Presentation Information
[P01-126]LC-Raman Screening: Unveiling Novel Microbial Metabolites via a Structure-Guided Approach
○Takuma Kyotani1,2, Takuji Nakashima3,4, Masahiro Ando3, Haruko Takeyama1,3,5 (1. Grad. Sch. Adv. Sci. Eng., Waseda Univ. (Japan), 2. Shimadzu Corp. (Japan), 3. Res. Org. Nano Life Innov., Waseda Univ. (Japan), 4. Fac. Integr. Environ. Stud., Univ. of Human Environ. (Japan), 5. Inst. Adv. Res. Biosyst. Dynam., Waseda Res. Inst. Sci. Eng., Waseda Univ. (Japan))
Keywords:
Microbial metabolites,Raman spectroscopy,LC-Raman,Screening method,Novel compounds
[Purpose]
Actinomycete-derived secondary metabolites are vital resources for drug discovery due to their structural diversity and potent biological activities. However, conventional screening strategies —relying primarily on bioactivity assays— face significant limitations: they are labor-intensive, time-consuming, and frequently lead to the redundant re-discovery of known compounds. To address these challenges, we developed a novel analytical platform, the LC-Raman system, which integrates liquid chromatography (LC) with Raman spectroscopy. By providing real-time molecular structural insights alongside chromatographic separation, this approach enables the direct selection of candidates based on their unique chemical signatures, moving beyond the constraints of bioactivity-centered screening. In this study, we established an LC-Raman screening protocol —a structure-based approach for identifying novel microbial products.
[Method]
Culture broths of actinomycetes isolated from soybean roots were subjected to organic solvent extraction to prepare analytical samples. Component separation was performed using reverse-phase LC. One-tenth of the eluate was spotted onto a custom 384-well plate at 5-second intervals. Raman spectra of the precipitates, formed after ambient drying of the solvent, were acquired. The obtained Raman spectra were analyzed using an in-house Raman spectral database.
[Results]
LC-Raman screening of the culture extracts identified various actinomycete metabolites, including amino acids, isoflavones, and lipids. Furthermore, two Raman spectra, which did not match any entries in the database and were attributed to secondary metabolites containing a thiazole skeleton, were identified as novel compound candidates. To validate these findings, we performed isolation, purification, and structural elucidation using NMR spectroscopy. The analysis confirmed that the candidate compounds were indeed novel compounds possessing a thiazole skeleton. Additionally, one of the identified novel compounds exhibited antimicrobial activity.
[Consideration]
A current challenge of the LC-Raman workflow is not the separation of multiple co-existing compounds, as our platform can already resolve and analyze such mixtures effectively. Rather, the main limitation lies in compound identification from Raman peaks. Although spectral annotation using our in-house Raman database is effective for known compounds, identification accuracy remains limited for previously uncharacterized compounds. Expanding the database and improving inference for unknown spectra will further enhance the utility of this screening platform.
[Conclusion]
Two novel sulfur-containing compounds were successfully identified through the LC-Raman screening of actinomycete culture extracts. This structure-based strategy will not only enhance discovery efficiency but also maximize the probability of identifying truly novel chemical scaffolds.
Actinomycete-derived secondary metabolites are vital resources for drug discovery due to their structural diversity and potent biological activities. However, conventional screening strategies —relying primarily on bioactivity assays— face significant limitations: they are labor-intensive, time-consuming, and frequently lead to the redundant re-discovery of known compounds. To address these challenges, we developed a novel analytical platform, the LC-Raman system, which integrates liquid chromatography (LC) with Raman spectroscopy. By providing real-time molecular structural insights alongside chromatographic separation, this approach enables the direct selection of candidates based on their unique chemical signatures, moving beyond the constraints of bioactivity-centered screening. In this study, we established an LC-Raman screening protocol —a structure-based approach for identifying novel microbial products.
[Method]
Culture broths of actinomycetes isolated from soybean roots were subjected to organic solvent extraction to prepare analytical samples. Component separation was performed using reverse-phase LC. One-tenth of the eluate was spotted onto a custom 384-well plate at 5-second intervals. Raman spectra of the precipitates, formed after ambient drying of the solvent, were acquired. The obtained Raman spectra were analyzed using an in-house Raman spectral database.
[Results]
LC-Raman screening of the culture extracts identified various actinomycete metabolites, including amino acids, isoflavones, and lipids. Furthermore, two Raman spectra, which did not match any entries in the database and were attributed to secondary metabolites containing a thiazole skeleton, were identified as novel compound candidates. To validate these findings, we performed isolation, purification, and structural elucidation using NMR spectroscopy. The analysis confirmed that the candidate compounds were indeed novel compounds possessing a thiazole skeleton. Additionally, one of the identified novel compounds exhibited antimicrobial activity.
[Consideration]
A current challenge of the LC-Raman workflow is not the separation of multiple co-existing compounds, as our platform can already resolve and analyze such mixtures effectively. Rather, the main limitation lies in compound identification from Raman peaks. Although spectral annotation using our in-house Raman database is effective for known compounds, identification accuracy remains limited for previously uncharacterized compounds. Expanding the database and improving inference for unknown spectra will further enhance the utility of this screening platform.
[Conclusion]
Two novel sulfur-containing compounds were successfully identified through the LC-Raman screening of actinomycete culture extracts. This structure-based strategy will not only enhance discovery efficiency but also maximize the probability of identifying truly novel chemical scaffolds.
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