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ACS Medicinal Chemistry Letters logoLink to ACS Medicinal Chemistry Letters
. 2024 Mar 12;15(4):524–532. doi: 10.1021/acsmedchemlett.4c00016

Lead Optimization of Small Molecule ENL YEATS Inhibitors to Enable In Vivo Studies: Discovery of TDI-11055

Mayako Michino †,*, Tanweer A Khan †,*, Michael W Miller †, Yoshiyuki Fukase †, Jeremie Vendome ‡, Carolina Adura §, J Fraser Glickman §, Yiman Liu ∥, Liling Wan ∥, C David Allis ⊥, Andrew W Stamford †, Peter T Meinke †,#, Louis M Renzetti ∇, Stacia Kargman †,∇, Nigel J Liverton †, David J Huggins †,○
PMCID: PMC11017412  PMID: 38628784

Abstract

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Eleven-nineteen leukemia (ENL) is an epigenetic reader protein that drives oncogenic transcriptional programs in acute myeloid leukemia (AML). AML is one of the deadliest hematopoietic malignancies, with an overall 5-year survival rate of 27%. The epigenetic reader activity of ENL is mediated by its YEATS domain that binds to acetyl and crotonyl marks on histone tails and colocalizes with promoters of actively transcribed genes that are essential for leukemia. Prior to the discovery of TDI-11055, existing inhibitors of ENL YEATS showed in vitro potency, but had not shown efficacy in in vivo animal models. During the course of the medicinal chemistry campaign described here, we identified ENL YEATS inhibitor TDI-11055 that has an improved pharmacokinetic profile and is appropriate for in vivo evaluation of the ENL YEATS inhibition mechanism in AML.

Keywords: epigenetics, ENL YEATS inhibitor, leukemia

Eleven-nineteen leukemia (ENL), also known as MLLT1, is an epigenetic reader protein that recognizes acetyl and crotonyl marks on histone tails via the well-conserved YEATS domain. Upon binding to acylation marks, ENL recruits transcriptional complexes to drive target gene activation. ENL has been strongly implicated in cancer. ENL is frequently fused with the mixed lineage leukemia gene (MLL1, also known as KMT2A) as a result of chromosomal translocations, and the resultant MLL-ENL fusion protein is a potent driver of acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL).4 Additionally, the wild-type ENL is required for the maintenance of AML that carries MLL fusions or NPM1 mutations. Mutational disruption of the interaction between the ENL YEATS domain and acylated histones has been shown to reduce the elongation of RNA polymerase II at ENL-target genes, leading to suppression of oncogenic gene expression programs in these AML subsets.5,6 Furthermore, a series of hotspot mutations in the ENL YEATS domain have been found in patients with AML and Wilms tumors.7,8 These mutations increase ENL’s transcriptional activity and drive hyperactivation of key cancer genes, and such a function requires the reader activity of ENL.9,10 Thus, pharmacological inhibition of the ENL YEATS domain reader activity represents a promising therapeutic strategy for AML and potentially other cancers.11,12

Analysis of the crystal structures of the ENL YEATS domain shows that it recognizes histone lysine acetylation and crotonylation with a tunnel-like acetyl-lysine (Kac) pocket formed by three loops L1/L4/L6 and side chains of the aromatic triad residues Phe28/Phe59/Tyr78.5 Several chemical probes for ENL YEATS have been reported in the literature (Figure 1). The peptide-based inhibitor, XL-13m (ENL IC50 = 0.56 μM by competitive photo-cross-linking assay), was developed with an expanded π system replacing the crotonyl group on the Lys side chain that forms π-stacking interaction with the aromatic triad in the Kac pocket.13 The first small molecule chemical probe, SGC-iMLLT (ENL IC50 = 0.26 μM by AlphaScreen assay), an analog optimized from a medium-throughput screening hit, has a benzimidazole-amide scaffold that binds to the Kac pocket, where the amide acts as an acetyl-lysine mimetic in a flipped orientation and forms a π-stacking interaction with the aromatic triad.14,15 Other derivatives with the benzimidazole-amide scaffold were reported from crystallography-based screen and rational design.16,17 Additional chemotypes such as isoxazole-amides and piperazine-ureas were later identified, having comparable or slightly weaker potency than the benzimidazole-amide inhibitors.18,19 More recently, alternative chemotypes with more potent in vitro potency such as amido-triazolopyridines (Cmp 11 ENL IC50 < 0.1 μM by AlphaScreen assay) and amido-imidazopyridines (SR-0813 ENL IC50 = 0.025 μM by HTRF) were identified.20,21 However, the in vitro potency of these compounds did not translate to cellular efficacy in ENL-dependent AML cells or in vivo efficacy in animal models of AML.20,21 While these published compounds convincingly supported the tractability of the ENL YEATS domain for drug discovery, each of them exhibited either suboptimal cellular activity or poor pharmacokinetic properties that limited further use for fully exploring the translational potential of ENL inhibition in cancer models.

Figure 1.

Figure 1

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Chemical probes for ENL YEATS in the literature.

We recently reported that an orally bioavailable ENL YEATS inhibitor, TDI-11055, shows promising in vitro and in vivo efficacy in models of MLL-r leukemia. Here, we describe the medicinal chemistry optimization that led to the identification of TDI-11055, starting from the published SGC inhibitor, SGC-iMLLT.14 At the time of our optimization effort, SGC-iMLLT and its derivatives reported by Moustakim et al.14 were the only small molecule ENL YEATS inhibitor series available. Optimization of ADME properties led to TDI-11055, the first small molecule inhibitor to show efficacy in both AML cells and in vivo animal models.22 TDI-11055 selectively suppressed the in vitro growth of AML cell lines and primary patient samples carrying MLL rearrangements or NPM1 mutations. At the molecular level, TDI-11055 treatment rapidly decreased the chromatin occupancy of ENL and its associated transcriptional complexes, including the Super Elongation Complex and DOT1L, leading to suppression of oncogenic gene expression programs. Furthermore, oral dosing with TDI-11055 showed efficacy in patient-derived xenograft mouse models of MLL-rearranged and NPM1-mutated AML without overt toxicity.

In vitro ENL YEATS inhibitory activity of the selected compounds was evaluated by a TR-FRET assay. Briefly, this is a protein interaction assay to detect compounds that prevent the interaction of ENL YEATS with the acylated histone peptide. The TR-FRET assay was used instead of the AlphaScreen assay commonly used in the literature, to avoid any potential assay interference caused by Ni-metal chelation.23 Our starting compound SGC-iMLLT showed an IC50 of 0.12 μM in the TR-FRET assay, comparable to the potency reported by Moustakim et al. (IC50 = 0.26 μM by AlphaScreen assay).14

We observed that SGC-iMLLT is an MDR1 substrate (MDR1 efflux ratio = 15), indicating susceptibility to efflux from cancer cells that may overexpress MDR1.24 To improve the MDR1 efflux liability and cell permeability, we designed compounds to mask the amide-NH, effectively reducing the HBD count via intramolecular interactions (Figure S1A).25−27 Introducing an ortho fluoro group into two biaryl compounds (3 and 5 vs 4 and 6) showed improved MDR1 efflux ratios while maintaining PAMPA permeability values (Table 1). The ortho fluoro compound 2 also showed a low MDR1 ratio of 0.75.

Table 1. Structure–Activity Relationship of RHS.

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a

Compounds were tested in a minimum of two independent assays and data are reported as mean ± SD. PAMPA unit, nm/sec; MDR1 unit, A → B, nm/sec, ratio (B → A/A → B).

We next explored the SAR of the benzimidazole core scaffold. We speculated that modification of the benzimidazole scaffold could lead to improved potency. Design was guided by FEP+ calculations using the cocrystal structure of SGC-iMLLT (PDB: 6HT1). A validation plot with the results of retrospective FEP+ calculations showed good agreement between the experimental and FEP+ predicted potencies (Figure S2). The mean unsigned error in the retrospective pIC50 predictions is 0.53 or approximately 4-fold error in the IC50 prediction. Prospective FEP+ predictions and the corresponding experimental results are listed in Table 2.

Table 2. Structure–Activity Relationship of Benzimidazole Core Scaffold.

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a

Compounds were tested in a minimum of two independent assays and data are reported as mean ± SD. *IC50 > 100 μM in one replicate. PAMPA unit, nm/sec; MDR1 unit, A → B, nm/sec, ratio (B → A/A → B).

As predicted by FEP+, reversing the amide of SGC-iMLLT was deleterious to binding, resulting in a ∼500-fold decrease in potency (7). This is likely due to the disruption of the hydrogen bonding interactions between the amide and Tyr78/Ser58. However, also as predicted by FEP+, replacing the benzimidazole of SGC-iMLLT with an indole (9) was tolerated, in line with the retained nitrogen atom making the key hydrogen bond with the backbone carbonyl of Ser76. Indeed, many modifications to the solvent exposed portions of the benzimidazole ring were also tolerated and, in some cases, beneficial. For example, replacing the indole of 11 with a 4-azabenzimidazole (10) yields a similar potency. In addition, replacing the benzimidazole of SGC-iMLLT with 5-azaindole (TDI-11055) leads to a small 3-fold increase in affinity. Similarly, replacing the indole of 11 with a 4-azaindole (12) also leads to a 3-fold increase in affinity. A plot of experimental vs predicted pIC50 values is shown in Figure S3. The mean unsigned error in the prospective pIC50 predictions is 0.71 or approximately 5-fold error in the IC50 prediction.

We considered the ability to modify the benzimidazole core and retain or improve potency to be useful in the context of modulating important druglike properties such as lipophilicity. Conversely, the SAR around the LHS pyrrolidine showed less tolerance for changes (Table 3). The basic amine moiety provided by the pyrrolidine is critical, as indicated by the 300-fold or greater loss in potency for the significantly less basic difluoropyrrolidine and aniline analogues (16 and 20). However, the basic azetidine analogue 15 maintains comparable potency to SGC-iMLLT, and a docking model of 15 shows that the charged nitrogen atom of azetidine can form a salt bridge with the Glu75 side chain, similarly to the pyrrolidine nitrogen atom in SGC-iMLLT (Figure 2A). Efforts to replace the pyrrolidine with bridged bicyclic derivatives such as the [3.2.1] and [3.3.1] analogs (18 and 19) were not well-tolerated. However, as predicted by docking, the analog 21, in which the pyrrolidine is connected to the benzimidazole via the C-2 carbon is well tolerated (Figure 2B). Gratifyingly, resolution of the indazole analog of 21 with this LHS C-linked connectivity afforded one enantiomer (23) with an affinity of 0.04 μM in the TR-FRET assay.

Table 3. Structure–Activity Relationship of LHS Pyrrolidine Modification.

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a

Compounds were tested in a minimum of two independent assays and data are reported as mean ± SD. *IC50 > 100 μM in one replicate. **Absolute stereochemistry not determined.

Figure 2.

Figure 2

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Predicted binding mode of 15 (A, slate sticks) and 23 (B, turquoise sticks) in the ENL YEATS domain based on the ENL YEATS structure (PDB: 6HT1). Both compounds can form a salt bridge with the Glu75 side chain, while only 23 showed improved potency.

As stated in previous work, SGC-iMLLT is cell-active and was found to be a suboptimal in vivo tool compound due to moderate cell activity and poor metabolic stability.14 Indeed, we confirmed that the SGC-iMLLT inhibitor displayed poor exposure when dosed orally in the rat (F% = 3; Table 4). Initial profiling had shown that this analogue was an MDR1 substrate (MDR1 efflux ratio = 15), and we reasoned that this may be one contributing factor to the low oral exposure. Also, MDR1 expression can often be upregulated in many types of cancers, which limits therapeutic intervention.24 Early SAR effort to improve the MDR1 efflux liability led to the identification of 4, which incorporated an ortho fluoro group, which may mask the amide-NH to the biaryl RHS. Interestingly, TDI-11055 identified from later SAR exploration was also found not to be an MDR1 substrate. Introducing a new nitrogen atom into the azaindole ring system of TDI-11055 may allow an intramolecular hydrogen bonding interaction with the tautomerized amide, contributing to the improved MDR1 efflux ratio (MDR1 efflux ratio = 1.4; Table 2, Figure S1B). Both 4 and TDI-11055 showed improved oral bioavailability (F% = 49 and 31, respectively) upon oral dosing in rats (Table 4). In addition, biophysical measurement of compound binding by isothermal titration calorimetry (ITC) showed that 4 and TDI-11055 have potent binding affinity to the ENL YEATS domain (Kd = 0.16 and 0.12 μM, respectively; Table 4, Figure S5). Furthermore, efficacy in human leukemia cells assessed by the cell viability assay demonstrated that 4 and TDI-11055 have profound inhibitory effects on cell proliferation in a concentration-dependent manner in the ENL-dependent MLL-r leukemia cell line (MV4;11; 8-day viability IC50 = 0.31 and 0.10 μM, respectively; Table 4).

Table 4. In Vitro ADME and In Vivo PK Properties of 1 (SGC-iMLLT), 5, and TDI-11055.

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Encouraged by the overall profile of TDI-11055, we measured a high-dose oral exposure in mice to determine if this compound would be appropriate for in vivo studies. A dose of 100 mg/kg in mice achieved unbound plasma exposures that exceeded the cell IC50 out to 15 h.22 Based on this pharmacokinetic profile, we chose TDI-11055 as a key tool compound to explore the inhibition of the ENL YEATS domain as a strategy against ENL-dependent AML in cellular and animal models. We recently reported extensive in vitro and in vivo functional and mechanistic studies with TDI-11055 in AML.22

The preparation of 4 is illustrated in Scheme 1. The boronic ester 4a was converted into the pyrazinyl acid 4b via palladium catalyzed coupling with 2-chloropyrazine with concomitant hydrolysis of the ester (Pd(PPh3)2Cl2, Na2CO3, dioxane/water, 90 °C). The acid 4b was then coupled with (S)-2-((2-methylpyrrolidin-1-yl)-1H-benzo[d]imidazo-6-amine to provide 4 (HBTU/pyridine).

Scheme 1. Synthesis of 4.

Scheme 1

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Reagents and conditions: (a) 2-chloropyrazine, Pd(PPh3)2Cl2, Na2CO3, dioxane, water, 90 °C, 16 h; (b) HBTU, pyridine, (S)-2-((2-methylpyrrolidin-1-yl)methyl)-1H-benzo[d]imidazol-6-amine.

In a similar fashion, the boronic ester 4a was coupled with 4-chloropyrimidine to provide the pyrimidinyl ester 6a using standard Pd catalyzed coupling conditions (Pd(PPh3)4, K3PO4, and DMF/water; Scheme 2). The ester in 6a was hydrolyzed to provide the acid 6b with LiOH-H20 in MeOH. The acid 6b was coupled with (S)-2-((2-methylpyrrolidin-1-yl)-1H-benzo[d]imidazo-6-amine to provide 6 (HBTU/pyridine).

Scheme 2. Synthesis of 6.

Scheme 2

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Reagents and conditions: (a) 4-chloropyrimidine-hydrochloride, Pd(PPh3)4, K3PO4, DMF, water, 95 °C, 12 h; (b) LiOH-H2O, water, MeOH, 20 °C 3 h; (c) HBTU, pyridine, (S)-2-((2-methylpyrrolidin-1-yl)methyl)-1H-benzo[d]imidazol-6-amine.

The preparation of the pyrrolo-pyridine analogue 8 (TDI-11055) is illustrated in Scheme 3. The acid 8a was converted to the alcohol 8b by sequential conversion into the methyl ester (TMS-diazomethane/MeOH) followed by reduction (LAH/THF). The Boc protected intermediate 8c was prepared from the alcohol 8b via a three-step sequence (oxidation/reductive amination/Boc protection). Chloro-pyridine 8c was converted into the amino-pyridine 8d using a two-step sequence (Pd-catalyzed coupling with tert-butyl carbamate followed by hydrolysis of the Boc group). The amino-pyridine 8d was coupled to 1-methyl-1H-indazole-5-carboxylic acid with HBTU/pyridine which provided 8 (TDI-11055).

Scheme 3. Synthesis of 8 (TDI-11055).

Scheme 3

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Reagents and conditions: (a) TMSCHN2, DCM, MeOH, 20 °C, 0.5 h; (b) LAH, THF, 0–20 °C 1 h; (c) Dess-Martin, DCM, 20 °C, 2 h; (d) NaBH(OAc)3, DCE, AcOH, (S)-2-methylpyrrolidine, 20 °C, 2 h; (e) Boc2O, DMAP, DCM, 25 °C, 12 h; (f) tert-butyl carbamate, Pd(OAc)2, Xphos, Cs2CO3, dioxane, 100 °C, 12 h; (g) HCl, ethyl acetate, 25 °C, 2 h; (h) HBTU, pyridine, 1-methyl-1H-indazole-5-carboxylic acid.

Scheme 4 illustrates the preparation of the indole analog 9. The aldehyde 9a was protected as the SEM intermediate 9b using standard conditions (NaH, SEMCl, DMF). Reductive amination of 9b with (S)-2-methylpyrrolidine provided 9c. The nitro group in 9c was reduced (Fe, NH4Cl, EtOH/water) to the SEM protected amino-indole 9d. The amino-indole 9d was converted to 9 by sequential amide bond formation followed by SEM deprotection.

Scheme 4. Synthesis of 9.

Scheme 4

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Reagents and conditions: (a) NaH, SEMCl, DMF, 0–20 °C, 1 h; (b) NaBH(OAc)3, DCE, AcOH, (S)-2-methylpyrrolidine, 20 °C, 2 h; (c) Fe, NH4Cl, EtOH, water, 80 °C, 0.5 h; (d) HBTU, pyridine, 1-methyl-1H-indazole-5-carboxylic acid; (e) TBAF, ethylenediamine, THF, 80 °C, 16 h.

The preparation of the imidazo-pyridine analogue 10 is illustrated in Scheme 5. 5-Bromopyridine-2,3-diamine was converted into the PMB protected imidazo-pyridine intermediate 10b via formation of the fused ring system (2-hydroxyacetic acid/mesitylene) followed by PMB protection of the imidazo-NH group. The alcohol in 10b was converted into the (S)-methyl pyrrolidine substituted intermediate 10c by a two-step procedure (oxidation to the aldehyde/reductive amination). Bromo-pyridine 10c was converted into the amino-pyridine 10d using a two-step procedure (Pd coupling with benzophenone imine followed by hydrolysis of the imine). The amine 10d was coupled to 2-fluoro-4-(pyrazin-2-yl)benzoic acid to provide 10 using HATU/TEA in DMF.

Scheme 5. Synthesis of 10.

Scheme 5

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Reagents and conditions: (a) 2-hydroxyacetic acid, mesitylene, 150 °C, 16 h; (b) PMBCl, K2CO3, DMF, 20 °C, 12 h; (c) MnO2, DCM, 15 °C, 12 h; (d) (S)-2-methylpyrrolidine, NaBH(OAc)3, AcOH, DCE, 15 0C, 12 h; (e) benzophenone imine, XPhos Pd G2, NaOtBu, toluene, 115 °C, 2 h; (f) aq. HCl, THF, 15 °C, 2 h; (g) 2-fluoro-4-(pyrazin-2-yl)benzoic acid, HATU, TEA, DMF, 15 °C, 12 h; (h) TFA, 90 °C, 12 h.

The preparation of pyrrolo-pyridine 12 is shown in Scheme 6. The methyl ester 12b was prepared from 2,5-dibromopyridin-3-amine (formation of the acid followed by esterification). The ester in 12b was converted into the aldehyde 12c by two steps (reduction to the alcohol followed by oxidation of the alcohol to the aldehyde). The aldehyde 12c was converted into the (S)-methyl pyrrolidine substituted intermediate 12d using standard reductive amination conditions. After protection of the NH in 12d (SEM group), bromo intermediate 12e was converted into the amino pyridine intermediate 12f using a two-step procedure (Pd coupling with benzophenone imine followed by hydrolysis of the imine group). The amino-pyridine intermediate 12f was converted into 12 via deprotection of the SEM group (HCl, water) followed by coupling with 2-fluoro-4-(pyrazin-2-yl)benzoic acid with HATU/TEA.

Scheme 6. Synthesis of 12.

Scheme 6

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Reagents and conditions: (a) 2-oxopropanoic acid, Pd(OAc)2, TEA, PPh3, DMF, 100 oC, 12 h; (b) TMSCHN2, MeOH, 25 °C, 2 h; (c) LAH, THF, 0–25 °C, 1 h; (d) Dess-Martin, DCM, 25 °C, 12 h; (e) NaBH(OAc)3, DCE, AcOH, (S)-2-methylpyrrolidine, 25 °C, 12 h; (f) NaH, SEMCl, THF, 0 °C, 3 h; (g) diphenylmethanimine, Pd2(dba)3, BINAP, NaOtBu, toluene, 110 °C, MW; (h) aq. HCl, THF, 25 °C, 3 h; (i) 2-fluoro-4-(pyrazin-2-yl)benzoic acid, HATU, TEA, DMF, 25 °C, 12 h.

The preparation of the pyrrolo-pyridazine 13 is shown in Scheme 7. 3,4,6-Trichloropyridazine 13a was converted into the PMB protected alkynylated intermediate 13b by displacement of the 4-chloro substituent with PMB-NH2 followed by Pd catalyzed Sonagashira coupling of 3,3-diethoxyprop-1-yne. The PMB protected alkyne intermediate 13b was cyclized to the pyrrolo-pyridazine (CuI/DMF/130 °C), and the diethoxy acetal was hydrolyzed (TsOH/THF/water) to provide the aldehyde 13c. Reductive amination of 13c with (S)-2-methylpyrrolidine provided 13d. The chloro-pyridazine 13d was converted into the amino-pyridazine 13e using conditions like those previously described (Pd catalyzed coupling of benzophenone imine followed by hydrolysis of the imine). Final deprotection of the PMB group in 13f provided 13 (TFA/anisole).

Scheme 7. Synthesis of 13.

Scheme 7

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Reagents and conditions: (a) PMBNH2, K2CO3, MeCN, 95 °C, 4 h; (b) 3,3-diethoxyprop-1-yne, Pd(PPh3)2Cl2, TEA, CuI, MeCN, 65 °C, 5 h, MW; (c) CuI, DMF, 130 °C, 12h; (d) TsOH, THF, water, 45 0C, 1 h; (e) NaBH(OAc)3, DCE, AcOH, (S)-2-methylpyrrolidine, 25 °C, 12 h; (f) benzophenone imine, BretPhos Pd G3, NaOtBu, THF 100 °C, 5 h; (g) aq. HCl, THF, 25 °C, 0.5 h; (h) 2-fluoro-4-(pyrazin-2-yl)benzoic acid, HATU, TEA, DMF, 15 °C, 12.5 h; (i) TFA, anisole, 130 °C, 6 h.

The C2 carbon linked pyrrolidine analogue 23 was prepared using conditions outlined in Scheme 8. 4-Nitrobenzene-1,2-diamine was coupled to (tert-butoxycarbonyl)-D-proline (EDCI/HOBt/DMF), and the resulting aminoamide was cyclized to 23b (AcOH/90 °C). Deprotection of the Boc group in 23b provided the free amine 23c (HCl/EtOAc). The nitro-pyrrolidine 23c was converted into the N-methyl amino indazole intermediate 23d by sequential reductive amination with formaldehyde and reduction of the nitro group using standard conditions. The amino-indazole 23d was coupled to 1-methyl-1H-indazole-5-carboxylic acid to provide 23 (HATU/TEA/DMF).

Scheme 8. Synthesis of 23.

Scheme 8

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Reagents and conditions: (a) 4-nitrobenzene-1,2-diamine, EDCI, HOBt, DMF, 15 °C, 12 h; (b) AcOH, 90 °C, 5 h; (c) HCl/EtOAc, 15 °C, 0.5 h; (d) formaldehyde, NaBH(OAc)3, DCM, MeOH, 15 °C, 2 h; (e) Pd/C, H2, MeOH, 15 °C, 1 h; (f) 1-methyl-1H-indazole-5-carboxylic acid, HATU, TEA, DMF, 15 °C, 12 h.

The epigenetic reader ENL has been identified as a potential drug target for AML. While inhibitors of the acetyl and crotonyl lysine binding YEATS domain have been described in the literature, none are effective in both AML cells and in vivo animal models. This prevented in vivo target validation of the ENL.

During the course of the medicinal chemistry campaign described here, we identified ADME liabilities in the published tool compound SGC-iMLLT and optimized it to design TDI-11055, the first compound demonstrating in vivo efficacy in murine models of AML.22 In addition, we identified a novel C-linked connectivity of pyrrolidine to the indole/benzimidazole core scaffold. Resulting compounds such as 23 show improved inhibitory activity against ENL YEATS. These tool compounds described here enable in vivo interrogation of ENL YEATS, facilitating the development of therapeutics for AML and exploration of its role in other malignancies.

Acknowledgments

The authors thank Michael Foley for critical advice and guidance at project initiation when the ENL YEATS project entered the TDI early stage portfolio. The research was supported by an NIH Pathway to Independence Award R00CA226399 (to L.W.), a V Foundation Scholar Award (to L.W.), and an American Society of Hematology Scholar Award (to L.W.). The authors gratefully acknowledge the MSKCC supercomputing resources made available for conducting the research reported in this paper (https://www.mskcc.org/research/ski/core-facilities/high-performance-computing-group). The authors thank Hao Zhang for assistance with 13C NMR characterization of compounds. The authors gratefully acknowledge the support to the project generously provided by the Sanders Tri-Institutional Therapeutics Discovery Institute (TDI), a 501(c)(3) organization. TDI receives financial support from Takeda Pharmaceutical Company, TDI’s parent institutes (Memorial Sloan Kettering Cancer Center, The Rockefeller University, and Weill Cornell Medicine) and from a generous contribution from Mr. Lewis Sanders and other philanthropic sources.

Glossary

Abbreviations

ENL

Eleven-nineteen leukemia

AML

acute myeloid leukemia

Kac

acetyl-lysine

ADMET

absorption distribution metabolism excretion toxicity

PK

pharmacokinetic

RHS

right hand side

LHS

left hand side

Supporting Information Available

The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acsmedchemlett.4c00016.

  • Spreadsheet of compound SMILES strings and the associated data (CSV)

  • Docking model of TDI-11055 bound to ENL YEATS (PDB)

  • Docking model of compound 15 bound to ENL YEATS (PDB)

  • Docking model of compound 23 bound to ENL YEATS (PDB)

  • Synthetic materials and methods for 2–23; HPLC traces for 2–7, 9–15, 18–21, and 23 and 24; biology assay methods; ADMET assay methods; rat pharmacokinetic studies; computational methods; Figures S1–S5 (PDF)

Author Present Address

+ Atai Life Sciences, 524 Broadway, New York, NY 10012

Author Present Address

▲ Ferring Research Institute, Inc., 4245 Sorrento Valley Blvd, San Diego, CA 92131

Author Present Address

□ Deerfield Discovery and Development, LLC, 345 Park Ave South, New York, NY 10010

Author Present Address

% Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place – MS 1000, Memphis, TN 38105

Author Contributions

& Authors contributed equally

The authors declare the following competing financial interest(s): T.A.K., M.M., M.W.M., Y.F., A.W.S., P.T.M., S.K., N.J.L., and D.J.H. are current or former employees of the Sanders Tri-Institutional Therapeutics Discovery Institute (TDI) and may benefit from the further development and licensure of molecules described herein.

Author Status

⧫ Deceased Jan 8, 2023

Supplementary Material

ml4c00016_si_001.csv (2.6KB, csv)
ml4c00016_si_002.pdb (275.8KB, pdb)
ml4c00016_si_003.pdb (275.5KB, pdb)
ml4c00016_si_004.pdb (275.5KB, pdb)
ml4c00016_si_005.pdf (1.3MB, pdf)

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

ml4c00016_si_001.csv (2.6KB, csv)
ml4c00016_si_002.pdb (275.8KB, pdb)
ml4c00016_si_003.pdb (275.5KB, pdb)
ml4c00016_si_004.pdb (275.5KB, pdb)
ml4c00016_si_005.pdf (1.3MB, pdf)

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