Life Sciences Division

Uncovering novel enzymatic activities to design bioinspired drug molecules

CEA

A team of CEA-CNRS researchers has just published pioneering results in two reviews, focusing on the biological synthesis of complex cyclodipeptides, which are molecules widely found in microorganisms. The team has uncovered a new family of enzymes presenting the standout feature of peptide-bonding cyclodipeptides using amino acids loaded on the transfer RNA. They also demonstrated that these enzymes work in tandem with other enzyme groups to alter the cyclodipeptides, conferring them novel biological activities. This research opens up promising new perspectives for the rational design of complex molecules, especially medical drugs.

Nature continues to demonstrate unparalleled genius in engineering biologically-active compounds. Research has arrived at the point where understanding the mechanisms regulating the synthesis of biologically-active compounds is one of the keys opening the door to a new therapeutic arsenal of bioinspired medicines.

Researchers from the Institute of Biotechnology – Saclay (CEA) and the Institute of Genetics and Microbiology (Paris-Sud 11 University, CNRS) have uncovered a new family of enzymes responsible for the first step in the biosynthesis of complex cyclodipeptides. These relatively small enzymes, baptised cyclodipeptide synthases (CDPS), have the ability to link two amino acids by forming two peptide bonds, thus generating a broad array of cyclodipeptides.
The standout feature of these enzymes is that they use amino acid-loaded transfer RNA (tRNA) as substrates. These pioneering results represent a potential breakthrough in the search for a catalytic enzyme peptide bond-forming mechanism similar to that of the ribosome, which itself uses these same loaded tRNA for protein synthesis.
This research also highlights the genetic-level pairing of cyclodipeptide synthases (CDPS) with other enzymes whose role is to impel changes on cyclodipeptides.
The results establish the existence of novel enzymes boasting the ability to biosynthesize peptide bonds and assign a new role for loaded tRNA, thus earning their recent publication in Nature Chem Biol.

This same research team has also extended its scope to focus on the CDPS-associated modifier enzymes. Particularly fruitful results have been obtained for Mycobacterium tuberculosis, the pathogenic agent that causes tuberculosis. The M. tuberculosis CDPS synthesizes a cyclodipeptide termed cyclo(L-tyr-L-tyr). In a PNAS-published paper, the authors showed that cyclo(L-tyr-L-tyr) is governed by a modifier enzyme: cytochrome P450 CYP121. Andrew Munro’s team (McLean et al. (2008), J. Biol. Chem. 283, 33406) recently demonstrated that cytochrome P450 CYP121 is an essential enzyme for M. tuberculosis viability, making it a novel therapeutic target. The work of the joint iBiTec-S/IGM team, by identifying the cytochrome’s natural substrate and enzymatic activity, paves the way to the rational design of inhibitors of this enzyme, and therefore a putative new class of antituberculosis agents.




The figure schematizes the metabolic pathway associating a CDPS (in green) with the CYP121 modifier enzyme (in orange) in Mycobacterium tuberculosis. The CDPS uses tRNA (in black and blue) loaded with tyrosyl residues (green fragments at the tips of the tRNA) to form the cyclodipeptide cyclo(L-tyr-L-tyr) (green, at centre). Cyclo(L-tyr-L-tyr) is then used as a substrate by CYP121 to catalyze the formation of a novel chemical entity (orange, at right) via an intramolecular carbon-carbon bridge.


This research also illustrates how studying the biosynthesis of natural molecules can surface novel enzymatic activities and uncover the role of tRNA in new mechanisms of biosynthesis. Taken together, these findings open up solid perspectives for the rational design of a broad array of molecular compounds, as well as new pharmacologically active drugs.

Research funded by the CEA, the CNRS and Paris-Sud 11 University. The research published in Nature Chem. Biol. was also partly funded by Kyowa Hakko Bio Co. Ltd.


Reference :

• Cyclodipeptide synthases are a family of tRNA-dependent peptide bond-forming enzymes. Gondry M., Sauguet L., Belin P., Thai R., Amouroux R., Tellier C., Tuphile K., Jacquet M., Braud S., Courçon M., Masson C., Dubois S., Lautru S., Lecoq A., Hashimoto S.-I., Genet R. and Pernodet J.-L. Nature Chem. Biol., 3 mai 2009, doi :10.1038/nchembio.175
• Identification and structural basis of the reaction catalyzed by CYP121, an essential cytochrome P450 in Mycobacterium tuberculosis. Belin P., Le Du M.-H., Fielding A., Lequin O, Jacquet M., Charbonnier J.-B., Lecoq A., Thai R., Courçon M., Masson C., Genet R., Pernodet J.-L. and Gondry M. Proc. Natl. Acad. Sci. USA, May 5, 2009, vol. 106 7426 –7431