Cotranslational folding in ab initio protein structure prediction and applications in de novo design;

PROTAC（蛋白水解靶向嵌合体）是异双功能分子。它们通过与感兴趣的蛋白质（POI）和E3连接酶结合来发挥功能。使POI与E3连接酶紧密接近导致多聚泛素化，这标志着POI被蛋白体降解。这种作用机制使PROTAC分子成为需要长期下调特定蛋白质的治疗的令人兴奋的候选者[1] [2]。许多PROTAC分子来源于具有已知蛋白质结合特性的小分子。一种常见的方法是将已知的小分子E3连接酶结合剂与已知通过连接区（通常为聚乙二醇或PEG）结合感兴趣蛋白的不同小分子拴在一起。该项目将关注称为IMID（免疫调节酰亚胺药物）的较小类别的分子。这类药物包括沙利度胺、来那度胺和泊马度胺。尽管在结构上与更传统的嵌合PROTAC分子不相似，但现在已知IMID通过PROTAC样机制表现出其药物作用。分子的酰亚胺组分-作为生物分子尿苷的类似物-在三重色氨酸疏水口袋中与E3连接酶蛋白cereblon结合。从cereblon E3连接酶蛋白突出的分子的邻苯二甲酰亚胺半部分改变了cereblon的表面拓扑结构图1 PROTACS作用机制：在没有protac分子的情况下，靶蛋白不降解;在protac存在下，靶蛋白与E3连接酶连接，这标志着它通过多聚泛素化[13]降解，这样它现在将与各种其他蛋白质结合，GSK的工作已经探索了在自然界中这些靶蛋白中发现的保守特征。虽然整体形状不同，但这些蛋白质都有一个与IMID/cereblon复合物结合的小基序。该基序在一级序列方面不保守，但在每种情况下结构相似。还有一个保守的甘氨酸残基，其可与IMID的邻苯二甲酰亚胺基序结合。GSK进行的试验表明，这种共有的基序（以下称为降解决定子）可以被添加到蛋白质中，并在IMID药物存在下用作降解的标记。这种方法被命名为IPID（IMID邻近诱导降解）。涉及具有可变GlySer接头长度的重组GFP-降解决定子杂交体的测定证明了概念的证明。GSK目前的研究目标是探索将这种开关纳入CAR-T细胞疗法（嵌合抗原受体T细胞疗法）的可能性，这是一种免疫疗法，其中T细胞被修饰以识别和破坏患者自身的癌细胞。通过其实现这一点的蛋白质包含与跨膜结构域融合的单克隆抗体的scFv区

PROTACs (proteolysis-targeting chimera) are heterobifunctional molecules. They function by binding to a protein of interest (POI) and an E3 ligase. Bringing the POI into close proximity with the E3 ligase leads to polyubiquitination, which marks the POI for degradation by the proteosome. This mechanism of action makes PROTAC molecules exciting candidates for therapies which require long-term downregulation of a specific protein [1] [2].Many PROTAC molecules are derived from small molecules with known protein binding properties. A frequent approach is to tether a known small molecule E3 ligase binder to a different small molecule that is known to bind the protein of interest via a linker region (usually polyethylene glycol, or PEG).This project will be concerned with a smaller class of molecules known as IMIDs (immunomodulatory imide drugs). Members of this drug class include thalidomide, lenalidomide, and pomalidomide. Although not structurally similar to the more traditional chimeric PROTAC molecules, it is now known that IMIDs exhibit their pharmaceutical effects via a PROTAC-like mechanism. The imide component of the molecule - acting as an analogue of the biomolecule uridine - binds to the E3 ligase protein cereblon in a triple tryptophan hydrophobic pocket. The phthalimide half of the molecule, protruding out from the cereblon E3 ligase protein, alters the surface topology of cereblonFigure 1 PROTACS mechanism of action: In the absence of the protac molecule, the target protein is not degraded; in the presence of the protac, the target protein is linked to an E3 ligase, which marks it for degradation via polyubiquitination [13]such that it will now bind with a variety of other proteins, which all become marked for degradation via the aforementioned route.Work by GSK has explored the conserved features found amongst these target proteins in nature. Although diverse in overall shape, these proteins all share a small motif which binds to the IMID/cereblon complex. This motif is not conserved in terms of primary sequence, but is structurally analogous in each case. There is also a conserved glycine residue, which accommodates binding of the phthalimde motif of the IMID. Any residue other than glycine in this position would be too sterically crowded.Tests carried out by GSK have shown that this shared motif, hereafter referred to as a degron, can be added to a protein and used as a tag for degradation in the presence of an IMID drug. This approach has been named IPID (IMID Proximity Induced Degradation). Assays involving recombinant GFP-degron hybrids with variable GlySer linker lengths demonstrate the proof of concept.A current research goal at GSK is to explore the possibility of including this switch in CAR-T cell therapy (chimeric antigen receptor T cell therapy), a form of immunotherapy where T cells are modified to recognise and destroy the patient's own cancer cells. The protein through which this is achieved comprises of the scFv region of a monoclonal antibody, fused to a transmembrane domain