Abstract
Natural products exhibit structural diversity, and biologically active natural products with unprecedented molecular skeletons can potentially be isolated from natural resources in the future. Although it has often been difficult to determine the structures and configurations of new compounds that do not resemble known compounds, the determination of the chemical structures, including the absolute stereo configuration, is very important in drug discovery research. In our efforts to find new bioactive natural products, we have identified novel compounds such as the ubiquitin–proteasome system inhibitors and osteoclast differentiation inhibitors. Various natural products, mixtures of stereoisomers of natural products, and compounds with novel skeletal structures were studied. In cases where it was difficult to determine the structures by NMR spectroscopy, we could successfully determine the chemical structures by computational chemistry. This review presents the results of structural analysis obtained using computational methods for several natural products that we have recently isolated.
Similar content being viewed by others
Avoid common mistakes on your manuscript.
Introduction
Natural products exhibit structural diversity and have been widely used for the development of pharmaceuticals. Detailed knowledge is essential for effective determination of the planar structure, relative configuration, and absolute configuration of potentially useful, naturally occurring compounds. The structural analyses of bioactive natural products that are structurally similar to known compounds are easier than that of compounds that do not resemble known compounds. It is also difficult to determine the absolute configuration of natural products if they consist of a mixture of stereoisomers.
We have previously identified bioactive natural products such as the ubiquitin–proteasome system inhibitors [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16] and osteoclast differentiation inhibitors [17,18,19,20,21,22]. Some of those natural products were compounds with unique substructures or mixtures of stereoisomers such as epimers or diastereomers. It was difficult to determine the structures and configurations of these complex compounds by NMR spectroscopy, because not enough information was available. However, we could successfully determine the chemical structures by computational chemistry. In this review, we describe techniques of structure determination for previously unknown natural products using computational methods.
Taichunamide C (1): diketopiperazine isolated from the fungus Aspergillus taichungensis
Notoamide analogs are isolated from Aspergillus fungi, and they contain tryptophan–proline diketopiperazine. We have isolated approximately 50 new notoamide analogs to date [23,24,25,26,27,28,29,30,31,32], and the biosynthetic mechanism of these alkaloids has also been studied [25,26,27,28,29, 32,33,34]. Seven structurally novel analogs, isolated from the metabolites of A. taichungensis (IBT19404), were analyzed, and their structures were determined [30]. Among these seven new analogs, compound 1 was the first natural product with a 1,2,4-dioxazolidine ring (Fig. 1). The absolute configuration of the bicyclic ring could be determined by analyzing the electronic circular dichroism (ECD) profiles recorded for the compound, because many known analogs have the same partial structure. Significant nuclear NOE correlation, such as between H-10 and H-30, was not observed during the determination of the relative configuration between C-2 and C-3. The relative configuration could not be determined by analyzing the NMR spectra of the compounds, because we were the first to report a compound containing a 1,2,4-dioxazolidine ring in the core structure, and reference spectra were not available in the literature. We decided to use computational methods to determine the absolute configuration. Since the absolute configurations of the centers, except for the C-2 and C-3 centers, were clear as described above, the possibility of the presence of four types of stereoisomers (2R,3R-, 2R,3S-, 2S,3R-, and 2S,3S-1) was investigated. Molecular mechanics conformational searches were performed for the four isomers using Merck molecular force field (MMFF), then density functional theory (DFT)-based calculations were used to optimize the structures of the obtained conformations. The calculated ECD profiles of the four stereoisomers were obtained using the time-dependent density functional theory (TDDFT) technique at the B3LYP/6-31G* level. The characteristic positive Cotton effect observed at 230 nm in the experimentally obtained ECD profile recorded for 1 agreed well with the effect observed in the calculated ECD profiles recorded for 2R,3R-1 (Fig. 2). Therefore, it could be concluded that the absolute configuration of 1 was 2R,3R,11S,17S,21R. The same conclusions could be drawn from the results obtained by calculations performed at the CAM-B3LYP and BHandHLYP levels [30].
Sulawesin A (2): a mixture of four diastereomers isolated from a marine sponge (Psammocinia sp.)
We isolated three new furanosesterterpene tetronic acids (sulawesins A–C (2–4)) and two known analogs (ircinins 1 and 2 (5 and 6)) (Fig. 3) from the Psammocinia sponge (North Sulawesi, Indonesia, September 2007) [12]. A comparison of the specific rotation values ([α]D) of compounds 5 and 6 (+ 8.0 (c 0.050, MeOH) and − 24 (c 0.050, MeOH), respectively) obtained by us with the values presented in the literature ((+)-5, [α]D = + 32.3 (c 0.050, MeOH); (+)-6, [α]D = + 34.8 (c 0.060, MeOH) [35]; (−)-18S-5, [α]D = − 34.12 (MeOH); (−)-18S-6, [α]D = − 40.20 (MeOH) [36]) indicated the presence of an optical mixture. We proved this hypothesis by isolating the (+)- and (−)-forms of the compound using a chiral column. This was the first time that 5 and 6 were obtained as optical mixtures (mixture of epimers; epimerization at C-18). It was presumed that compounds 2–4 consisted of epimers (epimerization at C-18).
The planar structures of 2 and 3 were determined by analyzing various spectral profiles. The 13C NMR chemical shifts of the structurally simple model compounds 7 (cis) and 8 (trans) (Fig. 4a) were calculated, and the chemical shifts were analyzed to determine the relative configurations at C-5 and C-9. The calculated chemical shifts corresponding to the C-5 and C-9 centers of the cis-isomer were significantly different from the calculated chemical shifts corresponding to the C-5 and C-9 centers of the trans-isomer. The experimentally obtained chemical shifts corresponding to the C-5 and C-9 centers in 2 and 3 matched well with the values calculated for the centers in the trans-isomer. This suggested that C-5/C-9 (in 2 and 3) was trans (Fig. 4b). Since it was presumed that 2 and 3 consisted of a mixture of epimers, the compounds were analyzed by HPLC with a chiral column. Four peaks (P1–P4) were detected in the chromatogram recorded for 2 (Fig. 5a), and the same result was obtained for 3. This suggested that each compound was a mixture of four diastereomers (5R,9R,18R, 5R,9R,18S, 5S,9S,18R, and 5S,9S,18S). An analysis of the ECD profiles of P1–P4 revealed the characteristic Cotton effect near 225 nm (Fig. 5b). Since 2 and 3 contained two chromophore units each, we investigated which chromophore corresponded to the peak at 225 nm. We designed 5R,9R-2A and 18R-2B as simplified model compounds and theoretically generated the ECD profiles for each compound. 5R,9R-2A exhibited a strong Cotton effect at 225 nm. The absolute configuration could be determined by analyzing the peak at 225 nm. The ECD profiles showed positive (for 2b/2c) and negative (for 2a/2d) Cotton effects at 225 nm, which suggested that the configuration of 2b/2c was 5R,9R and that of 2a/2d was 5S,9S. The absolute configuration at C-18 could not be determined, because the peak at 260 nm in the profile recorded for 2B was low in intensity. It was considered that the peak was hardly observed in the experimental ECD spectrum (Fig. 5b and c). Although 2 contained four diastereomers, the presence of the diastereomers was not observed by the NMR spectrum. Furthermore, analysis of the ECD profiles did not reveal the interaction between the two chromophores present in 2. These observations indicated that the two chromophores were connected by a long carbon chain. Hence, they did not influence each other.
Niphateolide A (9): a diterpene isolated from the marine sponge Niphates olemda
We isolated a new compound, niphateolide A (9) (Fig. 6), from the ethanol extract of the sponge Niphates olemda (Mantehage, North Sulawesi, Indonesia, December 2006) [10]. The analysis of various NMR spectra and molecular weights suggested that 9 was a diterpene containing a cyclopentylidene moiety and a γ-hydroxybutenolide moiety. It was a mixture of C-17 epimers (1:1). The NOE effect was analyzed to reveal that the configuration of 9 was 10R*,11R*. The ECD spectrum was generated computationally to determine the absolute configuration. Particular attention was paid to the following points. (1) The ECD profiles were usually recorded at wavelengths longer than 200 nm. Exciton-split CD profiles resulting from the correlation between the exocyclic double bond (C-6/C-7; 185 nm) and γ-hydroxybutenolide (207 nm) [37] were observed partially in the range beyond 200 nm. Therefore, we recorded the vacuum ultraviolet (VUV)-ECD spectrum at wavelengths shorter than 200 nm. (2) Since it was concluded that 9 was a mixture of epimers (epimerization at C-17), we theoretically generated the ECD profiles (at the B3LYP/6-31G* level) of the two epimers (10R,11R,17R- and 10R,11R,17S-9A). The spectral profile obtained by adding the two calculated ECD profiles (for 10R,11R-9A) reproduced the experimentally obtained spectral profile of 9 (Fig. 7). Hence, the absolute configuration of 9 could be determined as 10R,11R. The same conclusions were reached when different functionals, such as CAM-B3LYP and BHandHLP, were used for the calculations. For a mixture of stereoisomers, the experimentally obtained ECD profile could be reproduced by adding the calculated ECD profiles of each isomer.
Conclusion
In this study, we used computational methods to elucidate the chemical structures of natural products with partial structures that were previously unknown. The structures of natural products containing a mixture of stereoisomers, whose structures were difficult to determine solely by NMR spectroscopy, were also determined.
It is difficult to analyze the structure of new compounds with unprecedented molecular skeletons, because reference data are not available. In such cases (e.g., taichunamide C (1)), computational methods can be used to generate the 13C NMR spectra and ECD profiles. The computationally obtained spectra can be compared with the experimentally obtained spectra to determine the structure of the compounds. We observed that the ECD profiles of the sulawesins (2–4) and niphateolide A (9) were the summations of spectra of the Cotton effects observed for each chromophore. We also succeeded in determining the configuration when the compound consisted of a mixture of stereoisomers.
NMR spectroscopy and X-ray crystallography are commonly used to determine the structural properties of natural products. However, rapid and accurate determination of structural features may be achieved using computational methods, which may be particularly useful for analyzing previously unknown compounds. Natural products that can be used as safer and more effective pharmaceuticals may be identified using advanced structural analysis and computational techniques.
References
Yamanokuchi R, Imada K, Miyazaki M, Kato H, Watanabe T, Fujimuro M, Saeki Y, Yoshinaga S, Terasawa H, Iwasaki N, Rotinsulu H, Losung F, Mangindaan REP, Namikoshi M, de Voogd NJ, Yokosawa H, Tsukamoto S (2012) Hyrtioreticulins A-E, indole alkaloids inhibiting the ubiquitin-activating enzyme from the marine sponge Hyrtios reticulates. Bioorg Med Chem 20:4437–4442
Ushiyama S, Umaoka H, Kato H, Suwa Y, Morioka H, Rotinsulu H, Losung F, Mangindaan REP, de Voogd NJ, Yokosawa H, Tsukamoto S (2012) Manadosterols A and B, sulfonated sterol dimers inhibiting the Ubc13-Uev1A interaction, isolated from the marine sponge Lissodendryx fibrosa. J Nat Prod 75:1495–1499
Nakamura Y, Kato H, Nishikawa T, Iwasaki N, Suwa Y, Rotinsulu H, Losung F, Maarisit W, Mangindaan REP, Morioka H, Yokosawa H, Tsukamoto S (2013) Siladenoserinols A-L: new sulfonated serinol derivatives from a tunicate as inhibitors of p53-Hdm2 interaction. Org Lett 15:322–325
Imada K, Sakai E, Kato H, Kawabata T, Yoshinaga S, Nehira T, Terasawa H, Tsukamoto S (2013) Reticulatins A and B and hyrtioreticulin F from the marine sponge Hyrtios reticulatus. Tetrahedron 69:7051–7055
Sakai E, Kato H, Rotinsulu H, Losung F, Mangindaan REP, de Voogd NJ, Yokosawa H, Tsukamoto S (2014) Variabines A and B, new β-carboline alkaloids from the marine sponge Luffariella variabilis. J Nat Med 68:215–219
El-Desoky AH, Kato H, Eguchi K, Kawabata T, Fujiwara Y, Losung F, Mangindaan REP, de Voogd NJ, Takeya M, Yokosawa H, Tsukamoto S (2014) Acantholactam and pre-neo-kauluamine, manzamine-related alkaloids, from the Indonesian marine sponges, Acanthostrongylophora ingens. J Nat Prod 77:1536–1540
Furusato A, Kato H, Nehira T, Eguchi K, Kawabata T, Fujiwara Y, Mangindaan REP, de Voogd NJ, Takeya M, Yokosawa H, Tsukamoto S (2014) Acanthomanzamines A-E with new manzamine frameworks from the marine sponge Acanthostrongylophora ingens. Org Lett 16:3888–3891
Yamakuma M, Kato H, Matsuo K, El-Desoky AH, Kawabata T, Losung F, Mangindaan REP, de Voogd NJ, Yokosawa H, Tsukamoto S (2014) 1-Hydroxyethylhalenaquinone: a new proteasome inhibitor from the marine sponge Xestospongia sp. Heterocycles 89:2605–2610
Noda A, Sakai E, Kato H, Losung F, Mangindaan REP, de Voogd NJ, Yokosawa H, Tsukamoto S (2015) Strongylophorines, meroditerpenoids from the marine sponge Petrosia corticata, function as proteasome inhibitors. Bioorg Med Chem Lett 25:2650–2653
Kato H, Nehira T, Matsuo K, Kawabata T, Kobashigawa Y, Morioka H, Losung F, Mangindaan REP, de Voogd NJ, Yokosawa H, Tsukamoto S (2015) Niphateolide A: isolation from the marine sponge Niphates olemda and determination of its absolute configuration by an ECD analysis. Tetrahedron 71:6956–6960
Tanokashira N, Kukita S, Kato H, Nehira T, Angkouw ED, Mangindaan REP, de Voogd NJ, Tsukamoto S (2016) Petroquinones: trimeric and dimeric xestoquinone derivatives isolated from the marine sponge Petrosia alfiani. Tetrahedron 72:5530–5540
Afifi AH, Kagiyama I, El-Desoky AH, Kato H, Mangindaan REP, de Voogd NJ, Ammar NM, Hifnawy MS, Tsukamoto S (2017) Sulawesins A-C, furanosesterterpene tetronic acids that inhibit USP7, from a Psammocinia sp. marine sponge. J Nat Prod 80:2045–2050
El-Desoky AH, Kato H, Tsukamoto S (2017) Ceylonins G-I: spongian diterpenes from the marine sponge Spongia ceylonensis. J Nat Med 71:765–769
Inoue M, Hitora Y, Kato H, Losung F, Mangindaan REP, Tsukamoto S (2018) New geranyl flavonoids from the leaves of Artocarpus communis. J Nat Med 72:632–640
Torii M, Hitora Y, Kato H, Koyanagi Y, Kawahara T, Losung F, Mangindaan REP, Tsukamoto S (2018) Siladenoserinols M-P, sulfonated serinol derivatives from a tunicate. Tetrahedron 74:7516–7521
Kato H, El-Desoky AH, Takeishi Y, Nehira T, Angkouw ED, Mangindaan REP, de Voogd NJ, Tsukamoto S (2019) Tetradehydrohalicyclamine B, a new proteasome inhibitor from the marine sponge Acanthostrongylophora ingens. Bioorg Med Chem Lett 29:8–10
Tsukamoto S, Takeuchi T, Kawabata T, Kato H, Yamakuma M, Matsuo K, El-Desoky AH, Losung F, Mangindaan REP, de Voogd NJ, Arata Y, Yokosawa H (2014) Halenaquinone inhibits RANKL-induced osteoclastogenesis. Bioorg Med Chem Lett 24:5315–5317
El-Desoky AH, Kato H, Angkouw ED, Mangindaan REP, de Voogd NJ, Tsukamoto S (2016) Ceylonamides A-F, nitrogenous spongian diterpenes that inhibit RANKL-induced osteoclastogenesis, from the marine sponge Spongia ceylonensis. J Nat Prod 79:1922–1928
El-Desoky AH, Kato H, Kagiyama I, Hitora Y, Losung F, Mangindaan REP, de Voogd NJ, Tsukamoto S (2017) Ceylonins A-F, spongian diterpene derivatives that inhibit RANKL-induced formation of multinuclear osteoclasts, from the marine sponge Spongia ceylonensis. J Nat Prod 80:90–95
Kato H, Kai A, Kawabata T, Sunderhaus JD, McAfoos TJ, Finefield JM, Sugimoto Y, Williams RM, Tsukamoto S (2017) Enantioselective inhibitory abilities of enantiomers of notoamides against RANKL-induced formation of multinuclear osteoclasts. Bioorg Med Chem Lett 27:4975–4978
Fukumoto A, Hitora Y, Kai A, Kato H, Angkouw ED, Mangindaan REP, de Voogd NJ, Tsukamoto S (2018) Isolation of aaptic acid from the marine sponge Asptos lobata and inhibitory effect of aaptamines on RANKL-induced formation of multinuclear osteoclasts. Heterocycles 97:1219–1225
El-Beih AA, El-Desoky AH, Al-hammady MA, Elshamy A-SI, Hegazy M-EF, Kato H, Tsukamoto S (2018) New inhibitiors of RANKL-induced osteoclastogenesis from the marine sponge Siphonochalina siphonella. Fitoterapia 128:43–49
Kato H, Yoshida T, Tokue T, Nojiri Y, Hirota H, Ohta T, Williams RM, Tsukamoto S (2007) Notoamides A-D: new prenylated indole alkaloids isolated from a marine-derived fungus, Aspergillus sp. Angew Chem Int Ed 46:2254–2256
Tsukamoto S, Kato H, Samizo M, Nojiri Y, Onuki H, Hirota H, Ohta T (2008) Notoamides F-K, prenylated indole alkaloids isolated from a marine-derived Aspergillus sp. J Nat Prod 71:2064–2067
Tsukamoto S, Kawabata T, Kato H, Greshock TJ, Hirota H, Ohta T, Williams RM (2009) Isolation of antipodal (-)-versicolamide B and notoamides L-N from a marine-derived Aspergillus sp. Org Lett 11:1297–1300
Tsukamoto S, Kato H, Greshock TJ, Hirota H, Ohta T, Williams RM (2009) Isolation of notoamide E, a key precursor in the biosynthesis of prenylated indole alkaloids in a marine-derived fungus, Aspergillus sp. J Am Chem Soc 131:3834–3835
Sunderhaus JD, McAfoos TJ, Finefield JM, Kato H, Li S, Tsukamoto S, Sherman DH, Williams RM (2013) Synthesis and bioconversions of notoamide T: a biosynthetic precursor to stephacidin A and notoamide B. Org Lett 15:22–25
Kato H, Nakahara T, Yamaguchi M, Kagiyama I, Finefield JM, Sunderhaus JD, Sherman DH, Williams RM, Tsukamoto S (2015) Bioconversion of 6-epi-notoamide T produces metabolites of unprecedented structures in a marine-derived Aspergillus sp. Tetrahedron Lett 56:247–251
Kato H, Nakahara T, Sugimoto K, Matsuo K, Kagiyama I, Frisvad JC, Sherman DH, Williams RM, Tsukamoto S (2015) Isolation of notoamide S and enantiomeric 6-epi-stephacidin A from the fungus Aspergillus amoenus: biogenetic implications. Org Lett 17:700–703
Kagiyama I, Kato H, Nehira T, Frisvad JC, Sherman DH, Williams RM, Tsukamoto S (2016) Taichunamides: prenylated indole alkaloids from Aspergillus taichungensis (IBT 19404). Angew Chem Int Ed 55:1128–1132
Sugimoto K, Sadahiro Y, Kagiyama I, Kato H, Sherman DH, Williams RM, Tsukamoto S (2017) Isolation of amoenamide A and five antipodal prenylated alkaloids from Aspergillus amoenus NRRL 35600. Tetrahedron Lett 52:6923–6926
Kai A, Kato H, Sherman DH, Williams RM, Tsukamoto S (2018) Isolation of a new indoxyl alkaloid, Amoenamide B, from Aspergillus amoenus NRRL 35600: biosynthetic implications and correction of the structure of Speramide B. Tetrahedron Lett 59:4236–4240
Finefield JM, Kato H, Greshock TJ, Sherman DH, Tsukamoto S, Williams RM (2011) Biosynthetic stadies of the notoamides: isotopic synthesis of stephacidin A and incorporation into notoamide B and sclerotiamide. Org Lett 13:3802–3805
Kato H, Nakamura Y, Finefield JM, Umaoka H, Nakahara T, Williams RM, Tsukamoto S (2011) Study on the biosynthesis of the notoamides: Pinacol-type rearrangement of the isoprenyl unit in deoxybrevianamide E and 6-hydroxydeoxybrevianamide E. Tetrahedron Lett 52:6923–6926
Liu Y, Bae BH, Alam N, Hong J, Sim CJ, Lee CO, Im KS, Jung JH (2001) New cytotoxic sesterterpenes from the sponge Sarcotragus species. J Nat Prod 64:1301–1304
Manes LV, Crews P, Ksebati MB, Schmitz FJ (1986) The use of two-dimensional NMR and relaxation reagents to determine stereochemical features in acyclic sesterterpenes. J Nat Prod 49:787–793
Shao Y, Wang M-F, Ho C-T, Chin C-K, Yang S-W, Cordell GA, Lotter H, Wagner H (1998) Lingulatusin, two epimers of an unusual linear diterpene from Aster lingulatus. Phytochemistry 49:609–612
Acknowledgements
This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan.
Author information
Authors and Affiliations
Corresponding author
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
About this article
Cite this article
Kato, H. Structural analysis of previously unknown natural products using computational methods. J Nat Med 76, 719–724 (2022). https://doi.org/10.1007/s11418-022-01637-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11418-022-01637-y