Role of Natural Products in Evolution, in Evolution of Metabolic Pathways, ed. J. T. e. a. Romeo, Elsevier, 2000, pp. 1-24.
16 E. Mayr, Towards a New Philosophy of Biology: Observations of an Evolutionist, Harvard University Press, Boston, 1989.
17 C. G. Jones and R. D. Firn, Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 1991, 333, 273-280.
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5. Notes Added In Edit
A) Wikipedia has reasonable entries on secondary metabolites and natural products. The terms are used interchangeably in modern organic chemistry, perhaps if I'm being pedantic I'd say this was a bit sloppy of us, but there is a high degree of accuracy to their interchange and the anal retentive technical semantics of my field are far from exciting!
B) Speaking of technical wrangles in scientific fields, I freely admit that the above is massively over emphasising adaptation. As we are mostly dealing with microorganisms I think that horizontal gene transfer and simple genetic drift have a greater part to play. However, I haven't scoured the lit for this distinction over the last 2 or so years and I didn't find much on it the first time around. I may point Larry Moran at this and see what he knows because the evolution of bioactive secondary metabolites is a very important topic, and if I'm right about a few things (research proposals are being written) then secondary metabolites and secondary metabolism in certain species have big clues about certain stages of abiogenesis. And no I won't be more specific until I have some evidence!