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Parallel screening and cheminformatics modeling of flavonoid activated aptasensors

Xiu, Yu, Zhang, Ni, Prabhakaran, Pranesha, Jang, Sungho, Yuan, Qipeng, Breneman, Curt M., Jung, Gyoo Yeol, Vongsangnak, Wanwipa, Koffas, Mattheos A.G.·2022·Synthetic and Systems Biotechnology
DOI 10.1016/j.synbio.2022.07.006
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Abstract

A parallel screening of 27 different flavonoids and chalcones was conducted using 6 artificial naringenin-activated riboswitches (M1, M2, M3, O, L and H). A quantitative structure-property relationship approach was applied to understand the physicochemical properties of the flavonoid structures resulting in specificity differences relied on the fluorescence intensity of a green fluorescent protein reporter. Robust models of riboswitches M1, M2 and O that had good predictive power were constructed with descriptors selected for their high correlation. Increased electronegativity and hydrophilicity of the flavonoids structures were identified as two properties that increased binding affinity to RNA riboswitches. Hydroxyl groups at the C-3′ and C-4’ positions of the flavonoid molecule were strictly required for ligand-activation with riboswitches M1 and M2. Riboswitches O and L preferred multi-hydroxylated flavones as ligands. Substitutions on the A ring of the flavonoid molecule were not important in the molecular recognition process. O-glycosylated derivatives were not recognized by any of the riboswitches, presumably due to steric hindrances. Despite the challenges of detecting RNA conformational change after ligand binding, the resulting models elucidate important physicochemical features in the ligands for conformational structural studies of artificial aptamer complexes and for design of ligands having higher binding specificity.

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Metadata

Authors
Xiu, Y., Zhang, N., Prabhakaran, P., Jang, S., Yuan, Q., Breneman, C. M., Jung, G. Y., Vongsangnak, W., & Koffas, M. A. G.
Venue
Synthetic and Systems Biotechnology
Publisher
Elsevier BV
Published
2022-12
Volume
7
Issue
4
Pages
1148-1158
ISSN
2405-805X
DOI
10.1016/j.synbio.2022.07.006
Cited by
3
Language
en
Licence
Funders
  • Kasetsart University
  • Thailand Science Research and Innovation
  • Office of International Affairs
  • National Natural Science Foundation of China (21636001)
  • National Research Foundation of Korea
  • Beijing Municipal Commission of Education (KM20191417012)

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CoChat. (2026). Citation check: Parallel screening and cheminformatics modeling of flavonoid activated aptasensors. https://app.cochat.ai/papers/10.1016/j.synbio.2022.07.006
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Xiu, Y., Zhang, N., Prabhakaran, P., Jang, S., Yuan, Q., Breneman, C. M., Jung, G. Y., Vongsangnak, W., & Koffas, M. A. G. (2022). Parallel screening and cheminformatics modeling of flavonoid activated aptasensors. Synthetic and Systems Biotechnology. https://doi.org/10.1016/j.synbio.2022.07.006

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