Malachite Green Assay for the Discovery of Heat-Shock Protein 90 Inhibitors

Summary

The malachite green assay protocol is a simple and cost-effective method to discover heat shock protein 90 (Hsp90) suppressors, as well as other inhibitor compounds against ATP-dependent enzymes.

Abstract

Heat shock protein 90 (Hsp90) is a promising anticancer target because of its chaperoning effect on multiple oncogenic proteins. The activity of Hsp90 is dependent on its ability to hydrolyze adenosine triphosphate (ATP) to adenosine diphosphate (ADP) and free phosphate. The ATPase activity of Hsp90 is linked to its chaperoning function; ATP binds to the N-terminal domain of the Hsp90, and disrupting its binding was found to be the most successful strategy in suppressing Hsp90 function. The ATPase activity can be measured by a colorimetric malachite green assay, which determines the amount of free phosphate formed by ATP hydrolysis. Here, a procedure for determining the ATPase activity of yeast Hsp90 by using the malachite green phosphate assay kit is described. Further, detailed instructions for the discovery of Hsp90 inhibitors by taking geldanamycin as an authentic inhibitor is provided. Finally, the application of this assay protocol through the high-throughput screening (HTS) of inhibitor molecules against yeast Hsp90 is discussed.

Introduction

Heat shock protein 90 (Hsp90) is a molecular chaperone that maintains the stability of proteins responsible for the development and progression of cancer. In addition, proteins responsible for the development of resistance to antineoplastic agents are also clients of Hsp90¹. Hsp90 is overexpressed ubiquitously in all cancer cell types (>90% of cellular proteins), compared to normal cells where it may constitute less than 2% of total proteins. Moreover, the Hsp90 of cancer cells resides in a complex with co-chaperones, whereas in a normal cell it is present predominantly in a free, un-complexed state^2,3. In recent years, several Hsp90 inhibitors have been demonstrated to possess senolytic effects in in vitro and in vivo studies, where they have significantly improved the life span of mice^4,5,6. All the aforementioned findings substantiate the fact that Hsp90 inhibitors could be effective in multiple cancer types, with fewer adverse effects and reduced chances of developing resistance. The chaperoning function of Hsp90 is accomplished by binding ATP at the N-terminal domain of Hsp90 and hydrolyzing it into ADP and free phosphate⁷. Small molecules that competitively bind to the ATP binding pocket of Hsp90 were found to successfully suppress the chaperoning effect of the protein. To date, this remains the best strategy for Hsp90 inhibition, which is supported by the fact that such inhibitors have reached clinical trials⁸. One of them, Pimitespib, was approved in Japan for the treatment of gastrointestinal stromal tumor (GIST) in June 2022⁹. This is the first Hsp90 inhibitor approved since the druggability of the chaperone was established in 1994¹⁰.

The malachite green assay is a simple, sensitive, fast, and inexpensive procedure for the detection of inorganic phosphate, suitable for automation and high-throughput screening (HTS) of compounds against its desired target¹¹. The assay has been successfully employed for the screening of Hsp90 inhibitors in small lab-scale setups, as well as in a HTS^{12,13,14,15,16,17}. The assay uses a colorimetric method that determines the free inorganic phosphate formed due to the ATPase activity of Hsp90. The basis of this quantification is the formation of a phosphomolybdate complex between free phosphate and molybdenum, which subsequently reacts with malachite green to generate a green color (Figure 1). This rapid color formation is measured on a spectrophotometer, or on a plate reader, between 600-660 nm^18,19.

In the present protocol, the procedure for carrying out a malachite green assay with yeast Hsp90 and subsequent identification of inhibitors against the chaperone is described. The natural product molecule, geldanamycin (GA), with which the druggability of Hsp90 was first established, was taken as an authentic inhibitor¹⁰. HTS has become an integral part of the current drug discovery program, owing to the availability of a large number of molecules for testing. This technique has gained more significance in the past 2 years because of the urgent need for repurposing drugs for treating Covid-19 infection^20,21. Therefore, a detailed outline for the HTS of molecules against yeast Hsp90 protein by adopting the malachite green assay method is presented.

Protocol

1. Lab-scale malachite green assay

1. Preparation of assay buffer
   1. Prepare the assay buffer, as per the composition and preparation presented in Table 1.
2. Preparation of phosphate standards
   1. Use 1 mM phosphate standard, provided in the malachite green assay phosphate assay kit (stored at 4 °C).
   2. Pipette 40 µL of 1 mM phosphate standard in 960 µL of ultra-pure water to obtain 40 µM phosphate solution (premix solution). Add the premix solution with ultra-pure water, as per manufacturer's instructions, to form a serial dilution of phosphate from 0 to 40 µM.
3. Preparation of yeast Hsp90
   1. Use yeast Hsp90 with a glycerol stock concentration of 0.66 mg/mL. Thaw on ice just before use.
   2. Use 8 µL (5.98 µg, 0.80 µM) of yeast Hsp90 for measurable ATPase activity. Check that the optical density difference after the addition of malachite green reagent between the blank and positive control is at least 0.5 and less than 1.0. Here, the absorbance difference between the blank (without Hsp90) and positive control (with Hsp90) was found to be 0.510.
4. Preparation of ATP
   1. Transfer 1 mg of ATP to a vial containing 453.39 µL of ultra-pure water to obtain 4 mM of stock solution. Perform weight calculations based on anhydrous ATP (molecular weight [m.w.] = 551.14). Prepare ATP fresh, as it can spontaneously hydrolyze over time.
   2. Add 4 µL of ATP stock solution to each well to give a final well concentration of 0.2 mM (final total assay well volume of 80 µL). Add ATP as the last component to the reaction, using a multichannel pipette so that all the reactions start simultaneously.
5. Preparation of geldanamycin (GA)
   1. Prepare a 10 mM stock of GA by dissolving 1 mg in 178.37 µL of DMSO (m.w. = 560.64). Using the stock solution, prepare 4 mM, 0.8 mM, 0.16 mM, 0.032 mM, 0.0064 mM, and 0.00128 mM solution in DMSO by serial dilution.
   2. Add 2 µL of these stock solutions to each well to obtain a final well concentration of 0.1 mM, 0.02 mM, 0.004 mM, 0.0008 mM, 0.00016 mM, and 0.000032 mM, respectively.
   3. Prepare the wells as described in Table 2 and Table 3, with the wells containing the blank (buffer + water + DMSO) and negative control (Hsp90 in buffer + water + DMSO). The wells containing GA (Hsp90 in buffer + water + GA) serve as the positive control.
6. Preparation of well plates and order of addition
   1. Prepare 96-well plates with the layout presented in Table 2. For compounds that show absorbance at 620 nm, prepare a separate well for recording the absorbance at this wavelength. Do not prepare a separate well for GA, as GA does not show absorbance at 620 nm for the concentration used in the assay.
   2. Prepare each constituent with the total volume of each constituent, as presented in Table 3.
   3. Set up assay wells by adding ultra-pure water to each well. Following this, add the required amount of assay buffer and a compound solution (for example, GA solution).
   4. Then, add Hsp90 to the appropriate wells, and shake the plates for 2 min on a plate shaker at room temperature.
   5. Add 4 µL of ATP solution using a multi-channel pipette. Wrap the plate in aluminum foil and shake for 2 min on a plate shaker (200 rpm) at room temperature. Incubate the plate at 37 °C for 3 h.
7. Preparation and addition of malachite green reagent
   1. The malachite green reagent consists of reagents A (ammonium molybdate in 3M HCl) and B (malachite green and polyvinyl alcohol). Bring the reagent to room temperature before use. Mix reagents A and B at a 100:1 ratio (1,000 µL:10 µL). Prepare this within 3 h before use, since it is unstable and starts decomposing after 3 h.
   2. After 3 h of step 1.6.5, stop the reaction by adding 20 µL of malachite green reagent, added in the same order as ATP, using a multi-channel pipette.
   3. After a 15 min incubation at room temperature, measure the absorbance of the plate at 620 nm in a plate reader.

2. High-throughput screening of Hsp90 inhibitors by malachite green assay

NOTE: The protocol for high-throughput screening is similar to the lab-scale methodology. The final well volume in each case is 80 µL. However, there is a slight difference in the order of the addition of reagents. In the lab-scale based method, there are five stages of solution addition (34 µL of water, 32 µL of buffer, 2 µL compound in DMSO, 8 µL of Hsp90, and finally 4 µL of ATP solution). In contrast, with HTS there are three stages of addition (40 µL of buffer solution containing yeast Hsp90, 2 µL of DMSO in 18 µL of water containing the compounds, and finally 20 µL of ATP dissolved in water). The minimum amount of solution that can be pipetted accurately in the HTS setup is 20 µL. Hence, a difference in pipetting between lab and HTS scales is observed.

1. Preparation of assay buffer (pH 7.4)
   1. Use the same buffer in HTS as for the lab-scale malachite green assay (Table 1).
2. Preparation of yeast Hsp90
   1. Use protein with a glycerol stock concentration of 0.66 mg/mL. Thaw on ice just before use.
   2. Use 8 µL (5.98 µg, 0.80 µM) of yeast Hsp90 in each well, which provides measurable ATPase activity.
   3. Dilute the protein (8 µL) in buffer (32 µL) for each well. The final total working volume for each well is 40 µL in a total assay volume of 80 µL.
3. Preparation of 0.8 mM ATP
   1. Dissolve 1 mg of ATP in 2,267 µL of distilled water to obtain a 0.8 mM solution. The total working volume for each well is 20 µL in a total assay volume of 80 µL.
4. Preparation of geldanamycin (GA)/test compounds
   1. Prepare a 0.8 mM stock of GA in DMSO, as in step 1.5. Dilute 10 µL of the GA stock with 90 µL of water to give a final concentration of 80 µM.
   2. Use 20 µL of the 80 µM GA solution in appropriate assay wells (final total assay well volume = 80 µL), giving a final well concentration of 20 µM. This serves as a positive control.
   3. For test compounds, prepare solutions in DMSO as per their desired concentration for evaluation.
   4. Prepare 10 µL of DMSO in 90 µL of water for addition to blank (buffer + water + DMSO) and negative control wells (Hsp90 in buffer + water + DMSO). Prepare the test compounds in a similar fashion at a 100 µM final well concentration.
5. Design of assay plates and order of addition
   1. Use four main plates, one compound plate, and four addition plates containing stocks of reagents to set up the assay (Figure 2 and Table 4).
   2. In addition, plate A, add 90 µL of assay buffer in each well; in addition plate B, add 90 µL of buffer with Hsp90 in each well; in addition plates C and D, add 90 µL of ATP and 90 µL of malachite green reagent, respectively, in each well (Table 5 and Table 6).
   3. From addition plate A and plate B, transfer 40 µL of solution from each well to main plate 1 and 2, and 3 and 4, respectively, using an automated multichannel dispensing system. Here, the Biomek^(R) FX^P laboratory automation workstation was used (Figure 2 and Table 6).
   4. From each well of the compound plate, transfer 20 µL of the solution to main plates 1, 2, 3, and 4 (Figure 2). Shake the plates for 1 min in a shaker (200 rpm).
   5. From each well of the addition plate C (ATP), transfer 20 µL of solution to main plates 1, 2, 3, and 4 (Figure 2). Shake the plates for 1 min in a shaker (200 rpm).
   6. Incubate the plates for 3 h at 37 °C.
   7. Prepare the malachite green reagent as per step 1.7. After 3 h, transfer 20 µL of malachite green reagent from addition plate D into the wells of main plates 1 ,2, 3 and 4 (Figure 2).
   8. After a 15 min incubation at room temperature, measure the absorbance of the plate is at 620 nm in a plate reader.

Results

The results of the assay are interpreted in terms of absorbance due to free phosphate ion concentration. The absorbance by free phosphate due to ATP hydrolysis by the yeast Hsp90 at 620 nm is considered as 100% ATPase activity, or zero percentage protein inhibition. The inhibition of protein leads to the cessation of ATP hydrolysis (less free phosphate). which is reflected in terms of decreased absorbance at 620 nm.

Results of lab-scale malachite green assay
The standard...

Discussion

Hsp90 is a significant target for the discovery of novel anticancer drug molecules. Since its druggability was established in 1994¹⁰, 18 molecules have reached clinical trials. At present, seven molecules are in various phases of clinical trials, either alone or in combination²². All such small molecules are N-terminal ATP binding inhibitors. The other means of inhibiting the chaperone (C-terminal inhibitors, middle domain inhibitors) have not proceeded as fast as N-termina...

Materials

Name	Company	Catalog Number	Comments
1M Magnesium chloride solution in water	Sigma-Aldrich	63069-100ml
1M Potassium chloride solution in water	Sigma-Aldrich	60142-100ml
96-well plate	SPL Life Sciences	Not applicable
Adenosine 5′-triphosphate disodium salt hydrate	Sigma-Aldrich	A7699-5G
Biomek FX laboratory automation workstation	Beckman Coulter	Not applicable
Compounds 3-96	Not applicable	Not applicable	Histidine tagged yeast Hsp90 was obtained from Dr. Chrisostomos Prodromou, School of Life Sciences, University of Sussex, United Kingdom, and protein was expressed in KIST Gangneung Institute of Natural Products. Details cannot be disclosed due to patent infringement issues.
Dimethyl sulfoxide	Sigma-Aldrich	D8418
Geldanamycin, 99% (HPLC), powder	AK Scientific, Inc.	V2064
Invitroge UltraPure DNase/RNase-Free Distilled Water	ThermoFisher Scientific	10977015
Malachite Green Phosphate Assay  Assay kit	Sigma-Aldrich	MAK307-1KT
Multi-Detection Microplate Reader Synergy HT	Biotek Instruments, Inc.	Not applicable
Synergy HT multi-plate reader	Biotek Instruments, Inc.	Not applicable
Trizma hydrochloride buffer solution, pH7.4	Sigma-Aldrich	93313-1L
Yeast Hsp90	Not applicable	Not applicable	School of Life Sciences, University of Sussex, United Kingdom and protein was expressed in KIST Gangneung Institute of Natural Products. Primary Accession number: P02829