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Biochemical assay development and HTS
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The ATPase activity and the kinetic parameters of recombinant wild-type VCP and its mutants were evaluated by monitoring ADP formation in the reaction, using a modified NADH-coupled assay. As ADP and NADH are ATP-competitive inhibitors of VCP ATPase activity, the standard protocol for the NADH-coupled assay was modified into a two-step procedure. In the first part, an ATP-regenerating system (40 U/ml pyruvate kinase and 3 mM phosphoenolpyruvate) recycles the ADP produced by VCP activity, keeps the substrate concentration constant (thus preventing product inhibition) and accumulates a stoichiometric amount of pyruvate. In the second part, the VCP enzymatic reaction is quenched with 30 mM EDTA and 250 μM NADH and stoichiometrically oxidized by 40 U/ml lactic dehydrogenase to reduce accumulated pyruvate. The decrease of NADH concentration was measured at 340 nm using a Tecan Safire 2 reader plate. The assay was performed in 96- or 384-well UV plates in a reaction buffer with 50 mM Hepes, pH 7.5, 0.2 mg/ml BSA, 10 mM MgCl2 and 2 mM DTT. Experimental data were fitted with a cooperative equation obtaining a Ks* of about 60 μM and a Hill coefficient (n) of 2.0 ± 0.1.The HTS campaign was performed against a 1-million-compound library using a miniaturized assay in 1,536-well format and a more sensitive ADP detection system, Transcreener ADP FP. A 20-min preincubation of 10 nM VCP and 10 μM inhibitor was performed, after which 10 μM ATP was added to the reaction, which was allowed to proceed for 90 min before quenching. The average Z′ of the screening was 0.58, and the hit rate using 3× s.d. (38% inhibition) as cutoff was 1.7%. Primary hits with >60% inhibition at 10-μM concentration were pruned using physicochemical and structural filters to leave 7,516 compounds. At the end, reconfirmation was performed in duplicate on 3,988 primary hits, and 500 compounds were selected for a dose-response evaluation using the previously described NADH-modified coupled assay.The potency of the most interesting HTS hits was measured against both wild-type VCP and the C522T mutant. ATP concentrations that yielded the half-maximal velocity (Ks*) for each enzyme, corresponding to 60 μM and 130 μM for the wild type and C522T mutant, respectively, were used in the assay. To explore the dependency of reversible inhibitors from substrate concentration, their potency was evaluated also at saturating ATP concentration (1 mM) and compared to the potency of a standard ATP competitive inhibitor (AMP-PNP).
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References:
1Magnaghi, P., D'Alessio, R., Valsasina, B., Avanzi, N., Rizzi, S., Asa, D., Gasparri, F., Cozzi, L., Cucchi, U., Orrenius, C., Polucci, P., Ballinari, D., Perrera, C., Leone, A., Cervi, G., Casale, E., Xiao, Y., Wong, C., Anderson, D. J., Galvani, A., Donati, D., O'Brien, T., Jackson, P. K. and Isacchi, A. (2013) Covalent and allosteric inhibitors of the ATPase VCP/p97 induce cancer cell death. Nat Chem Biol. 9, 548-556
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