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Allosteric modulators are important regulation elements that bind the allosteric site beyond the active site, leading to the changes in dynamic and/or thermodynamic properties of the protein. Allosteric modulators have been a considerable interest as potential drugs with high selectivity and safety. However, current experimental methods have limitations to identify allosteric sites. Therefore, molecular dynamics simulation based on empirical force field becomes an important complement of experimental methods. Moreover, the precision and efficiency of current force fields need improvement. Deep learning and reweighting methods were used to train allosteric protein-specific precise force field (named APSF). Multiple allosteric proteins were used to evaluate the performance of APSF. The results indicate that APSFcan capture different types of allosteric pockets and sample multiple energy-minimum reference conformations of allosteric proteins. At the same time, the efficiency of conformation sampling for APSFis higher than that for ff14SB. These findings confirm that the newly developed force field APSFcan be effectively used to identify the allosteric pocket that can be further used to screen potential allosteric drugs based on these pockets.

Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) is a multidomain protein that plays a critical role in maintaining DNA methylation patterns through concurrent recognition of hemimethylated DNA and histone marks by various domains, and recruitment of DNA methyltransferase 1 (DNMT1). UHRF1 is overexpressed in various cancers, including breast cancer. The tandem tudor domain (TTD) of UHRF1 specifically and tightly binds to histone H3 di- or trimethylated at lysine 9 (H3K9me2 or H3K9me3, respectively), and this binding is essential for UHRF1 function. We developed an H3K9me3 peptide displacement assay, which was used to screen a library of 44,000 compounds for small molecules that disrupt the UHRF1-H3K9me3 interaction. This screen resulted in the identification of NV01, which bound to UHRF1-TTD with a Kdvalue of 5 μM. The structure of UHRF1-TTD in complex with NV01 confirmed binding to the H3K9me3-binding pocket. Limited structure-based optimization of NV01 led to the discovery of NV03 (Kdof 2.4 μM). These well-characterized small-molecule antagonists of the UHRF1-H3K9me2/3 interaction could be valuable starting chemical matter for developing more potent and cell-active probes toward further characterizing UHRF1 function, with possible applications as anticancer therapeutics.

Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) is a multidomain protein that plays a critical role in maintaining DNA methylation patterns through concurrent recognition of hemimethylated DNA and histone marks by various domains, and recruitment of DNA methyltransferase 1 (DNMT1). UHRF1 is overexpressed in various cancers, including breast cancer. The tandem tudor domain (TTD) of UHRF1 specifically and tightly binds to histone H3 di- or trimethylated at lysine 9 (H3K9me2 or H3K9me3, respectively), and this binding is essential for UHRF1 function. We developed an H3K9me3 peptide displacement assay, which was used to screen a library of 44,000 compounds for small molecules that disrupt the UHRF1-H3K9me3 interaction. This screen resulted in the identification of NV01, which bound to UHRF1-TTD with a Kdvalue of 5 μM. The structure of UHRF1-TTD in complex with NV01 confirmed binding to the H3K9me3-binding pocket. Limited structure-based optimization of NV01 led to the discovery of NV03 (Kdof 2.4 μM). These well-characterized small-molecule antagonists of the UHRF1-H3K9me2/3 interaction could be valuable starting chemical matter for developing more potent and cell-active probes toward further characterizing UHRF1 function, with possible applications as anticancer therapeutics.

Polycomb repressive complex 2 (PRC2) consists of three core subunits, EZH2, EED and SUZ12, and plays pivotal roles in transcriptional regulation. The catalytic subunit EZH2 methylates histone H3 lysine 27 (H3K27), and its activity is further enhanced by the binding of EED to trimethylated H3K27 (H3K27me3). Small-molecule inhibitors that compete with the cofactor S-adenosylmethionine (SAM) have been reported. Here we report the discovery of EED226, a potent and selective PRC2 inhibitor that directly binds to the H3K27me3 binding pocket of EED. EED226 induces a conformational change upon binding EED, leading to loss of PRC2 activity. EED226 shows similar activity to SAM-competitive inhibitors in blocking H3K27 methylation of PRC2 target genes and inducing regression of human lymphoma xenograft tumors. Interestingly, EED226 also effectively inhibits PRC2 containing a mutant EZH2 protein resistant to SAM-competitive inhibitors. Together, we show that EED226 inhibits PRC2 activity via an allosteric mechanism and offers an opportunity for treatment of PRC2-dependent cancers.

Polycomb Repressive Complex 2 (PRC2) plays an important role in transcriptional regulation during animal development and in cell differentiation, and alteration of PRC2 activity has been associated with cancer. On a molecular level, PRC2 catalyzes methylation of histone H3 lysine 27 (H3K27), resulting in mono-, di-, or trimethylated forms of H3K27, of which the trimethylated form H3K27me3 leads to transcriptional repression of polycomb target genes. Previously, we have shown that binding of the low-molecular-weight compound EED226 to the H3K27me3 binding pocket of the regulatory subunit EED can effectively inhibit PRC2 activity in cells and reduce tumor growth in mouse xenograft models. Here, we report the stepwise optimization of the tool compound EED226 toward the potent and selective EED inhibitor MAK683 (compound 22) and its subsequent preclinical characterization. Based on a balanced PK/PD profile, efficacy, and mitigated risk of forming reactive metabolites, MAK683 has been selected for clinical development.

{[2-(dimethylamino)ethyl]cyclopentadienyl}titanium trichloride (Cp^NTiCl3, 1) was activated with methylaluminoxane (MAO) to catalyze polymerizations of ethylene (E), propylene (P), ethylidene norbornene (ENB), vinylcyclohexene (VCH), and 1,4-hexadiene (HD). The dependence of homopolymerization activity (A) of 1/MAO on olefin concentration ([M]ⁿ) is n = 2.0 ± 0.5 for E and n = 1.8 ± 0.2 for P. The value of n is 2.4 ± 0.2 for CpTiCl3/MAO catalysis of ethylene polymerization; this system does not polymerize propylene. 1/MAO catalyzes HD polymerization at one-tenth of AH for 1-hexene, probably because of chelation effects in the HD case. The copolymerization of E and P has reactivity ratios of rE = 6.4 and rP = 0.29 at 20°C, and rErP = 1.9, which suggests 1/MAO may be a multisite catalyst. The copolymerization activity of CpTiCl3/MAO is 50 times smaller than that of Cp^NTiCl3/MAO. Terpolymerization of E/P/ENB has A of 10⁵ g of polymer/(mol of Ti h), incorporates up to 14 mol % (~ 40 wt %) of ENB, and high MW's of 1 to 3 × 10⁵. All of these parameters are surprisingly insensitive to the ENB concentration. The E/P/VCH terpolymerization has comparable A value of (1.3 ± 0.3) × 10⁵ g/(mol of Ti h). The incorporation of VCH in terpolymer increases with increasing [VCH]. Terpolymerization with HD occurs at about one-third of the A of either ENB or VCH; the product HD–EPDM is low in molecular weight and contains less than 4% of HD. These terpolymerization results are compared with those obtained previously for three zirconocene precursors: rac-ethylenebis(1-η⁵-indenyl)dichlorozirconium (6), rac-(dimethylsilylene)bis(1-η⁵-indenyl)dichlorozirconium (7), and ethylenebis(9-η⁵-fluorenyl)dichlorozirconium (8). The last compound is a particularly poor terpolymerization catalyst; it incorporates very little VCH or HD and no ENB at all. 7/MAO is a better catalyst for E/P/VCH terpolymerization, while 6/MAO is superior in E/P/HD terpolymerization. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: 319–328, 1998

Allostery is a fundamental and extensive mechanism of intramolecular signal transmission. Allosteric drugs possess several unique pharmacological advantages over traditional orthosteric drugs, including greater selectivity, better physicochemical properties, and lower off-target toxicity. However, owing to the complexity of allosteric regulation, experimental approaches for the development of allosteric modulators are traditionally serendipitous. Recently, the reversed allosteric communication theory has been proposed, providing a feasible tool for the unbiased detection of allosteric sites. Herein, we review the latest research on the reversed allosteric communication effect using the examples of sirtuin 6, epidermal growth factor receptor, 3-phosphoinositide-dependent protein kinase 1, and Related to A and C kinases (RAC) serine/threonine protein kinase B and recapitulate the methodologies of reversed allosteric communication strategy. The novel reversed allosteric communication strategy greatly expands the horizon of allosteric site identification and allosteric mechanism exploration and is expected to accelerate an end-to-end framework for drug discovery.