- Email: [email protected]
Naming natural products: Uses, abuses and a proposal for discussion
Phytochemistry 131 (2016) 7e8
Contents lists available at ScienceDirect
Phytochemistry journal homepage: www.elsevier.com/locate/phytochem
Editorial
Naming natural products: Uses, abuses and a proposal for discussion
Nowadays, when working with the isolation and characterization of an unknown substance, it does not need to be named: it is sufficient to know where it comes from and to have an idea of its properties. A unique code is enough to make sure the laboratory book is correctly filled in. If the compound is natural and has never described before, then a “trivial” name is frequently suggested when the article is send to an Editor. This is not the case with fully synthetic compounds, which are given systematic names obeying nomenclature rules. Unfortunately, this practice is not generally applied to natural products, for which trivial nomenclature is still prevalent. This habit is historical, as in the earlier literature compounds were frequently named before their structure was known. For example, strychnine and cholesterol were both named long before their structural elucidation. Strychnine was named after the plant it was extracted from: Strychnos nux-vomica L. and the naming of cholesterol found its roots in the Greek word chole “cοlή” (bile). This habit of naming compounds after their source, however, leads to problems. This was particularly brought to our attention in the course of reviewing alkaloids with the iboga skeleton. Among these compounds, a large number of “dimers” formed between a vobasan-type molecule substituted at position 3 and an ibogan , substituted on the aromatic ring have been described (Szabo 2008). What we believe to be fundamental literature, i.e. a reference book by Gabetta and Mustich “Spectral data of Indole Alkaloids” contained seven such molecules named voacamine, descarbomethoxyvoacamine, voacamidine, voacorine, conodurine, conoduramine and gabunine (Gabetta and Mustich, 1975). The pairs conodurine and conoduramine, voacamine and voacamidine correspond to different substitution positions on the aromatic ring of the ibogan moiety. So, in those days (late 1960s), four different etymologies were used to describe seven alkaloids and the name of gabunine was adopted, even if it was recognized by partial synthesis to be nor-conodurine (Cava et al., 1965). Among the seven historical compounds, only the trivial name voacamine was adopted in the literature and collected 54 citations, with the original article by Büchi et al. (1964) reaching a total of 84 citations (apps.webofknowledge.com). At the present time, there are more than fifty of these particular alkaloids with no less than eighteen names such as cononitarine, conodiparine, conodirinine, conodutarine and conodusarine (Kam and Sim, 2003; Kam et al., 2003, Kam and Pang, 2004). It is highly likely that newly described compounds will only be cited by their authors or by people writing review articles: this is unreasonable. http://dx.doi.org/10.1016/j.phytochem.2016.09.001 0031-9422/© 2016 Elsevier Ltd. All rights reserved.
Even though chemical correlations between compounds, which was the fundamental of organic chemistry, is almost out of practice, our recommendation is to try one's best not to multiply trivial names and to stick to known and accepted names. As an example of such a practice, one can mention the naming of a new saponin isolated from the seeds of several leguminous plants and which shared features with soyasaponin I from soybean (same triterpene, same three sugar substitution). The authority on soybean saponins was then Professor Isao Kitagawa (University of Osaka, Japan), from whom we requested permission to use a number in the series. His answer came rapidly (air mail at the time, not internet) and our compound was baptized soyasaponin VI (Massiot et al., 1992). Unfortunately, almost simultaneously, the same molecule was identified by two other groups from Japan and independently named soyasaponin bg (Kudou et al., 1992) and chromosaponin I (Tsurumi et al., 1992). It is worth noting that despite the number I, chromosaponin I remains the sole in its class. Such multiple naming of compounds adds confusion to the literature. In the alkaloid field, a similar story occurred but with a more harmonious end. Several groups were working on dimeric alkaloids from different plants of the Strychnos genus. These groups got along well and results were frequently exchanged even before publication. It turned out that four of us had the same molecule in hands (longicaudatine), arrived more or less at the same determination and decided to publish altogether (Massiot et al., 1983). Impact on literature duplication was consequently minimized with a single article in a good journal and dealing with a total of ten plant species. As an example with a less desirable outcome, we isolated a set of two very simple molecules from a marine sponge and for which we coined the name of jaspines from Jaspis sp., the marine sponge from which it was isolated (Ledroit et al., 2003). The structures were not complicated, biological activity was average and we were in no hurry to add them to the literature. It appeared that one of these molecules was published under the name of pachastrissamine, just a few months before our publication surfaced (Kuroda et al., 2002). This is most unfortunate but did not seem to deter the end users who almost equally cited both papers and the Japanese group currently has the lead with 94 citations versus 91. How to avoid these problems in the future? There is a systematic nomenclature system for the plants we study, ORCID numbers for researcher's identification, gene and protein sequence databases, InChiKeys for synthetic chemical substances, but no systematic database for tracking the assignment of trivial names to natural
8
Editorial / Phytochemistry 131 (2016) 7e8
products. As illustrated above, the same structure may have different names but also the same name may have been applied to different compounds, thus bringing confusion and encumbering the literature. It would clearly be useful to constitute a repository for the names of natural products either managed by learned societies or by a private institution such as Chapman and Hall, which runs the dictionary of natural products database. A further step would be to mimic the crystallographers who make the deposit of data on the CDB compulsory and have natural products chemists required deposit their spectral data in a freely accessible system before a newly discovered structure can be published. Acknowledgements de Reims ChampagneSupport by the CNRS and the Universite Ardenne is gratefully acknowledged. References Büchi, G., Manning, R.E., Monti, S.A., 1964. Voacamine þ voacorine. J. Amer. Chem. Soc. 86, 4631e4641. Cava, M.P., Talapatra, S.K., Weisbach, J.A., Douglas, B., Raffauf, R.F., Beal, J.L., 1965. Gabunine: A natural dimeric indole derived from perivine. Tet. Let. 931e935. Gabetta, B., Mustich, G., 1975. Spectral Data of Indole Alkaloids. Inverni Della Beffa (Milan, Italy). Kam, T.-S., Sim, K.-M., 2003. Conodirinines A and B, novel vobasine-iboga bisindoles incorporating an additional tetrahydro-1,3-oxazine unit on the vobasinyl moiety. Helv. Chim. Acta 86, 122e126. Kam, T.-S., Sim, K.-M., Pang, H.-S., 2003. New bisindole alkaloids from Tabernaemontana corymbosa. J. Nat. Prod. 66, 11e16. Kam, T.-S., Pang, H.-S., 2004. Conodusarine, a new biologically active bisindole
alkaloid from Tabernaemontana divaricata. Heterocycles 63, 845e850. Kudou, S., Tonomura, M., Tsukamoto, C., Shimoyamada, M., Uchida, T., Okubo, K., 1992. Isolation and structural elucidation of the major genuine soybean saponin. Biosci. Biotech. Biochem. 56, 142e143. Kuroda, H., Musman, M., Otani, I., Ichiba, T., Tanaka, J., Gravalos, D.G., Higa, T., 2002. Pachastrissamine, a cytotoxic anhydrophytosphingosine from a marine sponge Pachatrissa sp. J. Nat. Prod. 65, 1505e1506. Ledroit, V., Debitus, C., Lavaud, C., Massiot, G., 2003. Jaspines A and B: two new cytotoxic sphingosine derivatives from the marine sponge Jaspis sp. Tet. Let. 44, 225e228. ches, M., Mirand, C., Le Men-Olivier, L., Delaude, C., Baser, K.H.C., Massiot, G., Ze €mbom, J., Verpoorte, R., 1983. On Bavovada, R., Bisset, N.G., Hylands, P.J., Stro the blue coloring alkaloids from Strychnos species. J. Org. Chem. 48, 1869e1872. Massiot, G., Lavaud, C., Benkhaled, M., Le Men-Olivier, L., 1992. Soyasaponin VI, a new maltol conjugate from Alfalfa and Soybean. J. Nat. Prod. 55, 1339e1342. , L.F., 2008. Rigorous biogenetic network for a group of indole alkaloids Szabo derived from strictosidine. Molecules 13, 1875e1896. Tsurumi, S., Takage, T., Hashimoto, T., 1992. A g-pyronyl triterpenoid saponin from Pisum sativum. Phytochemistry 31, 2435e2438.
Catherine Lavaud, Georges Massiot* Universit e de Reims Champagne-Ardenne, Institut de Chimie Mol eculaire de Reims, UMR CNRS 7312, Case postale 44, UFR des Sciences Exactes et Naturelles, BP 1039, 51687 Reims Cedex 2, France * Corresponding author. E-mail addresses: [email protected] (C. Lavaud), [email protected] (G. Massiot).
2 May 2016 Available online 13 September 2016
Contents lists available at ScienceDirect
Phytochemistry journal homepage: www.elsevier.com/locate/phytochem
Editorial
Naming natural products: Uses, abuses and a proposal for discussion
Nowadays, when working with the isolation and characterization of an unknown substance, it does not need to be named: it is sufficient to know where it comes from and to have an idea of its properties. A unique code is enough to make sure the laboratory book is correctly filled in. If the compound is natural and has never described before, then a “trivial” name is frequently suggested when the article is send to an Editor. This is not the case with fully synthetic compounds, which are given systematic names obeying nomenclature rules. Unfortunately, this practice is not generally applied to natural products, for which trivial nomenclature is still prevalent. This habit is historical, as in the earlier literature compounds were frequently named before their structure was known. For example, strychnine and cholesterol were both named long before their structural elucidation. Strychnine was named after the plant it was extracted from: Strychnos nux-vomica L. and the naming of cholesterol found its roots in the Greek word chole “cοlή” (bile). This habit of naming compounds after their source, however, leads to problems. This was particularly brought to our attention in the course of reviewing alkaloids with the iboga skeleton. Among these compounds, a large number of “dimers” formed between a vobasan-type molecule substituted at position 3 and an ibogan , substituted on the aromatic ring have been described (Szabo 2008). What we believe to be fundamental literature, i.e. a reference book by Gabetta and Mustich “Spectral data of Indole Alkaloids” contained seven such molecules named voacamine, descarbomethoxyvoacamine, voacamidine, voacorine, conodurine, conoduramine and gabunine (Gabetta and Mustich, 1975). The pairs conodurine and conoduramine, voacamine and voacamidine correspond to different substitution positions on the aromatic ring of the ibogan moiety. So, in those days (late 1960s), four different etymologies were used to describe seven alkaloids and the name of gabunine was adopted, even if it was recognized by partial synthesis to be nor-conodurine (Cava et al., 1965). Among the seven historical compounds, only the trivial name voacamine was adopted in the literature and collected 54 citations, with the original article by Büchi et al. (1964) reaching a total of 84 citations (apps.webofknowledge.com). At the present time, there are more than fifty of these particular alkaloids with no less than eighteen names such as cononitarine, conodiparine, conodirinine, conodutarine and conodusarine (Kam and Sim, 2003; Kam et al., 2003, Kam and Pang, 2004). It is highly likely that newly described compounds will only be cited by their authors or by people writing review articles: this is unreasonable. http://dx.doi.org/10.1016/j.phytochem.2016.09.001 0031-9422/© 2016 Elsevier Ltd. All rights reserved.
Even though chemical correlations between compounds, which was the fundamental of organic chemistry, is almost out of practice, our recommendation is to try one's best not to multiply trivial names and to stick to known and accepted names. As an example of such a practice, one can mention the naming of a new saponin isolated from the seeds of several leguminous plants and which shared features with soyasaponin I from soybean (same triterpene, same three sugar substitution). The authority on soybean saponins was then Professor Isao Kitagawa (University of Osaka, Japan), from whom we requested permission to use a number in the series. His answer came rapidly (air mail at the time, not internet) and our compound was baptized soyasaponin VI (Massiot et al., 1992). Unfortunately, almost simultaneously, the same molecule was identified by two other groups from Japan and independently named soyasaponin bg (Kudou et al., 1992) and chromosaponin I (Tsurumi et al., 1992). It is worth noting that despite the number I, chromosaponin I remains the sole in its class. Such multiple naming of compounds adds confusion to the literature. In the alkaloid field, a similar story occurred but with a more harmonious end. Several groups were working on dimeric alkaloids from different plants of the Strychnos genus. These groups got along well and results were frequently exchanged even before publication. It turned out that four of us had the same molecule in hands (longicaudatine), arrived more or less at the same determination and decided to publish altogether (Massiot et al., 1983). Impact on literature duplication was consequently minimized with a single article in a good journal and dealing with a total of ten plant species. As an example with a less desirable outcome, we isolated a set of two very simple molecules from a marine sponge and for which we coined the name of jaspines from Jaspis sp., the marine sponge from which it was isolated (Ledroit et al., 2003). The structures were not complicated, biological activity was average and we were in no hurry to add them to the literature. It appeared that one of these molecules was published under the name of pachastrissamine, just a few months before our publication surfaced (Kuroda et al., 2002). This is most unfortunate but did not seem to deter the end users who almost equally cited both papers and the Japanese group currently has the lead with 94 citations versus 91. How to avoid these problems in the future? There is a systematic nomenclature system for the plants we study, ORCID numbers for researcher's identification, gene and protein sequence databases, InChiKeys for synthetic chemical substances, but no systematic database for tracking the assignment of trivial names to natural
8
Editorial / Phytochemistry 131 (2016) 7e8
products. As illustrated above, the same structure may have different names but also the same name may have been applied to different compounds, thus bringing confusion and encumbering the literature. It would clearly be useful to constitute a repository for the names of natural products either managed by learned societies or by a private institution such as Chapman and Hall, which runs the dictionary of natural products database. A further step would be to mimic the crystallographers who make the deposit of data on the CDB compulsory and have natural products chemists required deposit their spectral data in a freely accessible system before a newly discovered structure can be published. Acknowledgements de Reims ChampagneSupport by the CNRS and the Universite Ardenne is gratefully acknowledged. References Büchi, G., Manning, R.E., Monti, S.A., 1964. Voacamine þ voacorine. J. Amer. Chem. Soc. 86, 4631e4641. Cava, M.P., Talapatra, S.K., Weisbach, J.A., Douglas, B., Raffauf, R.F., Beal, J.L., 1965. Gabunine: A natural dimeric indole derived from perivine. Tet. Let. 931e935. Gabetta, B., Mustich, G., 1975. Spectral Data of Indole Alkaloids. Inverni Della Beffa (Milan, Italy). Kam, T.-S., Sim, K.-M., 2003. Conodirinines A and B, novel vobasine-iboga bisindoles incorporating an additional tetrahydro-1,3-oxazine unit on the vobasinyl moiety. Helv. Chim. Acta 86, 122e126. Kam, T.-S., Sim, K.-M., Pang, H.-S., 2003. New bisindole alkaloids from Tabernaemontana corymbosa. J. Nat. Prod. 66, 11e16. Kam, T.-S., Pang, H.-S., 2004. Conodusarine, a new biologically active bisindole
alkaloid from Tabernaemontana divaricata. Heterocycles 63, 845e850. Kudou, S., Tonomura, M., Tsukamoto, C., Shimoyamada, M., Uchida, T., Okubo, K., 1992. Isolation and structural elucidation of the major genuine soybean saponin. Biosci. Biotech. Biochem. 56, 142e143. Kuroda, H., Musman, M., Otani, I., Ichiba, T., Tanaka, J., Gravalos, D.G., Higa, T., 2002. Pachastrissamine, a cytotoxic anhydrophytosphingosine from a marine sponge Pachatrissa sp. J. Nat. Prod. 65, 1505e1506. Ledroit, V., Debitus, C., Lavaud, C., Massiot, G., 2003. Jaspines A and B: two new cytotoxic sphingosine derivatives from the marine sponge Jaspis sp. Tet. Let. 44, 225e228. ches, M., Mirand, C., Le Men-Olivier, L., Delaude, C., Baser, K.H.C., Massiot, G., Ze €mbom, J., Verpoorte, R., 1983. On Bavovada, R., Bisset, N.G., Hylands, P.J., Stro the blue coloring alkaloids from Strychnos species. J. Org. Chem. 48, 1869e1872. Massiot, G., Lavaud, C., Benkhaled, M., Le Men-Olivier, L., 1992. Soyasaponin VI, a new maltol conjugate from Alfalfa and Soybean. J. Nat. Prod. 55, 1339e1342. , L.F., 2008. Rigorous biogenetic network for a group of indole alkaloids Szabo derived from strictosidine. Molecules 13, 1875e1896. Tsurumi, S., Takage, T., Hashimoto, T., 1992. A g-pyronyl triterpenoid saponin from Pisum sativum. Phytochemistry 31, 2435e2438.
Catherine Lavaud, Georges Massiot* Universit e de Reims Champagne-Ardenne, Institut de Chimie Mol eculaire de Reims, UMR CNRS 7312, Case postale 44, UFR des Sciences Exactes et Naturelles, BP 1039, 51687 Reims Cedex 2, France * Corresponding author. E-mail addresses: [email protected] (C. Lavaud), [email protected] (G. Massiot).
2 May 2016 Available online 13 September 2016