Alkaloids are classified according to the amino acid that provides both the nitrogen atom and the fundamental portion of the alkaloid skeleton, and these are discussed in turn. Ornithine gives rise to pyrrolidine and tropane alkaloids, lysine to piperidine, quinolizidine, and indolizidine alkaloids, and nicotinic acid to pyridine alkaloids. Tyrosine produces phenylethylamines and simple tetrahydroisoquinoline alkaloids, but also many others in which phenolic oxidative coupling plays an important role, such as modified ben-zyltetrahydroisoquinoline, phenethylisoquinoline, terpenoid tetrahydroisoquinoline, and Amaryllidaceae alkaloids. Alkaloids derived from tryptophan are subdivided into simple indole, simple P-carboline, terpenoid indole, quinoline, pyrroloindole, and ergot alkaloids. Anthranilic acid acts as a precursor to quinazoline, quinoline and acridine alkaloids, whilst histidine gives imidazole derivatives. However, many alkaloids are not derived from an amino acid core, but arise by amination of another type of substrate, which may be acetate derived, phenylalanine derived, a terpene or a steroid, and examples are discussed. Purine alkaloids are constructed by pathways that resemble those for purines in nucleic acids. Monograph topics giving more detailed information on medicinal agents include belladonna, stramonium, hyoscyamus, duboisia and allied drugs, hyoscyamine, hyoscine and atropine, coca, lobelia, vitamin B3, tobacco, areca, catecholamines, lophophora, curare, opium, colchicum, ipecacuanha, galanthamine, serotonin, psilocybe, rauwolfia, catharanthus, iboga, nux-vomica, ellipticine, cinchona, camptothecin, physostigma, ergot, morning glories, pilocarpus, Conium maculatum, ephedra, khat, aconite, Solanum alkaloids, caffeine, theobromine and theophylline, coffee, tea, cola, cocoa, mate tea, guarana, saxitoxin, and tetrodotoxin.

The alkaloids are organic nitrogenous bases found mainly in plants, but also to a lesser extent in microorganisms and animals. One or more nitrogen atoms are present, typically as primary, secondary, or tertiary amines, and this usually confers basicity to the alkaloid, facilitating their isolation and purification since water-soluble salts can be formed in the presence of mineral acids. The name alkaloid is in fact derived from alkali. However, the degree of basicity varies greatly, depending on the structure of the alkaloid molecule, and the presence and location of other functional groups. Indeed, some alkaloids are essentially neutral. Alkaloids containing quaternary amines are also found in nature. The biological activity of many alkaloids is often dependent on the amine function being transformed into a quaternary system by protonation at physiological pHs.

Alkaloids are often classified according to the nature of the nitrogen-containing structure, e.g. pyrrolidine, piperidine, quinoline, isoquinoline, indole, etc, though the structural complexity of some examples rapidly expands the number of subdivisions. The nitrogen atoms in alkaloids originate from an amino acid, and, in general, the carbon skeleton of the particular amino acid precursor is also largely retained intact in the alkaloid structure, though the carboxylic acid carbon is often lost through decarboxylation. Accordingly, subdivision of alkaloids into groups based on amino acid precursors forms a rational and often illuminating approach to classification. Relatively few amino acid precursors are actually involved in alkaloid biosynthesis, the principal ones being ornithine, lysine, nicotinic acid, tyrosine, tryp-tophan, anthranilic acid, and histidine. Building blocks from the acetate, shikimate, or deoxyxylu-lose phosphate pathways are also frequently incorporated into the alkaloid structures. However, a large group of alkaloids are found to acquire their nitrogen atoms via transamination reactions, incorporating only the nitrogen from an amino acid, whilst the rest of the molecule may be derived from acetate or shikimate, or may be terpenoid or steroid in origin. The term 'pseudoalkaloid' is sometimes used to distinguish this group.

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