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Secondary metabolites are organic compounds that are not directly involved in the normal growth, development or reproduction of organisms. Unlike primary metabolites, absence of secondary metabolities results not in immediate death, but in long-term impairment of the organism's survivability/fecundity, or aesthetics, or may perhaps, result in no significant change at all. Secondary metabolites are often restricted to a narrow set of species within a phylogenetic group.

The function or importance of these compounds to the organism is usually of an ecological nature as they are used as defenses against predators, parasites and diseases, for interspecies competition, and to facilitate the reproductive processes (coloring agents, attractive smells, etc). Since these compounds are usually restricted to a much more limited group of organisms, they have long been of prime importance in taxonomic research.

Biomining is the process of seeking organisms for the purpose of exploiting their natural products for drug or other technological development directly, or as an inspiration for unnatural products. This will concern secondary metabolites in plants, bacteria, fungi and many marine organisms (sponges, tunicates, corals, snails). In some cases, higher organisms will host a microorganism which is the actual producer of the product in question, as part of a symbiotic relationship. Most of the secondary metabolites of interest to man fit into the following categories, and some fall into more than one:

These categories are broad categories which classify secondary metabolites based on their biosynthetic origin. Since secondary metabolites are often created by modified primary metabolite synthases, or "borrow" substrates of primary metabolite origin, these categories should not be interpreted as saying that all molecules in the category are secondary metabolites (for example the steroid category), but rather that there are secondary metabolites in these categories.

Small "small molecules"

• Alkaloids (usually a small, heavily derivatized amino acid):
  • Hyoscyamine, present in Datura stramonium
  • Atropine, present in Atropa belladonna, Deadly nightshade
  • Cocaine, present in Erythroxylon coca the Coca plant
  • Codeine and Morphine, present in Papaver somniferum, the opium poppy
  • Tetrodotoxin, a microbial product in Fugu and some salamanders
• Terpenoids (come from semiterpene oligomerization):
  • Azadirachtin A, (Neem tree)
  • Artemisinin, present in Artemisia annua Chinese wormwood
  • tetrahydrocannabinol, present in cannabis sativa
  • Steroids (Terpenes with a particular ring structure)
    • Saponins (plant steroids, often glycosylated)
• Glycosides (heavily modified sugar molecules):
  • Nojirimycin
  • Glucosinolates
• Phenols:
  • Resveratrol
• Phenazines:
  • Pyocyanin
  • Phenazine-1-carboxylic acid (and derivatives)

Big "small molecules", produced by large, modular, "molecular factories".

• Polyketides:
  • Erythromycin
  • Discodermolide
• Fatty acid synthase products :
  • FR-900848
  • U-106305
  • phloroglucinols
• Nonribosomal peptides:
  • Vancomycin
  • Thiostrepton
  • Ramoplanin
  • Teicoplanin
  • Gramicidin
  • Bacitracin
• Hybrids of the above three:
  • Epothilone

Non-"small molecules" - DNA, RNA, ribosome, or polysaccharide "classical" biopolymers.

• Ribosomal peptides:
  • Microcin-J25

Secondary metabolism