Talk:Natural product/Outline

Based on function

 * Kossel reference, and dispensable/indispensable and intrinsic/extrinsic dichotomies.

Following Albrecht Kossel's original proposal in 1891, natural products are often divided into two major classes, the primary and secondary metabolites. Primary metabolites have an intrinsic function that is essential to the survival of the organism that produces them. Secondary metabolites in contrast have an extrinsic function that mainly affects other organisms. Secondary metabolites are not essential to survival but do increase the competitiveness of the organism within its environment.

Primary metabolites

 * Essential cellular functions—nutrient assimilation, energy production, and growth/development.
 * Wide species distribution
 * Include carbohydrates, lipids, amino acids, and nucleic acids, proteins, macromolecular assemblies
 * includes enzymes, amino acids, cofactors
 * Includea cell membranes, cell walls, and cytoskeletal proteins
 * includes DNA, RNA


 * Includes primary signal molecule — hormones, growth factors
 * peptides
 * biogenic amine
 * steroid hormonea
 * auxins and gibberellin
 * etc.
 * primary metabolites
 * cyclic nucleotides,
 * diacyl glycerolS
 * ETC.

Primary metabolites as defined by Kossel are components of basic metabolic pathways that are required for life. They are associated with essential cellular functions such as nutrient assimilation, energy production, and growth/development. They have a wide species distribution that span many phyla and frequently more than one kingdom. Primary metabolites include carbohydrates, lipids, amino acids, and nucleic acids which are the basic building blocks of life.

Primary metabolites that are involved with energy production include respiratory and photosynthetic enzymes. Enzymes in turn are composed of amino acids and often non-peptidic cofactors that are essential for enzyme function. The basic structure of cells and of organisms are also composed of primary metabolites. These include cell membranes (phospholipids), cell walls (peptidoglycans), and cytoskeletons (proteins).

DNA and RNA which store and transmit genetic information are composed of nucleic acid primary metabolites.

First messengers are signaling molecules that control metabolism or cellular differentiation. These signaling molecules include hormones and growth factors in turn are composed of peptides, biogenic amines, steroid hormones, auxins, gibberellins, etc. These first messengers interact with cellular receptors which are composed of proteins. Cellular receptor in turn activate second messengers are used to relay the extracellular message to intracellular targets. These signaling molecules include the primary metabolites cyclic nucleotides, diacyl glycerol, etc.

Secondary metabolites

 * Dispensable, not absolutely required
 * Narrow species distribution.
 * Function of many unknown.
 * Confer a competitive advantage
 * Alternatively, no specific function, general presence of biosynthetic pathways provides general selective advantage

Includes pheromones Includes siderophores, Includes "competitive weapons"
 * repellants
 * venoms
 * toxins


 * Structural classes
 * alkaloids
 * phenylpropanoid
 * polyketides
 * terpenoids

Secondary in contrast to primary metabolites are dispensable and are not absolutely required for survival. Furthermore secondary metabolites typically have a narrow species distribution. Other than they are dispensable, the function of many secondary metabolites is otherwise unknown. It is assumed however that they confer a competitive advantage to the organism that produces them. An alternative view is that in analogy to the immune system, a majority of individual secondary metabolites have no specific function, but having the machinery in place to produce these diverse chemical structures is important so that a few useful secondary metabolites that are useful are produced and selected for.

Secondary metabolites are used for a broad range of purposes. These include pheromones that act as social signaling molecules with other individuals of the same species, signaling molecules that attract and activate symbiotic organisms, agents that solubilize and transport nutrients (siderophores, etc.), and competitive weapons (repellants, venoms, toxins, etc.) that are used against competitors, prey, and predators.

General structural classes of secondary metabolites include alkaloids, phenylpropanoids, polyketides, and terpenoids which are described in more detail in the biosynthesis section below.

Based on biosynthesis
Major classes of based on Dewick (2009)

Acetate pathway
Acetate pathway → fatty acids and polyketides

Shikimate pathway
Shikimate pathway → aromatic amino acids and phenylpropanoids

Mevalonate methyletrythritol phosphate pathways
Mevalonate pathway and methyletrythritol phosphate pathway → terpenoids and steroids

Amino acid pathways
amino acids → alkaloids

Based on source
(essentially a brief systematic summariy of sources appearing in the current "Natural sources" section, so phrases "marine NP", "fungal NP", etc, have meaning going forward)
 * prokaryotic
 * bacterial
 * archaeal
 * eukaryotic
 * plant
 * fungi
 * animal
 * marine/terrestrial

(discussion of difficulty of assigning single organism sources in commensal and other cases) (dividing current sections thus, removes issue of animals, plants having two possible locations in current outline, and having venom and toxins similarly confounded as to location; bottom line, a simpler basis of categories than the current is proposed) (propose need for substantial shortening of this section, to not overwhelm developing article, and to allow room for biological functions, examples)

Medical uses

 * Traditional medicine and ethnopharmacology
 * Modern pharmacotherapy
 * Marketed drugs
 * Oncology
 * Infectious diseases
 * Other areas
 * Off-market examples

Notable examples
(familiar or societally impactful cases, from red tide to yew needles)
 * microbial antibiotics
 * microbial mycotoxins
 * plant semiochemicals
 * plant colorants

Isolation, purification, and analytical techniques
(can include and wikilink to herbal remedies)
 * Sources and preparation
 * Crude extracts
 * Purifications
 * Analyses

Structure and properties

 * Structure determination
 * Property determination

Biotechnology applications

 * screening type assays, incl. HTS
 * individual compound assay
 * pharmacologic evaluation
 * tool compound use
 * toxicology

Commercial production

 * Via harvest
 * Via biotechnology
 * Microbial (incl. fermentation)
 * Plant tissue
 * Semisynthesis
 * Other

Chemical synthesis

 * Microbial transformations
 * Semisynthesis
 * Total synthesis
 * Combinatorial synthesis and biosynthesis

Research and teaching
(including remaining aspects of current "Impact on chemistry" section) (to include phylogenetics, systems biology, and chemoinformatics, as described in Sammuelsson)
 * Pharmacognosy
 * Chemical ecology
 * Ethnopharmacology
 * Chemistry
 * Other areas

Other commercial aspects
(including legal definitions and regulations)

History
(parts of what are now in the impact on chemistry, but mostly new, from a richly sourced literature, including significant societal impacts)