National Center for Bioinformatics, Quaid-i-Azam University, 45320 Islamabad, Pakistan.
J Chem Inf Model. 2020 Mar 23;60(3):1892-1909. doi: 10.1021/acs.jcim.0c00008. Epub 2020 Feb 7.
Myocyte enhancer factor 2 (MEF2; MEF2A-MEF2D) transcription factors regulate gene expression in a variety of developmental processes by binding to AT-rich DNA motifs via highly conserved N-terminal extensions known as MADS-box and MEF2 domains. Despite the fact that MEF2 proteins exhibit high similarity at their N-terminal regions and share a common consensus DNA binding motif, their functional preferences may vary significantly in the adjacent regions to the DNA binding core segment. The current study delineates the conformational paradigm, clustered recognition, and comparative DNA binding preferences for MEF2A and MEF2B-specific MADS-box/MEF2 domains at the YTA(A/T)4TAR consensus motif. In both MEF2A and MEF2B proteins, α1-helix plays a crucial role through acquiring more flexibility by attaining loop conformation. In comparison to apo-MEF2, an outward disposition of the distal portion of α1-helix and movement of its proximal part to β1 allows synergistic repositioning of the α1-α2 linker, C-terminal region, and MEF2 domain, resulting in the formation of a hydrophobic groove for DNA binding. In both instances, conformational switching of the helical content is the main contributing factor while preserving the overall β-topology to maintain the inside-out conformation of subdivided α1-helix flip. Multivariate statistical analysis reveals that MEF2B obscures less accessible conformational space for DNA binding as compared to the MEF2A-DNA complex. The presence of similar structural requirements and conserved residues including Arg10, Phe21, and Arg24 in accentuating the MEF2-specific DNA recognition mechanism led us to perform structure-based virtual screening for isolating novel inhibitors that are able to target MEF2-DNA binding regions. The top hits (acetamide, benzamide, carboxamide, and enamide) obtained through preliminary assay were scrutinized to binding potential analysis at the MEF2-DNA binding groove, energy values, absorption, distribution, toxicity, and Lipinski's rule of five assessments. Based on these findings, we propose valuable active drug-like molecules for selective applications against MEF2A and MEF2B. The current study may help in uncovering the atomistic-level mechanistic DNA binding patterns of MEF2 proteins, and data may be valuable in devising effective therapeutic strategies for MEF2-associated disorders.
肌细胞增强因子 2（MEF2；MEF2A-MEF2D）转录因子通过结合富含 AT 的 DNA 基序，通过高度保守的 N 端延伸（称为 MADS 盒和 MEF2 结构域）调节各种发育过程中的基因表达。尽管 MEF2 蛋白在其 N 端区域表现出高度相似性，并共享常见的共识 DNA 结合基序，但它们在 DNA 结合核心片段的相邻区域的功能偏好可能有很大差异。本研究描绘了 MEF2A 和 MEF2B 特异性 MADS 盒/MEF2 结构域在 YTA（A/T）4TAR 共识基序上的构象范例、聚类识别和比较 DNA 结合偏好。在 MEF2A 和 MEF2B 蛋白中，α1-螺旋通过获得更多的灵活性来达到环构象，从而发挥关键作用。与 apo-MEF2 相比，α1-螺旋的远端部分向外排列，其近端部分向β1移动，从而协同重新定位α1-α2 接头、C 端区域和 MEF2 结构域，形成 DNA 结合的疏水性凹槽。在这两种情况下，螺旋含量的构象转换是主要贡献因素，同时保持整体β拓扑结构以维持细分α1-螺旋翻转的内外翻转构象。多元统计分析表明，与 MEF2A-DNA 复合物相比，MEF2B 掩盖了较少可及的 DNA 结合构象空间。相似的结构要求和保守残基（包括 Arg10、Phe21 和 Arg24）的存在，强调了 MEF2 特异性 DNA 识别机制，使我们能够进行基于结构的虚拟筛选，以分离能够靶向 MEF2-DNA 结合区域的新型抑制剂。通过初步测定获得的顶级命中（乙酰胺、苯甲酰胺、羧酰胺和烯酰胺）通过结合潜力分析在 MEF2-DNA 结合槽、能量值、吸收、分布、毒性和 Lipinski 的五规则评估进行了详细检查。基于这些发现，我们提出了有价值的活性药物样分子，用于针对 MEF2A 和 MEF2B 的选择性应用。本研究可能有助于揭示 MEF2 蛋白的原子水平机械 DNA 结合模式，并且数据可能有助于设计针对 MEF2 相关疾病的有效治疗策略。
