Vaccinia H1-related (VHR) protein tyrosine phosphatase dephosphorylates and thereby inactivates extracellular signal-regulated kinases Erk1/2 and c-Jun N-terminal kinases Jnk1/2. These mitogen-activated protein (MAP) kinases mediate major signaling pathways triggered by extracellular growth factor, stress, or cytokines and regulate cellular processes such as differentiation, proliferation and apoptosis. Unlike many MAP kinase phosphatases (MKPs), VHR expression is not induced in response to activation of MAP kinases, but is instead regulated during cell cycle progression. The loss of VHR causes cell cycle arrest in HeLa carcinoma cells, suggesting that VHR inhibition may be a useful approach to halt the growth of cancer cells without detrimental effects on normal cells. Here we report the development of multidentate small-molecule inhibitors of VHR that inhibit its enzymatic activity at nanomolar concentrations and are selective for VHR over HePTP and MKP-1. This novel small molecular probe, ML113 (CID-6161281) appears to interact with both the phosphate-binding pocket and several distinct hydrophobic regions within VHR's active site. As a result, it will serve as a useful tool in probing these interactions and elucidating the molecular mechanism underlying the selectivity against this phosphatase, in addition to providing greater understanding of the functional consequences for cancer biology.
Assigned Assay Grant #: 1 R03 MH084230-01A1
Screening Center Name & PI: Burnham Center for Chemical Genomics & Dr John C Reed
Chemistry Center Name & PI: Burnham Center for Chemical Genomics & Dr John C Reed
Assay Submitter & Institution: Lutz Tautz & Burnham Institute for Medical Research
PubChem Summary Bioassay Identifier (AID): AID-1661
Probe Structure & Characteristics
(Cmpd internal # is MLS-0425632)
Recommendations for the scientific use of this probe
Loss of VHR phosphatase causes cell cycle arrest in HeLa carcinoma cells, suggesting that VHR inhibition may be a useful approach to halt the growth of cancer cells. VHR is also upregulated in several cervix cancer cell lines as well as in carcinomas of the uterine cervix. Here we report the development of multidentate small-molecule inhibitors of VHR that inhibit its enzymatic activity at nanomolar concentrations and are selective for VHR over HePTP and MKP-1.
This novel chemical probe appears to interact with both the phosphate-binding pocket and several distinct hydrophobic regions within VHR’s active site, so it will serve as a useful tool in probing these interactions and elucidating the molecular mechanism of selectivity against this phosphatase and the functional consequences for cancer biology.
The probe decreased the proliferation of cervix cancer cells at low micromolar concentrations, while growth of primary normal keratinocytes was not affected. Thus this probe may also be a starting point to develop drugs for the treatment of cervical cancer.
1. Scientific Rationale for Project
The overall goal is to develop selective and efficient VHR inhibitors for basic research on signal transduction processes and MAP kinase regulation. For the future, this work could also create proof-of concept evidence that VHR is a good drug target for the treatment of cervical cancer. Some of these inhibitors may turn out to be suitable for further development towards clinical use.
Background and Significance
The Vaccinia H1-related (VHR) protein tyrosine phosphatase is a relatively small member of the subclass of dual-specificity phosphatases (1) with only 185 amino acids (mw 21 kDa) and with no apparent targeting domain or docking site.) (2) Compared to the phospho-tyrosine (pTyr)- specific classical PTPs, the crystal structure of VHR revealed a much shallower active site, which allows VHR to act on both pTyr and phospho-threonine (pThr) in its substrates. (3) VHR dephosphorylates and thereby inactivates extracellular signal-regulated kinases Erk1/2 and c-Jun N-terminal kinases Jnk1/2, but not p38. (4–6) These mitogen-activated protein kinases (MAP kinases) mediate major signaling pathways triggered by extracellular growth factor, stress, or cytokines (7) and regulate cellular processes such as differentiation, proliferation and apoptosis. (8,9) Unlike many MKPs, VHR expression is not induced in response to activation of MAP kinases (10) but is instead regulated during cell cycle progression. (11) The loss of VHR causes cell cycle arrest in HeLa carcinoma cells, suggesting that VHR inhibition may be a useful approach to halt the growth of cancer cells without the detrimental effects on normal cells. The assay provider recently reported that VHR is upregulated in several cervical cancer cell lines as well as in squamous intraepithelial lesions and squamous cell carcinomas of the uterine cervix. (12)
2. Project Description
a. Original goal for probe characteristics
The ideal probe would be a new scaffold of improved potency (< 2–3 µM) over current probes in the literature and improved selectivity towards other phosphatases (at least 2-fold over either MKP-1 or HePTP). However, as there are very few potent phosphatase inhibitors and even fewer selective ones, any improvement in either potency or selectivity would be useful. Additionally activity in a cell based assay for direct substrates is a desired characteristic; however, if none of the scaffolds obtained by catalog or by medicinal chemistry efforts have cell activity, the probes will still be useful as in vitro biochemical tools.
In the original CPDP, several compounds are disclosed as prior art, but none are more than potent than ~ 4 µM, reported as selective for VHR1 nor cell active without cellular toxicity and are reiterated below from H. Park et al. “Discovery of VHR Phosphatase Inhibitors with Micromolar Activity based on Structure-Based Virtual Screening” (2008) J Med Chem 3:877 – 880 (the authors do not specify the stereochemistry as E or Z for these olefins. However, they do mention that the vendor is Interbioscreen).
There was no cell activity reported for compounds 1 – 6 in Figure 1, Table 1 (but they may have not been tested in cell assays). Compounds 1 and 2 were purchased and provided to the assay provider for cell activity testing and reference.
Additional VHR inhibitors (Table 2, Figure 2) were reported by Zhi et al. “Identification of a Potent Inhibitor of Human Dual-Specific Phosphatase, VHR, from Computer-Aided and NMR-Based Screening to Cellular Effects” (2007) ChemBioChem 8:2092–2099 GATPT is a stannous (tin containing compound and toxic) of no chemical interest or tractability. Has some reported cell activity, however it has been shown to be toxic.
The following publications refer to these existing probes with PMIDs: 7556642, 11563920, 11755399, 17933004, and 18236492.
b. Information for each Assay Implemented and Screening Run
i. PubChem Bioassay Name(s), AID(s), Assay-Type (Primary, DR, Counterscreen, Secondary)
ii. Assay Rationale & Description
The Vaccinia H1-related (VHR) PTP is a dual-specific Erk and Jnk phosphatase. This primary screen (AID-1992) is based on a biochemical assay that employs a colorimetric readout based on the enzyme’s ability to liberate phosphate from para-nitrophenyl phosphate (pNPP) and the reaction or the released phosphate with Biomol Green reagent. (13) Following initial screening the hits are confirmed for activity using the same assay but from re-ordered stock solutions in duplicate single concentrations (AID-1992), and then to determine the potency from full dose response curves (AID-2004).
- Recombinant VHR was provided by Prof. Lutz Tautz (Burnham Institute for Medical Research, San Diego, CA)
- Assay buffer: 0.1 M Bis-Tris pH 6.0 with 1 mM dithiothreitol (DTT)
- 4 mM pNPP
- BIOMOL Green 2:1 addition to quench a 70 uL reaction volume
Each reaction contained 180 nM VHR, 4 mM pNPP, and 0.02 mg/mL compound in 0.1 M Bis-Tris pH 6.0 reaction buffer with 1 mM dithiothreitol (DTT) present. The final volume amounted to 70 μL and contained 1.4% DMSO. The reaction was initiated by addition of pNPP after a preincubation of the enzyme with compounds for 10 min at room temperature. After 15 min, the reaction was quenched by addition of 140 μL BIOMOL GREEN reagent, and the pNPP hydrolysis was determined by measuring the absorbance of the complexed free phosphate at 620 nm. The nonenzymatic hydrolysis of the substrate was corrected by measuring the negative control without addition of enzyme. Other controls included a positive control (no inhibitor added), a background control (no substrate added), and a control with 200 µM of the general PTP inhibitor sodium orthovanadate. To quantitate the inhibitory efficacy of the library compounds, we determined the ratio of inhibition in comparison to the positive control. Every compound with >60% inhibition was cherry-picked and rescreened to confirm it as a hit (AID-1992) and confirmed for initial potency (AID-2004).
Rationale for confirmatory, counter and selectivity assays
VHR SAR assay
A higher sensitivity fluorogenic assay was developed and performed to study the structure-activity relationship on analogs of the confirmed VHR hits reported in AID-2004. This VHR biochemical assay (AID-2074) employs a fluorescent readout based on the enzyme’s ability to catalyze the hydrolysis of 6,8-difluoro-4-methylumbelliferyl phosphate (DiFMUP) in the presence of an inhibitor.
MAP kinase phosphatase 1 (MKP-1) is, like VHR, a dual-specific phosphatase and structurally closely related to VHR. MKP-1 also shares a physiological substrate with VHR, namely the extracellular signal-regulated kinases Erk1/2. Therefore, MKP-1 was chosen to assess the selectivity of the VHR1 inhibitors reported in AID-2004. This biochemical assay for MKP-1 (AID-2083) employs the same fluorescent readout as the VHR SAR assay.
Selectivity Assay (HePTP)
In contrast, the hematopoietic tyrosine phosphatase (HePTP) is a classical pTyr-specific phosphatase. HePTP shares a physiological substrate with VHR, namely the extracellular signal-regulated kinases Erk1/2, and therefore was chosen to assess the selectivity of the VHR1 inhibitors reported in AID-2004. This biochemical assay for HePTP (AID-2082) also employs the same fluorescent readout as the VHR SAR assay. The commonality of the assay format and readout ensure comparability of potency values in these three assays.
General assay protocol
The PTP-catalyzed hydrolysis of 6,8-difluoro-4-methylumbelliferyl phosphate (DiFMUP) in the presence of compound was assayed at 30°C in a 60 uL 96-well format reaction system in 150 mM Bis-Tris, pH 6.0, assay buffer having an ionic strength of 150 mM (adjusted with NaCl) and containing 1 mM DTT and 5%DMSO. At various concentrations of the compound, the initial rate at fixed DiFMUP concentration (equal to the corresponding Km value for each PTP) was determined using a FLx800 microplate reader (Bio-Tek Instruments, Inc.), an excitation wavelength of 360 nm, and measuring the emission of the fluorescent reaction product 6,8-difluoro-7-hydroxy-4-methylcoumarin (DiFMU) at 460 nm. The nonenzymatic hydrolysis of the substrate was corrected by measuring the control without addition of enzyme. The IC50 value was determined by plotting the relative activity versus inhibitor concentration and fitting to eq 1 using the software GraphPad Prism (GraphPad Software, Inc.).
In this case, Vi is the reaction velocity when the inhibitor concentration is [I], V0 is the reaction velocity with no inhibitor, and IC50=Ki + Ki[S]/Km.
iii. Summary of Results
We have completed the primary screen of 291,018 compounds from the MLSMR library (AID-1654) using a colorimetric assay that measures the enzyme’s ability to liberate phosphate from para-nitrophenyl phosphate (PNPP) and detection of the released phosphate with Biomol Green reagent. However, at this juncture no VHR compounds of <2–3 µM potency with selectivity against other phosphatases (e.g. HePTP) were found. This probe report describes the results of a parallel screen of the 49,840 drug-like molecules of the DIVERSet library from ChemBridge, Inc. (San Diego, CA), at the concentration of 0.02 mg/mL in a 96-well format using an in vitro colorimetric phosphatase assay, in collaboration with the assay provider. The average Z′ for this assay was 0.85, the signal to background ratio was 3.8, the signal to noise ratio was 46.6 and the signal window was 34.7. We found that 221 compounds inhibited VHR’s enzymatic activity to >60% (average of n=2) compared to a no-inhibitor control. For further evaluation, a total of 56 compounds were picked that inhibited VHR>90% (average of n=2). Michaelis-Menten kinetic studies revealed 21 hits that inhibited the enzyme with Ki values <20 µM (Table 5). Clustering the 21 compounds by a Tanimoto distance (15) of 0.5 resulted in 12 different clusters and singletons, respectively, indicating a quite diverse chemical space covered by these molecules. The most active hit, 2-((Z)-4-oxo-5-((E)-3-phenylallylidene)-2-thioxothiazolidin-3-yl)ethane-sulfonic acid, SID-17460170 (1), inhibited VHR with a Ki value of 0.81 µM. In a counter screen against the protein tyrosine phosphatase, HePTP, only 1 and 1,4-dimethoxyanthracene-9,10-dione, SID-17438068 (8), and (1E,4E)-1-[5-(3,4-dichlorophenyl)furan-2-yl]-5-(furan-2-yl)penta-1,4-dien-3-one, SID-17461020 (18) were found to be selective for VHR (Figure 3).
c. Probe Optimization
i. Description of SAR & chemistry strategy (including structure and data) that led to the probe
In Silico Docking
To study the molecular basis for inhibition of VHR, we first used in silico docking to dock SID-17460170 (1) and SID-17438068 (8) into the active site of the VHR crystal structure (PDB code1J4X, ref 16). Compound SID-17438068 (8) failed to dock into the catalytic pocket, further supporting an inhibition mechanism other than competitive. Because quinones like SID-17438068 (8) are known to deactivate PTPs by oxidizing the catalytic cysteine residue, (7) so we discarded SID-17438068 (8) from further investigation. As for compound SID-17460170 (1), the docking suggested that the sulfonic acid moiety functions as a phosphate mimic and binds into the catalytic pocket, forming a network of hydrogen bond interactions with the phosphate binding loop, also called P-loop (Figure 2B). In support of this, similar compounds lacking the sulfonic acid moiety did not inhibit VHR. Furthermore, the docking suggested that the oxo-thioxothiazolidine ring interacts with the rim of the catalytic pocket, whereas the diene linker and the phenyl ring make van der Waals interactions with a hydrophobic region, mainly formed by Leu25 and Tyr128 (Figure 2B, above).
SAR Analysis and Analogs of Lead Compound 1
By further analyzing the lipophilic potential of VHR’s active site surface area, we found a total of three distinct hydrophobic regions surrounding the catalytic pocket (Figure 2B). Compared to active site properties of solved PTP structures and homology models, (17) this feature seems to be rather unique to VHR and, therefore, could be exploited for designing selective inhibitors. The exposed hydrophobic patches are formed by Leu25/Tyr128 and Leu16/Tyr23, which make up large portions of the substrate binding site, (10) as well as by Phe68/Met69, which is part of a loop opposite of the catalytic pocket (Figure 2B). In an attempt to find analogs of 1 that could target more than one of these hydrophobic regions, we kept the oxo-thioxothiazolidinyl-ethanesulfonic acid moiety as hydrophilic pharmacophore, and subjected it to a substructure search among commercially available compounds. The pharmacophore model and limited R-group search is summarized below:
Six structures were identified that fulfilled the requirement of having additional multiple hydrophobic entities to interact with multiple hydrophobic regions in VHR’s active site. All compounds contained a 1-phenyl-substituted pyrazole ring, which at its 3-position linked to another, more variable entity (see Table 6). We obtained all six analogs and subjected them to direct measurements of VHR inhibition. Indeed, compounds CID-6161281, -6274486, -5932584, -5998084, and -6166563 (SA1-5) showed excellent IC50 values of 18, 71, 74, 78, and 268 nM, respectively (Table 6). An aromatic group in position ‘R’, such as the benzoxy group in compounds CID-6161281, -6274486, -5932584, and -5998084 (SA1-4), seemed to be very well accommodated by the protein, whereas sterically more demanding structures, such as the piperidinesulfonyl group in CID-6166563 (SA5) were less favorable. On the other hand, groups such as methyl in CID-6001181 (SA6) seemed to be too small to provide additional binding energy through van der Waals interactions. Interestingly, compounds CID-6161281, -6274486, -5932584, and -5998084 (SA1-4) only differ in their substituents at the benzoxy group. Chlorine in the para position was most favorable CID-6161281 (SA1), whereas substituents in the ortho-position, such as chlorine CID-6274486 (SA2) or fluorine CID-5932584 (SA3), had no effect on inhibitory activity against VHR in vitro. Testing the five best inhibitors CID-6161281, -6274486, -5932584, -5998084, and -6166563 (SA1-5) against a panel of related PTPs demonstrated that they were at least 1 order of magnitude less potent for MKP-1 and HePTP (Table 6). MKP-1 and HePTP share the same physiological substrate with VHR, namely, the MAP kinase Erk, and MKP-1 is structurally closely related to VHR.
a. Chemical name of probe compound
IUPAC: 2-[(5Z)-5-[[3-[4-[(4-chlorophenyl)methoxy]phenyl]-1-phenylpyrazol-4-yl]methylidene]-4-oxo-2-sulfanylidene-1,3-thiazolidin-3-yl]ethanesulfonic acid [ML113]
b. Probe chemical structure including stereochemistry
c. Structural verification information of probe SID
Probe SID number is SID-85256223 Purity: >95% (HPLC-MS)
d. PubChem CID (corresponding to the SID)
PubChem CID is 6161281 (corresponding to SID-85256223)
e. Availability from a vendor
This probe molecule is available from Princeton BioMolecular Research, Inc. (Monmouth Jct, NJ) with a catalog number of OSSK_022127 (www.princetonbio.com)
f. MLS#'s of probe molecule and five related samples that were submitted to the SMR collection
g. Mode of action for biological activity of probe
The resulting lead compound SID-17460170 (1) competitively inhibited VHR with a Ki value of 0.81 µM and exhibited a promising degree of selectivity for VHR among other PTPs. In silico docking of SID-17460170 (1) into the active site of VHR and SAR analysis suggested a binding mode, in which the sulfonic acid moiety of SID-17460170 (1) binds through a network of hydrogen bond interactions into the phosphate binding pocket, whereas the thiazolidine heterocycle interacts with the rim of the pocket and the phenyl-allyl moiety makes van der Waals interactions with side chains of hydrophobic amino acids that flank the active site. Besides highly improved potency against VHR with IC50 values as low as 18 nM, these multidentate inhibitors were at least 1 order of magnitude less potent for any other PTP tested, including HePTP and MKP-1, which share the same physiological substrate with VHR. This result provides a good example for a general applicable concept, in which targeting unique surface features outside of the catalytic pocket can generate selective small-molecule inhibitors for individual members of the PTP family. (18)
The assay provider, Dr. Tautz found that VHR inhibitors are able to pass cell membrane barriers and target VHR in cultured cells. (18) In particular, he tested the compounds in cervical cancer cells, which were shown earlier to express higher levels of endogenous VHR compared to noncancerous cells of the cervix. Indeed, incubation of the cancer cell line HeLa and CaSki with the inhibitors at 20 µM induced a very significant inhibition of cell proliferation after an incubation period as short as 24 h.
It is interesting to note that CID-5932584 (SA3) was more effective in inhibiting proliferation than CID-6161281 (SA1), although its IC50 value is four times higher in vitro. CID-5932584 (SA3) also exhibited greater antiproliferative effects than CID-6274486 (SA2) and CID-5998084 (SA4), both of which share similar IC50 values with CID-5932584 (SA3) in vitro.
These results suggest a beneficial role for the fluorine substituent (which is only present in CID-5932584 (SA3), maybe by facilitating better membrane permeability. The latter could be a limiting factor for these compounds, considering the substantially higher concentration that is needed to see clear effects in cells vs. inhibition of recombinant protein. Nonetheless, the fact that these inhibitors are not toxic to cells with low levels of endogenous VHR, such as primary normal keratinocytes, these compounds may well be a starting point for development of drugs for the treatment of cervical cancer and perhaps other cancers. Indeed, our results provide first evidence that pharmacological inhibition of VHR could be beneficial in treating such diseases. However, additional studies will be necessary to get better insights into the role of VHR phosphatase in cell cycle regulation and cancer and to test the activity of these compounds in vivo using mouse models.
Figure 4Effects of VHR inhibitors on proliferation and survival of cervix cancer cells
h. Detailed synthetic pathway for making probe
Compound is obtained commercially, but BCCG did prepare a synthetic route.
i. Summary of probe properties (solubility, absorbance/fluorescence, reactivity, toxicity, etc.)
This probe has demonstrated low micromolar potency for VHR and selectivity against HePTP and MKP-1. In PubChem this compounds has been tested in only the SAR assays associated with the VHR project.
While the probe compound CID6161281 [ML113] (MLS-0425632) contains a sulfonic acid that is expected to be fully negatively charged, however, it is also a very hydrophobic molecule. Consistent with these characteristics, it exhibited low solubility and permeability at all pHs tested (Table 8). It exhibits high plasma protein binding (both human and mouse). However, it has good stability in both human and mouse plasma. But, it has some instability in the presence of both human and mouse microsomes (determined by the exploratory pharmacology group). The probe compound has a LD50 >50µM towards Fa2N-4 immortalized human hepatocytes.
j. Probe properties
a. Comparative data on (1) probe, (2) similar compound structures (establishing SAR) and (3) prior probes
b. Comparative data showing probe specificity for target
Already summarized above in Table 6
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Lutz Tautz, Tomas Mustelin, Shuangding Wu, Sofie Vossius, Souad Rahmouni, Stefan Vasile, Eduard Sergienko, Derek Stonich, Hongbin Yuan, Ying Su, Russell Dahl, Yalda Mostofi, and Thomas DY Chung.
Received: October 31, 2009; Last Update: October 4, 2010.
National Center for Biotechnology Information (US), Bethesda (MD)
Tautz L, Mustelin T, Wu S, et al. Small-Molecule Inhibitors of Vaccinia-H1-Related Phosphatase VHR. 2009 Oct 31 [Updated 2010 Oct 4]. In: Probe Reports from the NIH Molecular Libraries Program [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-.