Dekker Frank J, de Mol Nico J, Bultinck Patrick, Kemmink Johan, Hilbers Hans W, Liskamp Rob M J
Department of Medicinal Chemistry, Utrecht Institute of Pharmaceutical Sciences, Faculty Pharmaceutical Sciences, Utrecht University, PO Box 80082, 3508TB Utrecht, The Netherlands.
Bioorg Med Chem. 2003 Mar 20;11(6):941-9. doi: 10.1016/s0968-0896(02)00536-9.
A general approach in drug design is making ligands more rigid in order to avoid loss in conformational entropy (deltaS(conf)) upon receptor binding. We hypothesized that in the high affinity binding of pYEEI peptide ligands to the p56(lck) SH2 domain this loss in deltaS(conf) might be diminished due to preorganization of the fourfold negatively charged pYEEI peptide in the bound, extended, conformation. A thermodynamic analysis was performed on the peptides Ac-pYEEI-NH(2), Ac-pYAAI-NH(2) and Ac-pYGGI-NH(2) using surface plasmon resonance (SPR) competition experiments to assay affinity constants at different temperatures. To study the effect of solution conformation and flexibility a computational conformation analysis was performed from which low energy conformations in solution were calculated, and S(conf) estimated. It was found that the calculated low energy conformations for especially the pYE moiety in solution resemble that in the bound state. In the calculated minimum energy conformation in solution isoleucine is bent towards the pY aromatic ring, the occurrence of such conformation is experimentally confirmed by NMR. The estimated values for S(conf) of the EE- and AA-peptide were similar, suggesting no predominant role of preorganization of the solution conformation due to electrostatic repulsion. Apparently the thermodynamics obey the same entropy-enthalpy compensation relationship, which also was found to hold for other peptides and peptidomimetics binding to p60(src) family SH2 domains. The implications of the results for drug design are discussed.
药物设计中的一种通用方法是使配体更加刚性，以避免受体结合时构象熵（deltaS(conf)）的损失。我们推测，在pYEEI肽配体与p56(lck) SH2结构域的高亲和力结合中，由于四倍带负电荷的pYEEI肽在结合时呈伸展构象的预组织，deltaS(conf)的这种损失可能会减少。使用表面等离子体共振（SPR）竞争实验对肽Ac-pYEEI-NH(2)、Ac-pYAAI-NH(2)和Ac-pYGGI-NH(2)进行了热力学分析，以测定不同温度下的亲和常数。为了研究溶液构象和灵活性的影响，进行了计算构象分析，从中计算出溶液中的低能构象，并估计了S(conf)。发现尤其是溶液中pYE部分的计算低能构象与结合状态下的相似。在计算出的溶液最低能量构象中，异亮氨酸向pY芳香环弯曲，这种构象的出现通过核磁共振实验得到证实。EE-肽和AA-肽的S(conf)估计值相似，表明由于静电排斥，溶液构象的预组织没有主要作用。显然，热力学遵循相同的熵-焓补偿关系，这也被发现适用于其他与p60(src)家族SH2结构域结合的肽和拟肽。讨论了结果对药物设计的影响。
