Joseph-McCarthy D, Tsang S K, Filman D J, Hogle J M, Karplus M
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
J Am Chem Soc. 2001 Dec 26;123(51):12758-69. doi: 10.1021/ja003972f.
Computational methods were used to design structure-based combinatorial libraries of antipicornaviral capsid-binding ligands. The multiple copy simultaneous search (MCSS) program was employed to calculate functionality maps for many diverse functional groups for both the poliovirus and rhinovirus capsid structures in the region of the known drug binding pocket. Based on the results of the MCSS calculations, small combinatorial libraries consisting of 10s or 100s of three-monomer compounds were designed and synthesized. Ligand binding was demonstrated by a noncell-based mass spectrometric assay, a functional immuno-precipitation assay, and crystallographic analysis of the complexes of the virus with two of the candidate ligands. The P1/Mahoney poliovirus strain was used in the experimental studies. A comparison showed that the MCSS calculations had correctly identified the observed binding site for all three monomer units in one ligand and for two out of three in the other ligand. The correct central monomer position in the second ligand was reproduced in calculations in which the several key residues lining the pocket were allowed to move. This study validates the computational methodology. It also illustrates that subtle changes in protein structure can lead to differences in docking results and points to the importance of including target flexibility, as well as ligand flexibility, in the design process.
采用计算方法设计基于结构的抗微小核糖核酸病毒衣壳结合配体组合文库。利用多重复本同时搜索（MCSS）程序，针对已知药物结合口袋区域的脊髓灰质炎病毒和鼻病毒衣壳结构，计算多种不同官能团的功能图谱。基于MCSS计算结果，设计并合成了由数十种或数百种三单体化合物组成的小型组合文库。通过非细胞质谱分析、功能性免疫沉淀分析以及病毒与两种候选配体复合物的晶体学分析，证实了配体结合。实验研究中使用了P1/Mahoney脊髓灰质炎病毒株。比较结果表明，MCSS计算正确识别出一种配体中所有三个单体单元以及另一种配体中三个单体单元中的两个的观察到的结合位点。在允许口袋内衬的几个关键残基移动的计算中，重现了第二种配体中正确的中心单体位置。这项研究验证了计算方法。它还表明蛋白质结构的细微变化会导致对接结果的差异，并指出在设计过程中纳入靶点灵活性以及配体灵活性的重要性。
