Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.
Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.
Protein Sci. 2023 Aug;32(8):e4713. doi: 10.1002/pro.4713.
Many protein therapeutics are competitive inhibitors that function by binding to endogenous proteins and preventing them from interacting with native partners. One effective strategy for engineering competitive inhibitors is to graft structural motifs from a native partner into a host protein. Here, we develop and experimentally test a computational protocol for embedding binding motifs in de novo designed proteins. The protocol uses an "inside-out" approach: Starting with a structural model of the binding motif docked against the target protein, the de novo protein is built by growing new structural elements off the termini of the binding motif. During backbone assembly, a score function favors backbones that introduce new tertiary contacts within the designed protein and do not introduce clashes with the target binding partner. Final sequences are designed and optimized using the molecular modeling program Rosetta. To test our protocol, we designed small helical proteins to inhibit the interaction between Gα and its effector PLC-β isozymes. Several of the designed proteins remain folded above 90°C and bind to Gα with equilibrium dissociation constants tighter than 80 nM. In cellular assays with oncogenic variants of Gα , the designed proteins inhibit activation of PLC-β isozymes and Dbl-family RhoGEFs. Our results demonstrate that computational protein design, in combination with motif grafting, can be used to directly generate potent inhibitors without further optimization via high throughput screening or selection.
许多蛋白质治疗药物是竞争性抑制剂,通过与内源性蛋白质结合并阻止它们与天然配体相互作用来发挥作用。工程竞争性抑制剂的一种有效策略是将天然配体的结构基序嫁接到宿主蛋白上。在这里,我们开发并实验测试了一种将结合基序嵌入从头设计的蛋白质中的计算方案。该方案使用“从内到外”的方法:从对接靶蛋白的结合基序的结构模型开始,通过在结合基序的末端生长新的结构元件来构建从头设计的蛋白质。在骨架组装过程中,评分函数有利于在设计的蛋白质中引入新的三级接触而不会与靶结合伴侣产生冲突的骨架。使用分子建模程序 Rosetta 设计和优化最终序列。为了测试我们的方案,我们设计了小型螺旋蛋白来抑制 Gα与其效应物 PLC-β同工酶之间的相互作用。设计的几种蛋白质在超过 90°C 的温度下仍保持折叠状态,与 Gα 的平衡解离常数小于 80 nM。在带有致癌 Gα 变体的细胞测定中,设计的蛋白质抑制 PLC-β同工酶和 Dbl 家族 RhoGEFs 的激活。我们的结果表明,计算蛋白质设计与基序嫁接相结合,可用于直接生成有效的抑制剂,而无需通过高通量筛选或选择进行进一步优化。