Discovery of 2-Indole-acylsulfonamide Myeloid Cell Leukemia 1 (Mcl-1) Inhibitors Using Fragment-Based Methods

Abstract

Myeloid cell leukemia-1 (Mcl-1) is a member of the Bcl-2 family of proteins responsible for the regulation of programmed cell death (PCD). Amplification of Mcl-1 is a common genetic aberration in human cancer whose overexpression contributes to the evasion of apoptosis and is one of the major resistance mechanisms for many chemotherapies. Mcl-1 mediates its effects primarily through interactions with pro-apoptotic BH3 containing proteins that achieve high affinity for the target by utilizing four hydrophobic pockets in its binding groove. Here we describe the discovery of Mcl-1 inhibitors using fragment based methods and structure-based design. These novel inhibitors exhibit low nanomolar binding affinities to Mcl-1 and greater than 500-fold selectivity over Bcl-xL. X-ray structures of lead Mcl-1 inhibitors when complexed to Mcl-1 provided detailed information on how these small-molecules bind to the target, and were used extensively to guide compound optimization.

Combination Therapy for Chronic Lymphoid Leukemia

“…It has been well documented that B cell lymphoma 2 protein (BCL-2) plays a major role in cellular apoptosis [4][5][6] and is a druggable target. Several small molecule inhibitors of BCL-2 are in active clinical studies [7,8] (Table 1). A phase 1 study of navitoclax showed activity in 50% of patients with relapsed or refractory CLL, but the drug was associated with dose-limiting thrombocytopenia owing to the inhibition of BCL2-like protein 1 (BCL-xL), a regulator of platelet senescence [9].…”

Peptide‐Directed Binding for the Discovery of Modulators of α‐Helix‐Mediated Protein–Protein Interactions: Proof‐of‐Concept Studies with the Apoptosis Regulator Mcl‐1

“…Additionally,t he Fmoc-propargylglycine moiety proved effective in several of the identified binders (18,20,21,23,and 25), but again was not afeature that was sufficient for binding on its own (Table S2). Concerns over the Fmoc protecting group were considered, but as these compounds are primarily meant as chemical probes or potential leads, further development may discover more effective alternatives.I ndeed, the Fmoc group is somewhat reminiscent of structural features present in Souers A-1210477…”

“…[16d] and Fesiks2 -indole-acylsulfonamides, [20] which are highly potent and selective Mcl-1 binders.I nterestingly,t he most potent small molecules did not result from the combination of the most potent small-molecule peptide hybrids 2 and 9,asmight be expected. Thec ombination of 2 and 9 demonstrated no appreciable ability to inhibit the interaction of Mcl-1 and FITC-Noxa.…”

“…Compounds 18,20,21,and 23 induced an increase in caspase-3 activation in BxPC-3 cells 4h after treatment, as indicated by the cleavage of DEVD-pNa and asubsequent increase in optical density at 405 nm. [26] Compounds 18 (Figure 2A).…”

Peptide‐Directed Binding for the Discovery of Modulators of α‐Helix‐Mediated Protein–Protein Interactions: Proof‐of‐Concept Studies with the Apoptosis Regulator Mcl‐1

“…Concerns over the Fmoc protecting group were considered, but as these compounds are primarily meant as chemical probes or potential leads, further development may discover more effective alternatives. Indeed, the Fmoc group is somewhat reminiscent of structural features present in Souers’ A‐121047716d and Fesik's 2‐indole‐acylsulfonamides,20 which are highly potent and selective Mcl‐1 binders. Interestingly, the most potent small molecules did not result from the combination of the most potent small‐molecule peptide hybrids 2 and 9 , as might be expected.…”