We thank George Zheng for providing H4K12CoA. We thank members of the Gruber Lab for helpful discussions and feedback. We thank support from the NIH/NCI (1K08CA245024), CPRIT (RR200090, RP210041), and the V Foundation (V2022-022).

1. Method 1: Producing and purifying recombinant HAT1/Rbap46 complex
<ol>
	<li>Thawing, recovering, and expanding HEK293f cells
	<ol>
		<li>Thaw 1-10 million HEK293f mammalian cells26 into 30 mL freestyle 293 expression media in a 100 mL flask. Incubate in 8% CO2 at 37 &#176;C while rotating at 60 rpm.</li>
		<li>The next day, count and check cell viability, then adjust rotation speed to 120 rpm. Expand to 300 mL culture in a 1 L flask, maintaining seeding density at ...

Development of a Click-Based Assay for Screening HAT1 Enzyme Activity

<ol>
	<li>Kleff, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+a+gene+encoding+a+yeast+histone+H4+acetyltransferase.">Identification of a gene encoding a yeast histone H4 acetyltransferase.</a> J Biol Chem. 270 (42), 24674-24677 (1995).</li><li>Parthun, M. R., Widom, J., Gottschling, D. 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J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HAT1+coordinates+histone+production+and+acetylation+via+H4+promoter+binding.">HAT1 coordinates histone production and acetylation via H4 promoter binding.</a> Mol Cell. 75 (4), 711-724 e5 (2019).</li><li>Fan, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Overexpressed+histone+acetyltransferase+1+regulates+cancer+immunity+by+increasing+programmed+death-ligand+1+expression+in+pancreatic+cancer.">Overexpressed histone acetyltransferase 1 regulates cancer immunity by increasing programmed death-ligand 1 expression in pancreatic cancer.</a> J Exp Clin Cancer Res. 38 (1), 47 (2019).</li><li>Xia, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MicroRNA-377+exerts+a+potent+suppressive+role+in+osteosarcoma+through+the+involvement+of+the+histone+acetyltransferase+1-mediated+Wnt+axis.">MicroRNA-377 exerts a potent suppressive role in osteosarcoma through the involvement of the histone acetyltransferase 1-mediated Wnt axis.</a> J Cell Physiol. 234 (12), 22787-22798 (2019).</li><li>Yang, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histone+acetyltransferase+1+is+a+succinyltransferase+for+histones+and+non-histones+and+promotes+tumorigenesis.">Histone acetyltransferase 1 is a succinyltransferase for histones and non-histones and promotes tumorigenesis.</a> EMBO Rep. 22 (2), e50967 (2021).</li><li>Xue, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNAi+screening+identifies+HAT1+as+a+potential+drug+target+in+esophageal+squamous+cell+carcinoma.">RNAi screening identifies HAT1 as a potential drug target in esophageal squamous cell carcinoma.</a> Int J Clin Exp Pathol. 7 (7), 3898-3907 (2014).</li><li>Zhang, W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structural+plasticity+of+histones+H3-H4+facilitates+their+allosteric+exchange+between+RbAp48+and+ASF1.">Structural plasticity of histones H3-H4 facilitates their allosteric exchange between RbAp48 and ASF1.</a> Nat Struct Mol Biol. 20 (1), 29-35 (2013).</li><li>Campos, E. I., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+program+for+processing+newly+synthesized+histones+H3.1+and+H4.">The program for processing newly synthesized histones H3.1 and H4.</a> Nat Struct Mol Biol. 17 (11), 1343-1351 (2010).</li><li>Agudelo Garcia, P. 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L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assay+interference+and+off-target+liabilities+of+reported+histone+acetyltransferase+inhibitors.">Assay interference and off-target liabilities of reported histone acetyltransferase inhibitors.</a> Nat Commun. 8 (1), 1527 (2017).</li><li>Baell, J. B., Miao, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histone+acetyltransferase+inhibitors:+where+art+thou.">Histone acetyltransferase inhibitors: where art thou.</a> Future Med Chem. 8 (13), 1525-1528 (2016).</li><li>Lasko, L. 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B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Inhibitors+of+histone+acetyltransferases+KAT6A/B+induce+senescence+and+arrest+tumour+growth.">Inhibitors of histone acetyltransferases KAT6A/B induce senescence and arrest tumour growth.</a> Nature. 560 (7717), 253-257 (2018).</li><li>Falk, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+efficient+high-throughput+screening+method+for+MYST+family+acetyltransferases,+a+new+class+of+epigenetic+drug+targets.">An efficient high-throughput screening method for MYST family acetyltransferases, a new class of epigenetic drug targets.</a> J Biomol Screen. 16 (10), 1196-1205 (2011).</li><li>He, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chemical+biology+approaches+for+investigating+the+functions+of+lysine+acetyltransferases.">Chemical biology approaches for investigating the functions of lysine acetyltransferases.</a> Angew Chem Int Ed Engl. 57 (5), 1162-1184 (2018).</li><li>Lipchik, A. 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D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Acetyl-click+screening+platform+identifies+small-molecule+inhibitors+of+histone+acetyltransferase+1+(HAT1).">Acetyl-click screening platform identifies small-molecule inhibitors of histone acetyltransferase 1 (HAT1).</a> J Med Chem. 66 (8), 5774-5801 (2023).</li><li>Ngo, L., Brown, T., Zheng, Y. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Bisubstrate+inhibitors+to+target+histone+acetyltransferase+1+(HAT1).">Bisubstrate inhibitors to target histone acetyltransferase 1 (HAT1).</a> Chem Biol Drug Des. 93 (5), 865-873 (2019).</li><li>Parker, C. G., Pratt, M. 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In the past decade, click chemistry became prominent20, enabling the precise design of interacting chemical structures. Within this context, various bioorthogonal covalent connections21 have emerged as promising options for forming complexes in their natural environment. Click chemistry employs pairs of functional groups that exhibit rapid and selective reactions, commonly known as &#34;click reactions.&#34; These reactions occur efficiently in environmentally friendly, gen...

Among the numerous eukaryotic acetyltransferases, HAT1 was the initial histone acetyltransferase to be isolated1,2,3. Subsequent investigations have firmly established its pivotal role in chromatin replication, particularly in the synthesis of new nucleosomes during S-phase4. Our research endeavors led to the recognition that HAT1 is highly stimulated by epidermal growth factor (EGF) treatment in mammary cells5. Furthermore, it has come to light that HAT1 is required for rapid cell proliferation and tumor formation in vivo6,7,8,9. Data indicate that HAT1 is critical in coordinating anabolic and epigenetic processes for cell division, driving tumor growth.
HAT1 di-acetylates the amino-terminal tail of histone H4 on lysines 5 and 12 in complex with the chaperone protein Rbap46, which binds the histone and presents the amino-terminus to HAT1. Histone tetramers or disomes10, together with HAT1/Rbap46 and other histone chaperones11, are then imported to the nucleus. Histones are then released to be deposited at the replication fork, or other sites to support gene activation or repression. The function of the HAT1 di-acetylation mark on histone H4 is not fully understood. It is likely quickly removed within a span of 15-30 min by the action of histone deacetylases12,13,14,15 after H4 is inserted into chromatin. Thus, the HAT1 di-acetylation mark is not propagated in chromatin and may not serve a true epigenetic role, although a role in the recruitment of chromatin-modifying enzymes to nascent chromatin has been postulated12. Also, HAT1 does not directly acetylate chromatin; its activity is restricted to soluble histones.
The development of small-molecule histone acetyltransferase inhibitors has been hampered by nonspecific and low-throughput assays, often resulting in the generation of biologically reactive compounds16,17.&#160;The gold-standard assay to measure acetyltransferase activities requires the use of 3H-acetyl-coA, which limits throughput and requires radiation. Nonetheless, recently, specific and highly potent small molecule acetyltransferase inhibitors targeting CBP/p30018 and KAT6A/B19,20 have been described and confirmed through the use of 3H-acetyl-CoA. Moving forward, improved assays to achieve better throughput and avoid laboratory hazards are being devised.
Recent advances in acetylation monitoring21 have used click chemistry to enable enzymatic reaction monitoring. There are a variety of click-enabled precursors that are accessible by simple synthetic routes or available for purchase that can be incorporated into enzyme reactions. These reactions are typically carried out in recombinant systems, although cell-based assays are also feasible22. The advantage of click-enabled co-factors and substrates is that screening can directly measure enzyme activity without the need for coupled read-out systems that are often perturbed by screening compounds and require additional handling steps. This allows for inhibitor treatments only during the enzymatic step, whereas all downstream functionalization and detection steps are carried out after extensive washing to remove compounds, thus limiting the potential for assay interference to occur. These advantages make the design of click-enabled assays preferable to coupled assays that commonly rely on the detection of free coenzyme A.
One important consideration is the acceptance of click-enabled co-factors into the enzyme active site. Existing click-enabled co-factors may not be fully compatible with the active site optimized for the native co-factor. Structural information and modeling can be used to design amino acid substitutions to enlarge the active site to incorporate altered substrates23. This may enable screening with improved enzyme kinetics and lower substrate and enzyme levels. The drawback of this approach is that altered catalytic pockets may not identify inhibitors that interact strongly with the native enzyme. Ultimately, a combination of approaches is required to identify and validate potential enzyme inhibitors.
Here, we describe a method developed to purify and assay HAT1 enzyme activity using the click co-factor 4-pentynoyl-CoA24. This assay (Figure 1) uses the native enzyme sequence in complex with its required partner protein Rbap46, which has been shown to boost enzyme activity. Purification of the enzyme from human cells allows for enzyme activation in cellulo, which may preserve stimulating post-translational modifications important for full enzyme activity. Design and optimization of recombinant enzyme assays for high-throughput chemical screens have successfully been used to identify and characterize HAT1 small molecule inhibitors.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>4P CoA</td>
			<td>Cayman Chemical</td>
			<td>10547</td>
			<td>Click chemistry co-factor</td>
		</tr>
		<tr>
			<td>Amplex Red</td>
			<td>Fisher Sci</td>
			<td>A12222</td>
			<td>Fluorescence substrate</td>
		</tr>
		<tr>
			<td>Biotin-PEG-Azide</td>
			<td>Alfa Aesar</td>
			<td>J64996MC</td>
			<td>Click chemistry</td>
		</tr>
		<tr>
			<td>Copper Sulfate</td>
			<td>Sigma-aldrich</td>
			<td>&#160;7758-98-7</td>
			<td>Click chemistry</td>
		</tr>
		<tr>
			<td>DMSO</td>
			<td>Fisher Scientific</td>
			<td>&#160;67-68-5</td>
			<td>diluent</td>
		</tr>
		<tr>
			<td>DTT</td>
			<td>Acros Organics</td>
			<td>03-12-3483</td>
			<td>reducting agent</td>
		</tr>
		<tr>
			<td>Forskolin</td>
			<td>VWR</td>
			<td>102987-310</td>
			<td>Protein expression</td>
		</tr>
		<tr>
			<td>Freestyle 293 Expression Medium</td>
			<td>Thermo Fisher</td>
			<td>12338018</td>
			<td>Media</td>
		</tr>
		<tr>
			<td>Freestyle 293-F cells</td>
			<td>Thermo Fisher</td>
			<td>R790-07</td>
			<td>Protein expression</td>
		</tr>
		<tr>
			<td>H4-peptide/1-23-GGK-biotin</td>
			<td>Anaspec</td>
			<td>AS65097</td>
			<td>peptide substrate</td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Sigma-aldrich</td>
			<td>&#160;7365-45-9</td>
			<td>EB buffer</td>
		</tr>
		<tr>
			<td>Hydrogen peroxide 30% solution</td>
			<td>Sigma-aldrich</td>
			<td>&#160;Z00183-99-0</td>
			<td>initiator</td>
		</tr>
		<tr>
			<td>M2 FLAG antibody slurry</td>
			<td>Millipore-Sigma</td>
			<td>A2220</td>
			<td>Protein purification</td>
		</tr>
		<tr>
			<td>Macrosep 10K Filter (Pall Lab)</td>
			<td>VWR</td>
			<td>89131-980</td>
			<td>Protein purification</td>
		</tr>
		<tr>
			<td>Neutravidin Plate</td>
			<td>Thermo Sci</td>
			<td>15127</td>
			<td>BSA-pre-blocked</td>
		</tr>
		<tr>
			<td>NP40 (IGEPAL)</td>
			<td>MP Biomedical</td>
			<td>198596</td>
			<td>20x buffer</td>
		</tr>
		<tr>
			<td>pHEK-293 plasmid</td>
			<td>Takara Bio</td>
			<td>3390</td>
			<td>Protein expression</td>
		</tr>
		<tr>
			<td>Phosphate Buffered Saline 10x</td>
			<td>Alfa Aesar</td>
			<td>&#160;Z00082-33-6</td>
			<td>wash buffer</td>
		</tr>
		<tr>
			<td>Pra peptide</td>
			<td>Genscript</td>
			<td>Custom synthesis</td>
			<td>biotinylated</td>
		</tr>
		<tr>
			<td>Sodium Ascorbate</td>
			<td>Sigma-aldrich</td>
			<td>&#160;134-03-2</td>
			<td>Click chemistry</td>
		</tr>
		<tr>
			<td>Sodium chloride</td>
			<td>Sigma-aldrich</td>
			<td>&#160;7647-14-5</td>
			<td>EB buffer</td>
		</tr>
		<tr>
			<td>Sodium phosphate</td>
			<td>VWR International</td>
			<td>7558-80-7</td>
			<td>buffer</td>
		</tr>
		<tr>
			<td>Streptavidin</td>
			<td>EMD Millipore</td>
			<td>189730</td>
			<td>competitor</td>
		</tr>
		<tr>
			<td>Streptavidin-HRP</td>
			<td>Cell Signaling</td>
			<td>3999S</td>
			<td>enzyme</td>
		</tr>
		<tr>
			<td>THPTA ligand</td>
			<td>Fisher Sci</td>
			<td>1010-500</td>
			<td>Click chemistry</td>
		</tr>
		<tr>
			<td>Tris base</td>
			<td>Sigma-aldrich</td>
			<td>&#160;77-86-1</td>
			<td>20x buffer</td>
		</tr>
		<tr>
			<td>Triton-X 100</td>
			<td>VWR International</td>
			<td>&#160;9002-93-1</td>
			<td>EB buffer</td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>Sigma-aldrich</td>
			<td>&#160;9005-64-5</td>
			<td>Wash buffer</td>
		</tr>
		<tr>
			<td>Urea</td>
			<td>Sigma-Aldrich</td>
			<td>57-13-6</td>
			<td>quencher</td>
		</tr>
	</tbody>
</table>

an acetyl-click chemistry assay to measure histone acetyltransferase 1 acetylation

HAT1, also known as Histone acetyltransferase 1, plays a crucial role in chromatin synthesis by stabilizing and acetylating nascent H4 before nucleosome assembly. It is required for tumor growth in various systems, making it a potential target for cancer treatment. To facilitate the identification of compounds that can inhibit HAT1 enzymatic activity, we have devised an acetyl-click assay for rapid screening. In this simple assay, we employ recombinant HAT1/Rbap46, which is purified from activated human cells. The method utilizes the acetyl-CoA analog 4-pentynoyl-CoA (4P) in a click-chemistry approach. This involves the enzymatic transfer of an alkyne handle through a HAT1-dependent acylation reaction to a biotinylated H4 N-terminal peptide. The captured peptide is then immobilized on neutravidin plates, followed by click-chemistry functionalization with biotin-azide. Subsequently, streptavidin-peroxidase recruitment is employed to oxidize amplex red, resulting in a quantitative fluorescent output. By introducing chemical inhibitors during the acylation reaction, we can quantify enzymatic inhibition based on a reduction of the fluorescence signal. Importantly, this reaction is scalable, allowing for high throughput screening of potential inhibitors for HAT1 enzymatic activity.

Author Spotlight: Developing Acetyl-Click Assay for HAT1 Inhibitor Screening

An Acetyl-Click Chemistry Assay to Measure Histone Acetyltransferase 1 Acetylation

Our developed acetyl-click assay serves as a tool to assess HAT1 acetyl transferase activity, which is key in isolating H4 histones before nucleosome incorporation. We aim to use this method for high throughput screening of small molecule inhibitors against the HAT1 enzyme. This method measures enzymatic activity directly on the peptide substrate.This offers advantages compared to other enzymatic assays by avoiding biologic variability and antibody related costs. This is also high throughput and can be adapted to use with other acetyl transferases. We have recently published a small molecule HAT1 inhibitor based on this assay that has activity in cells and animals.We continue to use this assay to screen additional chemical libraries and perform structure activity relationships. We are advancing methods to track histone production, folding, chaperoning, and chromatin integration. This highlights the need for improved chemical tools to explore biological mechanisms and stimulate drug discovery.Our goal is to demonstrate that targeting histone production can have therapeutic benefit for diseases such as cancer.

Standard curves in duplicate (16 wells) should be included on every plate to ensure proper assay performance. Standard curve data should be set up in table form, with a range of 100% to 0% according to the ratio of Pra-containing peptide to native H4 peptide in solution (Table 1). Amplex red signal will be the highest in 100% pra/0% native H4 peptide wells, and lowest in 0% pra/100% native H4 peptide wells. After fluorescence has been detected and wells are averaged, the resulting standards graph should ...

Watch this Scientific Journal Video about Author Spotlight: Developing Acetyl-Click Assay for HAT1 Inhibitor Screening at JoVE.com

Quick and accurate chemical assays to screen for specific inhibitors are an important tool in the drug development arsenal. Here, we present a scalable acetyl-click chemistry assay to measure the inhibition of HAT1 acetylation activity.

HAT1, also known as Histone acetyltransferase 1, plays a crucial role in chromatin synthesis by stabilizing and acetylating nascent H4 before nucleosome ...

an-acetyl-click-chemistry-assay-to-measure-histone-acetyltransferase