Identification of novel indole derivatives as highly potent and efficacious LSD1 inhibitors

Highlights

• Structure-based optimization of novel indole derivatives is described by a bioelectronic isosteric strategy.

• The in vivo PK studies indicated compound B35 possessed favorable metabolic stability.

• Compound B35 regulated genes are associated with transcriptional dislocation in PI3K/AKT pathway.

Abstract

Lysine-specific demethylase 1 (LSD1) is a FAD-dependent histone demethylase to catalyze the demethylation of H3K4 and H3K9 and thus is an attractive target for therapeutic cancer. Starting with a high micromolar compound 17i, structure-based optimization of novel indole derivatives is described by a bioelectronic isosteric strategy. Grounded by molecular modeling, medicinal chemistry has efficiently yielded low nanomolar LSD1 inhibitors. One of the compounds, B35, exhibited excellent LSD1 inhibition (IC₅₀ = 0.050 ± 0.005 μM) and anti-proliferation against A549 cells (IC₅₀ = 0.74 ± 0.14 μM). The further PK studies indicated compound B35 possessed favorable metabolic stability, in which the plasma t_1/2 of p.o. and i.v. were 6.27 ± 0.72 h and 8.78 ± 1.31 h, respectively. Additionally, inhibitor B35 shows a strong antitumor effect and good safety in vivo. Meanwhile, compound B35 regulated genes are closely associated with transcriptional dislocation in cancer and PI3K/AKT pathway involving IGFBP3. Taken together, B35 could be a potent LSD1 inhibitor for further drug development.

Introduction

LSD1 belongs to oxidative enzymes and takes flavin adenine dinucleotide (FAD) as a cofactor, specifically removing the methyl groups from histone and non-histone substrates to regulate the gene transcription [[1], [2], [3], [4], [5], [6]]. LSD1 has long been considered a pivotal target for cancer therapy due to its essential roles in gene expression regulation and cancer initiation [[7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17]]. Overexpressed LSD1 can lead to abnormal silencing of tumor suppressor genes and associate with a poor prognosis of tumors. Meanwhile, knockdown or inhibition of LSD1 could reactivate the expression of tumor suppressor genes in cell and animal models [[18], [19], [20], [21], [22], [23], [24], [25], [26], [27], [28], [29], [30], [31]]. Thus, the inhibition of LSD1 is an effective strategy for cancer treatment.

Various scaffold inhibitors against LSD1 have been reported in literature [[32], [33], [34], [35], [36], [37], [38], [39], [40], [41], [42], [43], [44], [45], [46], [47], [48]] with two main types of inhibitors that can be considered: irreversible and reversible inhibitors. Tranylcypromine (compound 1, TCP [42]) (Fig. 1) moderately inhibited LSD1 as a first reported irreversible inhibitor by covalent adducting to cofactor FAD. However, TCP and (TCP)-based irreversible inhibitors are often accompanied by poor selectivity and side effects because of the covalent adducting to cofactor FAD. Meanwhile, reversible inhibitors such as compounds 2–5 ^{8,17,44,45,47,49,50}(Fig. 1) have achieved good potency against the LSD1 enzyme. Of note, compound 6 (CC-90011) [50], as a reversible LSD1 inhibitor, has been used in clinical trials for relapsed/refractory solid tumors and non-Hodgkin's lymphomas in phase 1 trials (clinicaltrials.gov identifier: NCT02875223) and SCLC in phase 1/2 trials (clinicaltrials.gov identifier: NCT03850067).

In previous work, our group had reported a series of benzofuran derivatives to target LSD1, which showed potent anti-cancer activities [49]. Among them, inhibitor 17i (compound 4 in Fig. 1) as the representative LSD1 inhibitor (IC₅₀ = 65 nM) exhibited a great therapeutic effect in vitro. As depicted in Fig. 2, the predicted binding mode of 17i in the active site cavity of the LSD1 was performed by molecular docking.

Interestingly, we find that the space near the benzofuran ring is not occupied (Fig. 2B), which is possible to improve the activity by extending the benzofuran ring to occupy the active site cavity. Meanwhile, the cellular effect of compound 17i is in the micromolar levels, which is also necessary for further development. In this work, we thus used indole moiety to replace benzofuran ring, which is the most constructive scaffold with significant chemical properties and pharmacological behaviors in anti-cancer drug research. Meanwhile, the conformation of the terminal basic fragment is restricted by replacing methylene with amide at the 3-position of indole (Fig. 3). Our structure-based effort improved the cellular effect of LSD1 inhibitors and physicochemical properties and is discussed herein.