Bridging the maytansine and vinca sites: cryptophycins target β-tubulin's T5-loop

Anne-Catherine Abel; Tobias Mühlethaler; Cedric Dessin; Thomas Schachtsiek; Benedikt Sammet; Timothy Sharpe; Michel O Steinmetz; Norbert Sewald; Andrea E Prota

doi:10.1016/j.jbc.2024.107363

Bridging the maytansine and vinca sites: cryptophycins target β-tubulin's T5-loop

J Biol Chem. 2024 May 10:107363. doi: 10.1016/j.jbc.2024.107363. Online ahead of print.

Authors

Anne-Catherine Abel¹, Tobias Mühlethaler², Cedric Dessin³, Thomas Schachtsiek³, Benedikt Sammet³, Timothy Sharpe², Michel O Steinmetz¹, Norbert Sewald⁴, Andrea E Prota⁵

Affiliations

¹ Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland; Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
² Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
³ Organic and Bioorganic Chemistry, Department of Chemistry, University of Bielefeld, Universitätsstraße 25, 3361 Bielefeld, Germany.
⁴ Organic and Bioorganic Chemistry, Department of Chemistry, University of Bielefeld, Universitätsstraße 25, 3361 Bielefeld, Germany. Electronic address: nortbert.sewald@uni-bielefeld.de.
⁵ Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland. Electronic address: andrea.prota@psi.ch.

PMID: 38735475
DOI: 10.1016/j.jbc.2024.107363

Abstract

Cryptophycins are microtubule-targeting agents (MTAs) that belong to the most potent antimitotic compounds known to date; however, their exact molecular mechanism of action remains unclear. Here, we present the 2.2 Å resolution X-ray crystal structure of a potent cryptophycin derivative bound to the αβ-tubulin heterodimer. The structure addresses conformational issues present in a previous 3.3 Å resolution cryo-electron microscopy structure of cryptophycin-52 bound to the maytansine site of β-tubulin. It further provides atomic details on interactions of cryptophycins, which had not been described previously, including ones that are in line with structure-activity relationship (SAR) studies. Interestingly, we discovered a second cryptophycin-binding site that involves the T5-loop of β-tubulin, a critical secondary structure element involved in the exchange of the guanosine nucleotide and in the formation of longitudinal tubulin contacts in microtubules. Cryptophycins are the first natural ligands found to bind to this new "βT5-loop site" that bridges the maytansine and vinca sites. Our results offer unique avenues to rationally design novel MTAs with the capacity to modulate T5-loop dynamics and to simultaneously engage multiple β-tubulin binding sites.

Keywords: anticancer drug; cryptophycins; crystal structure; microtubule targeting agents; protein drug interactions; structural biology; tubulin.