Discovery of potent BET bromodomain 1 stereoselective inhibitors using DNA-encoded chemical library selections

Abstract

Significance BET bromodomain inhibition is therapeutic in multiple diseases; however, pan-BET inhibitors have induced significant myelosuppression and gastrointestinal toxicity, perhaps due to inhibition of both tandem bromodomains (BD) of all BET family members. However, selective inhibition of just the first BD (BD1) phenocopies pan-BET inhibitor activity in preclinical models of cancer, other diseases, and, for BRDT, in the testes for a contraceptive effect. Here, we leveraged our multibillion-molecule collection of DNA-encoded chemical libraries (DECLs) to identify BET BD1-selective inhibitors of specific chirality with high potency, stability, and good cellular activity. Our findings highlight the robustness and efficiency of the DECL platform to identify specific, potent protein binders that have promise as potential anticancer and anti-inflammatory agents and as male contraceptives.

Discovery of Highly Potent and BMPR2-Selective Kinase Inhibitors Using DNA-Encoded Chemical Library Screening

“…DECL selection was performed as previously described. − Briefly, 53 different DECLs (total of 4.17 billion molecules) were combined and incubated with 0.2 μM of BMPR2-His kinase domain in 150 μL of a selection buffer (25 mM Tris–HCl pH 7.5, 150 mM NaCl, 10 mM MgCl2,1 mM CHAPS, 1 mM TCEP, 10 mM imidazole, and 0.1 mg/mL Sheared Salmon Sperm DNA). The same library pool without protein was incubated under the same conditions as the NTC to assess background binding of DECL molecules to the affinity resin.…”

“…To address the bias of count data caused by factors such as sample size and library diversity, we developed an in-house normalized z -score to quantify the enrichment of n-synthons. , A higher z -score indicates a more significant enrichment in the selection. The normalized z -score is calculated on the basis of modeling the selection data as binomial distribution. , The DNA sequencing process is considered as a random sampling process, and the z -score indicates the probability of observing k times out of n independent samples. The normalized z -score is calculated as follows: z n = p 0 − p normali p normali ( 1 − p i ) where p 0 is observed populations of n-synthons, whereas p i represents the expected populations of n-synthons.…”

“…The discovery of kinase inhibitors has relied on high-throughput screening and other strategies to identify hit compounds as starting points. Compound optimization is then achieved using concerted medicinal chemistry to generate more potent and selective lead-like compounds. − This pathway can be tremendously time-consuming and is greatly facilitated by structure. Recent studies have also used DNA-encoded chemistry technology (DEC-Tec) as a strategy to find kinase-selective leads. − To uncover kinase inhibitors with specificity for BMPR2, we used DEC-Tec to screen our multibillion compound library collection of small molecules using the kinase domain of BMPR2.…”

Recent progress and structural analyses of domain‐selective BET inhibitors

“…While this manuscript was in review, the reverse of this selection experiment was also performed by the same group to identify BD1-selective molecule CDD-787 with over 500-fold selectivity (see Table 3 below). 107 The binding pose of CDD-1102 in a crystal structure with BRDT-BD1 shows unique features of molecular recognition. Whereas traditional K ac mimics directly interact with the carboxamide nitrogen of a conserved asparagine residue and through a conserved water molecule to a tyrosine residue deeper in the binding pocket (Asn351 and Try308 in BRDT), CDD-1102 does not directly interact with the carboxamide of Asn351 and displaces the conserved water (Figure 27B).…”

Incorporation of viridicatin alkaloid-like scaffolds into DNA-encoded chemical libraries

“…After tagged barcode amplification and sequencing, the optimal binder can be thus identified in the selection of DELs. 20–25 Generally, the encoded libraries are constructed via iterative steps of combinatory synthesis and enzymatic encoding ligation. 26–30 Numerous reaction toolkits, which must be DNA-compatible, have been thereby developed and employed to construct encoded libraries, and the building blocks (BBs) for library construction should be conveniently accessible or commercially available to expand the chemical diversities to more complicated molecular architectures beyond encoding early-stage peptide-like libraries.…”