Acetylene containing cyclo(L-Tyr-L-Tyr)-analogs as mechanism-based inhibitors of CYP121A1 from Mycobacterium tuberculosis

Sandra Ortega Ugalde, Kerstin Wallraven, Alexander Speer, Wilbert Bitter, Tom N. Grossmann*, Jan N.M. Commandeur

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review


Tuberculosis (TB) is a globally significant infective disease that is caused by a single infectious agent, Mycobacterium tuberculosis (Mtb). Because of the rise in the number of multidrug-resistant (MDR) TB strains, identification of alternative drug targets for the development of drugs with different mechanism of actions is desired. CYP121A1, one of the twenty cytochrome P450 enzymes encoded in the Mtb genome, was previously shown to be essential for bacterial growth. This enzyme catalyzes the intramolecular C–C crosslinking reaction of the cyclopeptide cyclo(L-tyr-L-tyr) (cYY) yielding the metabolite mycocyclosin. In the present study, acetylene-substituted cYY-analogs were synthesized and evaluated as potential mechanism-based inhibitors of CYP121A1. The acetylene-substituted cYY-analogs were capable of binding to CYP121A1 with affinities comparable with cYY, and exhibited a Type I binding mode, indicative of a substrate-like binding, mandatory for metabolism. Only the cYY-analogs which contain an acetylene-substitution at one (2a) or both (3) para-positions of cYY showed mechanism-based inhibition of CYP121A1 activity. The values of KI and kinact were 236 µM and 0.045 min−1, respectively, for compound 2a, and 145 µM and 0.015 min−1, repectively, for compound 3 The inactivation could neither be reversed by dialysis nor be prevented by including glutathione. LC-MS analysis demonstrated that the inactivation results from covalent binding to the apoprotein, whereas the heme was unmodified. Interestingly, the mass increment of the CYP121A1 apoprotein was significantly smaller than was expected from the ketene formed by oxidation of the acetylene-group, indicative for a secondary cleavage reaction in the active site of CYP121A1. Although the two acetylene-containing cYY-analogs showed significant mechanism-based inhibition, growth inhibition of the Mtb strains was only observed at millimolar concentrations. This low efficacy may be due to insufficient irreversible inactivation of CYP121A1 and/or insufficient cellular uptake. Although the identified mechanism-based inhibitors have no perspective for Mtb-treatment, this study is the first proof-of-principle that mechanism-based inhibition of CYP121A1 is feasible and may provide the basis for new strategies in the design and development of compounds against this promising therapeutic target.

Original languageEnglish
Article number113938
Pages (from-to)1-14
Number of pages14
JournalBiochemical Pharmacology
Early online date26 Mar 2020
Publication statusPublished - Jul 2020


This project was funded by The Netherlands Organization for Scientific Research (grant no. 022.005.031 to S. Ortega Ugalde). We thank the European Research Council for support (ERC; ERC starting grant, no. 678623 to T.N. Grossmann ).

FundersFunder number
Netherlands Organization for Scientific Research
Horizon 2020 Framework Programme678623
European Research Council
Nederlandse Organisatie voor Wetenschappelijk Onderzoek022.005.031


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