Design of the First‐in‐Class,Highly Potent Irreversible Inhibitor Targeting the Menin‐MLL Protein–Protein Interaction

The structure‐based design of M‐525 as the first‐in‐class, highly potent, irreversible small‐molecule inhibitor of the menin‐MLL interaction is presented. M‐525 targets cellular menin protein at sub‐nanomolar concentrations and achieves low nanomolar potencies in cell growth inhibition and in the suppression of MLL‐regulated gene expression in MLL leukemia cells. M‐525 demonstrates high cellular specificity over non‐MLL leukemia cells and is more than 30 times more potent than its corresponding reversible inhibitors. Mass spectrometric analysis and co‐crystal structure of M‐525 in complex with menin firmly establish its mode of action. A single administration of M‐525 effectively suppresses MLL‐regulated gene expression in tumor tissue. An efficient procedure was developed to synthesize M‐525. This study demonstrates that irreversible inhibition of menin may be a promising therapeutic strategy for MLL leukemia.     

A Chemical Inhibitor of the Skp2/p300 Interaction that Promotes p53‐Mediated Apoptosis

Skp2 is thought to have two critical roles in tumorigenesis. As part of the SCF^Skp2 ubiquitin ligase, Skp2 drives the cell cycle by mediating the degradation of cell cycle proteins. Besides the proteolytic activity, Skp2 also blocks p53‐mediated apoptosis by outcompeting p53 for binding p300. Herein, we exploit the Skp2/p300 interaction as a new target for Skp2 inhibition. An affinity‐based high‐throughput screen of a combinatorial cyclic peptoid library identified an inhibitor that binds to Skp2 and interferes with the Skp2/p300 interaction. We show that antagonism of the Skp2/p300 interaction by the inhibitor leads to p300‐mediated p53 acetylation, resulting in p53‐mediated apoptosis in cancer cells, without affecting Skp2 proteolytic activity. Our results suggest that inhibition of the Skp2/p300 interaction has a great potential as a new anticancer strategy, and our Skp2 inhibitor can be developed as a chemical probe to delineate Skp2 non‐proteolytic function in tumorigenesis.     

Charge density distribution and electrostatic moments of N‐(4‐chloro‐3‐ trifluromethyl‐phenyl)‐2‐ethoxy‐benzamide molecule at the active site of p300 enzyme: A quantum chemical and theoretical charge density study

A Charge density analysis of CTB molecule in gas phase (Form I ) and the same present at the active site (Form II ) of p300 enzyme were performed for the wave functions obtained from the Density functional method (B3LYP) with the basis set 6‐311G**. This study has been carried out to understand the nature of conformational modification, charge redistribution and the change of electrostatic moments of the CTB molecule when present at the active site of p300. The difference of charge density distribution between both forms of CTB molecule explicitly indicates the effect of intermolecular interaction on CTB molecule in the active site. The dipole moment of CTB in the gas phase (9.6 D) has been significantly decreased (4.27 D) when it present at the active site of p300; this large variation is attributed to the charge redistribution in CTB, due to the intermolecular interaction between the CTB and the receptor p300 molecule. The electrostatic potential maps differentiate the difference of electrostatic potential between the two forms. A large electronegative region is found at the vicinity of oxygen and fluorine atoms. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

CBP/P300溴结构域联芳基类抑制剂三维定量构效关系研究

CREB结合蛋白(CBP)和与其高度同源的P300蛋白是组蛋白乙酰化酶的两个亚型,两者通过它们的溴结构域(bromodomain,BRD)与染色质结合,目前,CBP/P300已经成为人类在肿瘤靶点领域中的研究热点。本研究基于CBP/P300溴结构域联芳基类抑制剂建立三维定量构效关系,采用比较分子力场分析法(Co MFA)和比较分子相似性指数分析法(Co MSIA)分别建立35个已知活性抑制剂的3D-QSAR模型,以确定CBP/P300溴结构域联芳基类抑制剂分子结构与生物活性之间的定量关系。Co MFA和Co MSIA模型活性数据p IC50的预测值与实验值基本一致,说明这两个模型具有较高的预测能力和统计学意义。根据Co MFA和Co MSIA模型所提供的立体场、静电场、疏水场、氢键给体场、氢键供体场等信息提出了改善此类抑制剂活性的药物设计思路,为指导设计具有更高活性的新分子和预测更加有效的CBP/P300溴结构域抑制剂提供理论依据。     

Solution NMR Structure of a Ligand/Hybrid‐2‐G‐Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding

Telomeric G‐quadruplexes have recently emerged as drug targets in cancer research. Herein, we present the first NMR structure of a telomeric DNA G‐quadruplex that adopts the biologically relevant hybrid‐2 conformation in a ligand‐bound state. We solved the complex with a metalorganic gold(III) ligand that stabilizes G‐quadruplexes. Analysis of the free and bound structures reveals structural changes in the capping region of the G‐quadruplex. The ligand is sandwiched between one terminal G‐tetrad and a flanking nucleotide. This complex structure involves a major structural rearrangement compared to the free G‐quadruplex structure as observed for other G‐quadruplexes in different conformations, invalidating simple docking approaches to ligand–G‐quadruplex structure determination.     

A PDE6δ‐KRas Inhibitor Chemotype with up to Seven H‐Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2

Small‐molecule inhibition of the interaction between the KRas oncoprotein and the chaperone PDE6δ impairs KRas spatial organization and signaling in cells. However, despite potent binding in vitro (K _D<10 nm ), interference with Ras signaling and growth inhibition require 5–20 μm compound concentrations. We demonstrate that these findings can be explained by fast release of high‐affinity inhibitors from PDE6δ by the release factor Arl2. This limitation is overcome by novel highly selective inhibitors that bind to PDE6δ with up to 7 hydrogen bonds, resulting in picomolar affinity. Their release by Arl2 is greatly decreased, and representative compounds selectively inhibit growth of KRas mutated and ‐dependent cells with the highest activity recorded yet. Our findings indicate that very potent inhibitors of the KRas‐PDE6δ interaction may impair the growth of tumors driven by oncogenic KRas.     

Analysis of pair interaction in a bipolar mesogen 4‐(4‐hydroxylbutyloxy)‐4′‐cyano‐biphenyl: A comparative study based on semiempirical and DFT methods

Structure of 4‐(4‐hydroxylbutyloxy)‐4′‐cyano‐biphenyl (H4CBP) molecule has been optimized using density functional B3LYP with 6‐31G (d) basis set taking crystallographic geometry as input. Using the optimized geometry, electronic structure of the H4CBP molecule has been evaluated on the basis of semiempirical methods and DFT calculations. Intermolecular interaction energy between a pair of H4CBP molecules has been evaluated by using Rayleigh–Schrodinger perturbation theory modified with multicentered multipole expansion method for the electrostatic part while dispersion and repulsion terms have been calculated using Kitaigorodskii formula. The results obtained through semiempirical and DFT calculations have been compared for various interacting conditions, viz.: (a) stacking, (b) in‐plane, and (c) terminal interactions. A comparative analysis of the results has been carried out with a view to examine suitability of different methods to study molecular aggregations in moderately large organic systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

General π‐Electron‐Assisted Strategy for Ir,Pt, Ru,Pd, Fe,Ni Single‐Atom Electrocatalysts with Bifunctional Active Sites for Highly Efficient Water Splitting

Both the hydrogen evolution reaction (HER) and the oxygen evolution reaction (OER) are crucial to water splitting, but require alternative active sites. Now, a general π‐electron‐assisted strategy to anchor single‐atom sites (M=Ir, Pt, Ru, Pd, Fe, Ni) on a heterogeneous support is reported. The M atoms can simultaneously anchor on two distinct domains of the hybrid support, four‐fold N/C atoms (M@NC), and centers of Co octahedra (M@Co), which are expected to serve as bifunctional electrocatalysts towards the HER and the OER. The Ir catalyst exhibits the best water‐splitting performance, showing a low applied potential of 1.603 V to achieve 10 mA cm^?2 in 1.0 m KOH solution with cycling over 5 h. DFT calculations indicate that the Ir@Co (Ir) sites can accelerate the OER, while the Ir@NC₃ sites are responsible for the enhanced HER, clarifying the unprecedented performance of this bifunctional catalyst towards full water splitting.