Mechanism of Cardiac Troponin C Calcium Sensitivity Modulation by Small Molecules Illuminated by Umbrella Sampling Simulations
Mechanism of Cardiac Troponin C Calcium Sensitivity Modulation by Small Molecules Illuminated by Umbrella Sampling Simulations
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DOI：
10.1021/acs.jcim.9b00256
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发表时间：
2019-06-01
影响因子：
5.6
通讯作者：
Lindert, Steffen
中科院分区：
文献类型：
--
作者：
Bowman, Jacob D.;Coldren, William H.;Lindert, Steffen
心肌肌钙蛋白C（cTnC）结合细胞内钙，随后结合心肌肌钙蛋白I（cTnI），启动心肌收缩。由于其在收缩中的作用，cTnC一直是寻找小分子以治疗干扰正常肌肉收缩的疾病（如遗传性心肌病）的治疗靶点。结构研究表明，小分子如苄普地尔、dfbp-o、3-甲基二苯胺（DPA）和W7的结合位置是cTnC（cNTnC）调节结构域中的疏水口袋，但尚未显示这些小分子对打开该结构域的能量学的影响。在这里，我们描述了一个应用程序的伞形采样方法，用于阐明这些钙敏感性调节剂的cNTnC疏水补丁开放的自由能的影响。我们发现，所有这些分子降低开放的自由能在cTnI的情况下，苄普地尔促进最小的吸能转换。然而，在cTnI的存在下，我们看到由于DPA和dfbp-o结合导致的开放构型的稳定，以及苄普地尔和W7赋予的开放构型的不稳定。在常规MD模拟中，预测的不良结合分子NSC 34337在3 ns以下离开疏水补丁，表明仅疏水补丁结合剂稳定开放构象。总之，这项研究提出了一种新的方法来研究小分子对疏水补丁开放的影响，通过雨伞采样，它提出了钙敏感性调节的机制。
Cardiac troponin C (cTnC) binds intracellular calcium and subsequently cardiac troponin I (cTnI), initiating cardiac muscle contraction. Due to its role in contraction, cTnC has been a therapeutic target in the search for small molecules to treat conditions that interfere with normal muscle contraction like the heritable cardiomyopathies. Structural studies have shown the binding location of small molecules such as bepridil, dfbp-o, 3-methyldiphenylamine (DPA), and W7 to be a hydrophobic pocket in the regulatory domain of cTnC (cNTnC) but have not shown the influence of these small molecules on the energetics of opening this domain. Here we describe an application of an umbrella sampling method used to elucidate the impact these calcium sensitivity modulators have on the free energy of cNTnC hydrophobic patch opening. We found that all these molecules lowered the free energy of opening in the absence of the cTnI, with bepridil facilitating the least endergonic transformation. In the presence of cTnI, however, we saw a stabilization of the open configuration due to DPA and dfbp-o binding, and a destabilization of the open configuration imparted by bepridil and W7. Predicted poor binding molecule NSC34337 left the hydrophobic patch in under 3 ns in conventional MD simulations suggesting that only hydrophobic patch binders stabilized the open conformation. In conclusion, this study presents a novel approach to study the impact of small molecules on hydrophobic patch opening through umbrella sampling, and it proposes mechanisms for calcium sensitivity modulation.