The relevance of K i calculation for bi-substrate enzymes illustrated by kinetic evaluation of a novel lysine (K) acetyltransferase 8 inhibitor

Abstract

Histone acetyltransferases (HATs) are important mediators of epigenetic post-translational modifications of histones that play important roles in health and disease. A disturbance of these modifications can result in disease states, such as cancer or inflammatory diseases. Inhibitors of HATs (HATi) such as lysine (K) acetyltransferase 8 (KAT8), could be used to study the epigenetic processes in diseases related to these enzymes or to investigate HATs as therapeutic targets. However, the development of HATi is challenged by the difficulties in kinetic characterization of HAT enzymes and their inhibitors to enable calculation of a reproducible inhibitory potency. In this study, a fragment screening approach was used, enabling identification of 4-amino-1-naphthol, which potently inhibited KAT8. The inhibitor was investigated for enzyme inhibition using kinetic and calorimetric binding studies. This allowed for calculation of the K values for both the free enzyme as well as the acetylated intermediate. Importantly, it revealed a striking difference in binding affinity between the acetylated enzyme and the free enzyme, which could not be revealed by the IC value. This shows that kinetic characterization of inhibitors and calculation of K values is crucial for determining the binding constants of HAT inhibitors. We anticipate that more comprehensive characterization of enzyme inhibition, as described here, is needed to advance the field of HAT inhibitors.

The Process and Strategy for Developing Selective Histone Deacetylase 3 Inhibitors

“…During the last decades, epigenetics has been established as a crucial factor in cancer and inflammatory diseases [ 1 , 2 ]. Epigenetics encompasses all inheritable changes in gene expression of eukaryotic cells without changes in the genetic code.…”

Comparison of Constituents and Antioxidant Activity of Above-Ground and Underground Parts of Dryopteris crassirhizoma Nakai Based on HS-SPME-GC-MS and UPLC/Q-TOF-MS

“…4-Amino-1-naphthol is a water-soluble therapeutic agent that possesses vitamin K activity [ 33 ] and can potently inhibit KAT8 (lysine (K) acetyltransferase 8 (KAT8)) [ 34 ]. In addition, 4-amino-1-naphthol is a model mediating compound used to stimulate color removal and power production in microbial fuel cells (MFCs) [ 35 ].…”

First-in-Class Selective Inhibitors of the Lysine Acetyltransferase KAT8

“…Specifically, II also targets KAT3B and III is a KAT5 inhibitor. Another KAT8i is the fragment 4-amino-1-naphtol ( IV , IC 50 = 9.7 μM), 23 which, however, inhibits KAT2B and KAT3B more efficiently. 23 Recently, Zhang and co-workers reported a new series of KAT8i with the most potent compounds DC_M01_6 ( V ) and DC_M01_7 ( VI ) possessing IC 50 values of 7.7 and 6 μM, respectively ( Figure 1 ).…”

“…Another KAT8i is the fragment 4-amino-1-naphtol ( IV , IC 50 = 9.7 μM), 23 which, however, inhibits KAT2B and KAT3B more efficiently. 23 Recently, Zhang and co-workers reported a new series of KAT8i with the most potent compounds DC_M01_6 ( V ) and DC_M01_7 ( VI ) possessing IC 50 values of 7.7 and 6 μM, respectively ( Figure 1 ). 24 Although these molecules could decrease H4K16 acetylation and inhibit the proliferation of HCT116 colon cancer cells, their selectivity over other KAT isoforms was not evaluated.…”