Chemical biology is a research approach that applies small molecules as chemical tools to dissect biological processes.
The application of small molecules to study a biological system is referred to as 'Chemical Biology'. Typically, these molecules interfere with the function of target proteins and consequently lead to disruption of biological processes. When these molecules are applied to cells or whole organisms, the consequences of this perturbation can be studied at the molecular level. As such, these chemical probes allow researchers to unravel the role of cellular and molecular components in a complex biological network, even inside living organisms. Next to the application as chemical probes, small molecules can also be used as starting points for the discovery and development of novel drugs and agrochemicals.
Chemical Biology to study Plant Development
Brassinosteroids (BRs) are plant steroid hormones essential in controlling plant growth and development. BRs bind to the plasma membrane-localized receptor BRI1 and consequently activate an intracellular signaling cascade. Central in BR signaling, the glycogen synthase kinase 3 (GSK3)-like kinase BIN2 and the Ser/Thr phosphatase BSU1 modulate the phosphorylation state of transcription factors, which in turn regulate BR-responsive gene expression. By phenotypic compound screening in Arabidopsis thaliana, we have identified a small non-steroidal molecule that induces constitutive BR-responses in planta similar to the action of brassinolide, the most potent naturally occurring BR. Genetic and biochemical data demonstrate that application of this compound activates the signaling pathway downstream of BRI1 by inhibiting BIN2 kinase activity, hence the name bikinin for BIN2 kinase inhibitor. Bikinin acts as an ATP competitor and inhibits, next to BIN2, six other Arabidopsis thaliana GSK3s in vitro. In silico modeling and in vitro kinase assays with mutated BIN2 allowed us to pinpoint the residues in the ATP-binding pocket of GSK3s that have an effect on bikinin binding affinity. Comparative transcriptome analysis of bikinin and brassinolide demonstrated that simultaneous inhibition of seven GSK3s exclusively activates BR responses. By using bikinin as a chemical tool, we could demonstrate that GSK3 inhibition is the sole activation mode of BR signaling and GSK3-independent BR responses are unlikely to occur. The project was done in collaboration with the brassinosteroid group (De Rybel B, Audenaert D, et al. 2009).
Spatial expansion of the root system and root branching is achieved through the development of lateral roots and is to a large extent controlled by the plant hormone auxin. However, studying root branching by application of auxin or auxin-like molecules is complicated by their pleiotropic effects on virtually every aspect of plant growth and development. We have developed and miniaturized a reporter-based assay in Arabidopsis thaliana, which marks lateral root development events and allows to screen for novel compounds that promote root branching. Screening of a diverse compound collection led to the identification of naxillin, the first non-auxin-like synthetic molecule that selectively induces lateral root development. Transcriptome analysis showed that naxillin induces only a subset of the auxin-responsive genes. In addition, the induced auxin response is restricted to the basal meristem, the zone where pericycle cells establish their lateral root founder cell identity. Genetic and biochemical analysis demonstrated that naxillin enhances the conversion of indole-3-butyric acid (IBA) into the active auxin indole-3-acetic acid (IAA) in the root cap. The application of naxillin revealed the role of IBA-derived IAA as a specific lateral root-inducing agent and highlights the contribution of the root cap in root branching as an important source for IBA-derived IAA (De Rybel B, Audenaert D, et al. 2012).
Other chemical biology projects
In collaboration with other academic groups, we have been involved in assay development and compound screening projects for a diversity of plant biological processes. The assays that have been developed include plant cell-based assays (secondary metabolism, flavonoid production) and Arabidopsis-based assays (general growth and development, drought tolerance, photorespiration, lignin biosynthesis, auxin signaling, gibberellin signaling, ethylene signaling), which have been successfully implemented for compound screenings.
VIB Compound Screening Facility (VIB-CSF)
Xuan W, Audenaert D, Parizot B, Möller BK, Njo MF, De Rybel B, De Rop G, Van Isterdael G, Mähönen AP, Vanneste S, Beeckman T. Root Cap-Derived Auxin Pre-patterns the Longitudinal Axis of the Arabidopsis Root. Curr Biol. 2015;25:1381-1388. [pmid]
Kerchev PI, De Clercq I, Denecker J, Mühlenbock P, Kumpf R, Nguyen L, Audenaert D, Dejonghe W, Van Breusegem F. Mitochondrial perturbation negatively affects auxin signaling. Mol Plant. 2014;7:1138-1150. [full text]
Hu Y, Callebert P, Vandemoortel I, Nguyen L, Audenaert D, Verschraegen L, Vandenbussche F, Van Der Straeten D. TR-DB: an open-access database of compounds affecting the ethylene-induced triple response in Arabidopsis. Plant Physiol Biochem. 2014;75:128-137. [pmid]
Audenaert D, Nguyen L, De Rybel B, Beeckman T. Fully automated compound screening in Arabidopsis thaliana seedlings. Methods Mol Biol. 2014;1056:3-9. [pmid]
Audenaert D, De Rybel B, Nguyen L, Beeckman T. Small-molecule screens to study lateral root development. Methods Mol Biol. 2013;959:189-195. [pmid]
De Rybel B*, Audenaert D*, Xuan W, Overvoorde P, Strader LC, Kepinski S, Hoye R, Brisbois R, Parizot B, Vanneste S, Liu X, Gilday A, Graham IA, Nguyen L, Jansen L, Njo MF, Inzé D, Bartel B, Beeckman T. A role for the root cap in root branching revealed by the non-auxin probe naxillin. Nat Chem Biol. 2012;8:798-805. (* equal contribution) [pmid]
De Rybel B*, Audenaert D*, Beeckman T, Kepinski S. The past, present and future of chemical biology in auxin research. ACS Chem Biol. 2009;4:987-998 (* equal contribution) [full text]
De Rybel B*, Audenaert D*, Vert G, Rozhon W, Mayerhofer J, Peelman F, Coutuer S, Denayer T, Jansen L, Nguyen L, Vanhoutte I, Beemster G, Vleminckx K, Jonak C, Chory J, Inzé D, Russinova E and Beeckman T. Chemical inhibition of a subset of Arabidopsis thaliana GSK3-like kinases activates brassinosteroid signaling. Chemistry & Biology. 2009;16, 594–604 (* equal contribution) [full text]