`
`Contents lists available at ScienceDirect
`
`Bioorganic & Medicinal Chemistry
`
`journal homepage: www.elsevier.com/locate/bmc
`
`Discovery of DC_H31 as potential mutant IDH1 inhibitor through NADPH-
`based high throughput screening
`Zhe Duana,1, Jingqiu Liub,1, Liping Niuc, Jun Wangb, Mingqian Fenga,⁎
`
`, Hua Chenc,⁎
`
`, Cheng Luob,⁎
`
`a College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
`b State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
`c Key Laboratory of Chemical Biology of Hebei Province, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, China
`
`A R T I C L E I N F O
`
`A B S T R A C T
`
`Keywords:
`IDH1 mutation
`High-throughput screening
`Pan-inhibitor
`2-HG
`Gliomas
`
`IDH1 mutations are early events in the development of IDH-mutant gliomas and leukemias and are associated
`with various regulation of molecular process. Mutations of active site in IDH1 could lead to high levels of 2-HG
`and the suppression of cellular differentiation, while these changes can be reversed by molecule inhibitors target
`mutant IDH1. Here, through in-house developed enzymatic assay-based high throughput screening platform, we
`discovered DC_H31 as a novel IDH1-R132H/C inhibitor, with the IC50 value of 0.41 μmol/L and 2.7 μmol/L
`respectively. In addition, saturable SPR binding assay indicated that DC_H31 bound to IDH1-R132H/C due to
`specific interaction. Further computational docking studies and structure-activity relationship (SAR) suggest that
`DC_H31 could occupy the allosteric pocket between the two monomers of IDH1-R132H homodimer, which
`accounts for its inhibitory ability. And it is possible to conclude that DC_H31 acts via an allosteric mechanism of
`inhibition. At the cellular level, DC_H31 could inhibit cell proliferation, promote cell differentiation and reduce
`the production of 2-HG with a dose-dependent manner in HT1080 cells. Taken together, DC_H31 is a potent
`selective inhibitor of IDH1-R132H/C both in vitro and in vivo, which can promote the development of more
`potent pan-inhibitors against IDH1-R132H/C through further structural decoration and provide a new insight for
`the pharmacological treatment of gliomas.
`
`Isocitrate dehydrogenase 1 (IDH1) is a homodimeric metabolic en-
`zyme that participates in lipid metabolism and glycolytic pathway and
`catalyzes the oxidative decarboxylation of isocitrate to generate a-ke-
`toglutarate (α-KG) and CO2, accompanied with consuming NADP+ to
`produce NADPH.1 Whole-genome sequencing revealed IDH1 mutations
`were frequent in low-grade gliomas (70–80%) and acute myeloid leu-
`kemia (AML) (10–15%).2–4 The most prevalent heterozygous mutated
`residues in IDH1 are located in the enzyme active cavity corresponding
`to amino acid residue 1325 that replaces an active-site arginine residue
`with inactive missense mutation histidine and cystein, accounting to
`92%. These mutations render IDH1-R132H/C a neomorphic activity
`that reduce α-ketoglutarate (α-KG) to the oncometabolite 2-hydro-
`xyglutarate (2-HG) with concomitant reduction of NADPH,6 and finally
`cause reduction of cellular concentration of α-KG and the accumulation
`of the D-2HG.7 α-KG is a substrate of prolyl hydroxylase domain pro-
`teins (PHD) which could lead to hydroxylation and degradation of
`hypoxia inducible factor (HIF). The high level 2-HG may inhibit ten-
`eleven translocation 2 (TET2), PHD and histone demethylases, which
`
`could induce changes in the cell methylome and epigenetic profiles,
`resulting in blockade of cell differentiation and cell proliferation.8,9
`Previous studies also demonstrated that the accumulation of 2-HG
`might be utilized diagnostically in oncology clinics.5,10–15 Therefore,
`due to the pivotal role of IDH1 mutations in tumorigenesis makes IDH1-
`R132H/C becoming a promising novel therapeutic target.16
`IDH1 mutations are therapeutically advantageous for inhibiting
`IDH1-mutant gliomas.17,18 There are several types of drugs targeting
`IDH1 mutations, such as metabolism inhibitors, demethylating agents,
`and vaccines.5,19–23 Small molecule inhibitors targeting mutant IDH1
`would lead to reduction of 2-HG and regulate related metabolic path-
`ways. Among the small molecule inhibitors, Ivossidenib (AG-120) is a
`specific and progressing IDH1-R132H/C inhibitor that restores normal
`cellular process to AML patients and approved by FDA in 2018.19,24
`Nevertheless, there is still urgent need to develop novel pan-inhibitors
`for IDH1-R132H/C for treatment of gliomas.
`In the current study, a new mutation–specific inhibitor, named
`DC_H31, was identified by a high-throughput screening. DC_H31 can
`
`⁎ Corresponding authors.
`E-mail addresses: fengmingqian@mail.hzau.edu.cn (M. Feng), hua-todd@hbu.edu.cn (H. Chen), cluo@simm.ac.cn (C. Luo).
`1 These authors contributed equally.
`
`https://doi.org/10.1016/j.bmc.2019.05.040
`Received 12 April 2019; Received in revised form 24 May 2019; Accepted 27 May 2019
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`Fig. 1. The diagram of NADPH-based high throughput screening assay. A) The flowchart of biochemical assay-based high throughput screening for the discovery of
`DC_H31. B) The Z′ factor determination of established biochemical assays. C) Proportional fluorescence signal at different NADPH concentrations. D) The IC50
`determination of AGI-5198 against IDH1-R132H measured by biochemical assays. (Each point represents the mean ± SD of three replicates).
`
`reduce the production of 2-HG in HT1080 cells. The identification of
`this lead molecule may help us deep understand the mechanism of the
`action and develop better drugs of the class with improved therapeutic
`effects.
`In our study, a new reliable and robust NADPH-based HTS assay
`targeting IDH1-R132H/C was developed to identify mutant-specific
`inhibitor. IDH1-R132H/C catalyze the convert of α-KG to 2-HG medi-
`ated with NADPH consumption with a concomitant decrease in fluor-
`escence at 460 nm, therefore inhibition of IDH1-R132H/C enzyme ac-
`tivity by small molecule was evaluated by a fluorescent assays of
`NADPH depletion. In the assay, the remaining NADPH, which is in-
`versely proportional to IDH1-R132H/C activity, was measured at the
`endpoint of
`the reaction by fluorescent
`reader
`(λex = 355 nm,
`λem = 460 nm) (Fig. 1A), and the fluorescence signal is proportional to
`the NADPH concentration (Fig. 1C). The Z′ factor of the biochemical
`assay was 0.76 and S/B ratio was 7.6 demonstrated the confidence of
`this NADPH fluorescence-based biochemical assay (Fig. 1B). The fea-
`sibility of this HTS method was further verified by testing the inhibitory
`activities of the positive compound AGI-5198,17,18 the IC50 value for the
`compound through this method was 82 nmol/L (Fig. 1D), which was in
`line with previous reports. All these data demonstrate that the assay is
`reliable and robust and can be used for molecular screening target
`mutant IDH1 and wide type (WT) IDH1. Compared to existing mutant
`IDH1-mediated NADPH consumption of a diaphorase/resazurin-based
`detection assay,25 the assay saved diaphorase converts resazurin into
`resorufin steps, needed less time and simplified screening process for
`drug discovery of mutant IDH1.
`A library containing 25,000 compounds with diverse structures was
`screened by this NADPH-based HTS assay using DMSO as a negative
`control and non-enzymatic reaction as a positive control to indicate an
`inhibition. Through primary HTS with a single concentration (10 μmol/
`
`L), 71 compounds which inhibitory activity more than 80% were se-
`lected and confirmed in an IDH1-R132C and WT IDH1 assay, and we
`obtained 6 compounds screened from secondary round screening, as
`shown in Fig. 2A. After that, all of these 6 compounds were identified
`by a selection criteria that inhibition as varies with a serious of con-
`centrations between 50 μmol/L to 0.068 μmol/L (Fig. 2B). Finally,
`DC_H31 was identified as a potential inhibitor with an IC50 value of
`0.41 μmol/L for IDH1-R132H and 2.7 μmol/L for IDH1-R132C, but in-
`hibited WT IDH1 minimally (Fig. 2C and D).
`To further investigating the interaction of compound DC_H31 and
`IDH1-R132H/C, Surface Plasmon Resonance (SPR), an optical tech-
`nique for hit validation,26 was utilized to measure the interactions be-
`tween the newly discovered DC_H31 towards IDH1-R132H/C and WT
`IDH1. The data were fit in both kinetic and equilibrium modes. Com-
`pound DC_H31 could directly bind to IDH1-R132H and IDH1-R132C
`with an equilibrium dissociation constant KD of 3.8 μmol/L and
`0.72 μmol/L (Fig. 3A and B), while the KD value for WT IDH1 was
`noticeably higher, over 50 μmol/L (Fig. 3C). The result is similar to the
`IDH1-R132H/C IC50 and WT IDH1 IC50 value, suggesting that DC_H31
`is a potential selective inhibitor to bind IDH1-R132H/C directly.
`The selective and effective inhibitory activity of DC_H31 against
`IDH1-R132H/C prompted us to disclose the molecular mechanism of
`the inhibitory activity of DC_H31. Molecular docking study was em-
`ployed to reveal the binding mode and structural details of its inter-
`actions with mutant IDH1. The crystal structures of IDH1-R132H (PDB
`ID: 5LGE)27 were selected and a putative binding mode was generated
`by Glide program with XP mode of the maestro. The results suggested
`that DC_H31 occupied the allosteric pocket between the two monomers
`far away from the mutation site with 12.6 Å (Fig. 4A). The binding site
`is also not located at the active site, Tyr139, because of highly polarity
`as defined by the amino acids lining the site.28 The allosteric pocket
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`Fig. 2. The results of high throughput screening and preliminary hit validation. A) Activity of 71 compounds screened from primary HTS in biochemical assays in WT
`IDH1 (x axis) versus that in IDH1-R132C (y axis). The selected 6 compounds are shown in red. B) IC50 value of 6 compounds screened from secondary round
`screening. C) The IC50 determination of DC_H31 against WT IDH1, IDH1-R132H and IDH1-R132C measured by biochemical assays. (Each point represents the
`mean ± SD of three replicates. D) The chemical structure of DC_H31. (For interpretation of the references to colour in this figure legend, the reader is referred to the
`web version of this article.)
`
`lined on three sides by Tyr285, Trp124, Met259, Trp267, and the re-
`maining side was formed by residues in a regulatory segment such as
`Ser280, Gln27729 (Fig. 4B). An assumption was proposed that DC_H31
`inhibits the IDH1-R132H enzyme function through an allosteric me-
`chanism of inhibition.
`We next synthesized a series of derivatives (Scheme 1) and eval-
`uated the structure-activity relationships (SAR) of DC_H31 and its de-
`rivatives based on the results of biochemistry assay to validate the
`scaffold authenticity of DC_H31. DC_H31 formed two hydrogen bond to
`the carbonyl group of Gln277 and hydroxyl group Ser280 respectively.
`The hydroxyl in the scaffold of DC_H31 formed a hydrogen bond to the
`carbonyl group of Gln277, which may clearly explain the different in-
`hibitory activity between DC_H31 and CH-H-16 or CH-H-17 (Table 1).
`Inhibitory activity totally disappeared when the hydroxyl was moved
`from DC_H31. Another hydrogen bond was observed between nitrogen
`atom of morpholine group and Ser280. Obviously, the hydrogen bond is
`vital to the inhibitory activity, which accounts for the huge difference
`in inhibitory activity between CH-H-3, CH-H-4 and DC_H31. However,
`the oxygen atom at the morpholine group had less importance, and the
`activity was no much change when the oxygen atom was replaced by a
`nitrogenous group (CH-H-2). However, the activity gradually decreased
`
`when the nitrogenous group was linked with various lengths of chains
`because of the steric hindrance, such as compounds CH-H-5 to CH-H-
`11.
`
`Besides polar interactions as mentioned above, a highly hydro-
`phobic environment surrounded by the allosteric pocket may contribute
`to stabilize the DC_H31 conformation in the pocket. In addition, it
`should be noticed that the pyridine group of the molecular forms three
`edge-to-face interaction with Trp124, Tyr285, Trp267 in three different
`directions respectively and is stabilized by powerful hydrophobic forces
`around the pocket (Fig. 4C). In addition, any chemical modifications on
`this group could reduce the inhibitory activity. It is clear that the
`pyridine group plays a crucial role to the improvement in inhibitory
`activity, which clarifies the molecular mechanism for better inhibitory
`activity of DC_H31 compared to its analogues (CH-H12, CH-H13, and
`CH-H14).
`When the IDH1-R132H:DC_H31 conformation was overlaid to the
`WT IDH1 structure (PDB: 1 T09),30 we found the α10 regulatory seg-
`ment (seg-2), a partially α-helix structure, in WT IDH1 conformation
`blocked the homologous allosteric site which was bound by DC_H31 in
`IDH1-R132H (Fig. 4D). In the WT IDH1 structures, Arg132 formed an
`ionic interaction with Asn271 of
`the seg-2, whereas the ionic
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`Fig. 3. DC_H31 binds to IDH1-R132H/C but not WT IDH1 by Surface Plasmon Resonance measurements. A) DC_H31 binds to IDH1-R132H with the KD is 3.8 μmol/L.
`B) DC_H31 binds to IDH1-R132C with the KD is 0.72 μmol/L. C) DC_H31 could not observably bind to WT IDH1 under the same detection conditions with IDH1-
`R132H/C.
`
`interaction did not produce because of the mutation of Arg to His in
`IDH1-R132H.6,30 Destabilization of seg-2 due to the lacking of the
`R132:N271 interaction may afford DC_H31 have access to the allosteric
`site of IDH1-R132H achieving mutant selectivity. Taken together, mu-
`tant selectivity for IDH1 is achieved by the intrinsic lability of reg-
`ulatory segment in IDH1-R132H compared to WT IDH1. However, we
`need further confirmation to verify that the long distance between
`H132 to the allosteric pocket is the reason for the pan-inhibitory ac-
`tivity.
`As HT1080 cells produced the high level of 2-HG due to the neo-
`morphic enzyme function of the missense mutation in IDH1, to further
`demonstrate the inhibition of IDH1 mutation in cells by DC_H31, the 2-
`HG assay was carried out with 0.625 μmol/L, 1.25 μmol/L, 2.5 μmol/L,
`
`5 μmol/L DC_H31.6 As shown in the Fig. 5A, 2-HG levels declined to
`half of DMSO control when DC_H31 concentration up to 1.25 μmol/L,
`and measurements of 2-HG production in a culture medium of HT1080
`cells demonstrated dose-dependent inhibition after 48 h of treatment.
`As mentioned above, inhibiting the mutation could affect cells
`proliferation. HT1080 cell line harboring IDH1-R132C mutation and U-
`87 MG cell line, a WT IDH1 cell, were chosen for the cell proliferation
`assay to evaluate the cellular activity of DC_H31. As shown in Fig. 5B
`and C, inhibition of HT1080 cell proliferation was observed in a dose-
`dependent manner after 72 h treatment with a range of concentrations
`of DC_H31. The compound could inhibit HT1080 cells growth with the
`IC50 value of 5 μmol/L while the minimal effect on the proliferation of
`U-87 MG cells was seen with the IC50 value of 48.7 μmol/L. Noticeably,
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`Fig. 4. Putative binding mode between DC_H31 and IDH1-R132H. A) Overview of the allosteric binding pocket between the two monomers. H132 is shown as gray
`sticks. B) Detailed view of the allosteric binding pocket for DC_H31 (green). Hydrogen bonds (yellow) are indicated by yellow dotted line. C) Schematic diagram
`showing predicted interactions between IDH1-R132H and DC_H31. DC_H31 is colored in purple. Hydrophobic interactions are plotted in red arcs. D) Overlay of one
`monomer of the IDH1-R132H (gray) bound to DC_H31 (green) and the WT IDH1 (wheat). Regulatory segment in IDH1-R132H and WT IDH1 is depicted in yellow and
`lavender respectively. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)
`
`Scheme 1. Synthesis of the compounds CH-H-X.
`Conditions and reagents: (a) R1Br, Mg, I2, THF,
`30 °C; (b) 3,5-di-tert-butyl-4-hydroxybenzaldehyde
`or 3,5-di-tert-butylbenzaldehyde, 30 °C, two steps:
`65–70% yields; (c) 1) MsCl, CH2Cl2, rt; 2) R3XH
`(X = N; O; S), DMF, 80–90 °C, two steps: 50–70%
`yields.
`
`HT1080 cells were more sensitive to inhibition by DC_H31 than U-87
`MG cells, at the nearly 10-fold difference between the two cell lines.
`Furthermore, in order to determine whether DC_H31 could induce
`differentiation in HT1080 cells, SRY-box2 (SOX2) and glial fibrillary
`acidic protein (GFAP) which are used to indicate the degree of differ-
`entiation of HT108031 were selected to determine the inhibition of
`DC_H31 against the transcription of IDH1-R132C downstream genes.
`After the treatment with 1 μmol/L DC_H31 or DMSO for 6 days, quan-
`titative fluorescence real-time PCR (qRT-PCR) was used to measure the
`transcription of the two genes in HT1080 cells. As shown in Fig. 5D,
`DC_H31 could inhibit the transcription of SOX2 genes and upregulate
`the transcription of GFAP genes. Meanwhile, western blot assay was
`performed to evaluate the alteration of the protein GFAP. As shown in
`Fig. 5E, treatment with 0.5 μmol/L DC_H31 induced the expression of
`GFAP compared to DMSO control, confirming the inhibitory activity of
`DC_H31 with on-target behavior.
`
`IDH1–R132H/C are highly attractive targets for the treatment of
`gliomas and AML. Although many IDH inhibitors have been dis-
`covered since the first report in 2012, there is still pressing need to
`develop novel pan-inhibitors for IDH1-R132H/C. In this study, we
`identified a small molecular, DC_H31, that could potentially inhibit
`both IDH1-R132H and IDH1-R132C with an IC50 value of 0.41 μmol/
`L and 2.7 μmol/L respectively. At the cellular level, DC_H31 effec-
`tively inhibited the proliferation of HT1080 cells and was capable of
`reducing 2-HG levels in the HT1080 cell line. In addition, the tran-
`scription of mutant IDH1 downstream genes was altered by DC_H31,
`and the protein abundance of GFAP also increased which validated
`inhibitory activity of this compound. Molecular docking studies re-
`vealed the potential binding mechanism of DC_H31 with IDH1-
`R132H and facilitated to discovery better mutant IDH1 inhibitors.
`Overall, these results demonstrate that DC_H31 deserves further
`structure optimization as a pan-inhibitor of IDH1-R132H and IDH1-
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`Table 1
`Structures and biochemical IC50 (μmol/L) data for DC_H31 and its analogues.
`
`Compounds
`
`R1
`
`CH-H-1
`
`CH-H-2
`
`CH-H-3
`
`CH-H-4
`
`CH-H-5
`
`CH-H-6
`
`CH-H-7
`
`CH-H-8
`
`CH-H-9
`
`CH-H-10
`
`CH-H-11
`
`CH-H-12
`
`CH-H-13
`
`CH-H-14
`
`CH-H-15
`
`CH-H-16
`
`R2
`
`OH
`
`OH
`
`OH
`
`OH
`
`OH
`
`OH
`
`OH
`
`OH
`
`OH
`
`OH
`
`OH
`
`OH
`
`OH
`
`OH
`
`H
`
`H
`
`R3
`
`Biochemical IC50(μmol/L)
`
`IDH1-R132H
`
`IDH1-R132C
`
`WT IDH1
`
`0.41
`
`3.0
`
`> 50
`
`> 50
`
`12
`
`> 50
`
`> 50
`
`> 50
`
`> 50
`
`4.76
`
`> 50
`
`> 50
`
`> 50
`
`20
`
`> 50
`
`> 50
`
`2.7
`
`4.9
`
`> 50
`
`> 50
`
`4.8
`
`> 50
`
`9
`
`18
`
`> 50
`
`7
`
`9
`
`> 50
`
`> 50
`
`4.7
`
`> 50
`
`> 50
`
`43.7
`
`∼50
`
`> 50
`
`> 50
`
`6.4
`
`> 50
`
`12.79
`
`31
`
`> 50
`
`3
`
`8.5
`
`> 50
`
`> 50
`
`0.8
`
`> 50
`
`> 50
`
`Note: The IC50 values for IDH1-R132H and IDH1-R132C and WT IDH1 are the mean of three determinations performed as described method.
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`Z. Duan, et al.
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`
`Fig. 5. DC_H31 decreases intracellular 2-HG production and affects cell proliferation and differentiation. A) DC_H31 inhibits intracellular 2-HG production in
`HT1080 cells within 48 h. B) And C) DC_31 inhibits HT1080 cell proliferation but have weak effect on U87-MG. D) qRT-PCR results of Sox2 and GFAP expression in
`HT1080 cells treatment with DC_H31 after 6 days. E) DC_H31 increases expression of GFAP and promotes HT1080 cell differentiation in the presence of DC_H31 for
`6 days. (Error bar are mean ± S.D. for three replicates).
`
`R132C for their potential use in the chemotherapeutics of patients
`with IDH1-mutant gliomas and AML.
`
`Acknowledgements
`
`Funding: This work was funded by Large-scale Protein Preparation
`System at the National Facility for Protein Science in Shanghai (NFPS),
`Zhanjiang Lab, and China for providing technical support and assis-
`tance in data collection and analysis. We gratefully acknowledge fi-
`nancial support from the National Natural Science Foundation of China
`(21472208, 81625022, and 81430084 to C.L.); K.C. Wong Education
`Foundation to C.L., Chinese Academy of Sciences (XDA12020353 and
`XDA12050401)
`and
`China
`Postdoctoral
`Science
`Foundation
`(2017M621571 to L.Y.).
`
`Author contributions
`
`Cheng Luo, Mingqian Feng, Zhe Duan and Jingqiu Liu designed the
`study, Zhe Duan and Jingqiu Liu performed the assays, Hua Chen and
`Liping Niu instructed the chemical synthesis including DC_H31 and the
`derivatives, Jun Wang performed molecular docking analysis, Zhe Duan
`and Jingqiu Liu analyzed data wrote the manuscript with input from all
`of the authors.
`
`Appendix A. Supplementary data
`
`Supplementary data to this article can be found online at https://
`doi.org/10.1016/j.bmc.2019.05.040.
`
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