Overcoming resistance to KRAS inhibitors through a fragment-based chemoproteomics approach

摘要 近年来的一项重大突破是针对KRASG12C的选择性抑制剂的开发 在肺癌、结肠癌和其他罕见的癌症类型中发现突变。Sotorasib和Adagrasib的应答率均为 近40%的KRASG12C突变肺癌。尽管取得了这些进展，但仍有两个主要问题需要解决 地址。首先，相当一部分患者的肿瘤没有消退。第二，回应是 暂时性的，耐药性的出现会导致肿瘤的进展。虽然基因组机制有 已被证实驱动获得性耐药，相当大的肿瘤组缺乏明显的基因组机制 似乎依赖于转录重编程或表观遗传机制。我们已经产生了细胞系 概括了非基因组抗性机制的模型：(I)识别与以下因素相关的靶标 (2)开发先导化合物，以服务于未来的药物发现工作。识别这两个新目标 和先导化合物，我们将利用一种新的基于片段的化学蛋白质组学方法。片断状探针 与更大、修饰更多的类药物分子相比，具有明显的优势，因为它们(I)较小且 (Ii)更简单的结构，可以与更发达和更复杂的目标结合位点结合 因此，碎片状分子是识别新靶点和探索未知生物的独特工具 目标空间。我们在Sotorasib耐药细胞模型中的初步数据表明，该屏幕能够识别 与药物敏感亲本相比，耐药细胞中活性增强的片段。此外，使用 一组功能化的20个片段，我们展示了在KRASG12C突变体H1792细胞中识别的能力 利用化学蛋白质组学研究这些片段的靶点。目标1将检验我们可以识别的假设 与未经处理的药物敏感细胞相比，具有增强Sotorasib耐药细胞活性的片段。 我们将利用Sotorasib耐药的额外细胞系模型，并使用非KRASG12C突变肺癌 模型和非肿瘤肺上皮细胞的选择性增强。目标2我们将检验以下假设 驱动耐药表型的因素可以通过化学蛋白质组学进行鉴定。我们将在我们的20个月中评估目标 功能化片段文库以及评估在我们的较大片段筛选中确定的靶标。通过使用 这种方法能够探测到明显更大的生物靶标空间，我们期望识别出唯一的 KRASG12C抑制剂耐药细胞的靶点。与此同时，我们的方法将确定具有吸引力的化学铅 这些目标是未来专门的药物发现项目的目标。

Abstract A major breakthrough in recent years has been the development of selective inhibitors that target KRASG12C mutations found in lung, colon, and other rare cancer typ. Both sotorasib and adagrasib have response rates of nearly 40% in KRASG12C mutant lung cancer. Despite this advance, there remains two major problems to address. First, a substantial group of patients fail to have tumor regressions. Second, the responses are transient, with the emergence of resistance leading to tumor progression. While genomic mechanisms have been identified that drive acquired resistance, a sizeable group of tumors lack obvious genomic mechanisms and appear to rely on transcriptional reprogramming or epigenetic mechanisms. We have generated cell line models that recapitulate non-genomic mechanisms of resistance to (i) identify such targets associated with resistance and (ii) develop lead compounds to serve in future drug discovery efforts. To identify both new targets and lead compounds, we will leverage a new fragment based chemoproteomics approach. Fragment-like probes have the distinct advantage over larger, more decorated drug-like molecules because of their (i) smaller size and (ii) simpler structures that can engage target binding sites that are inaccessible to more developed and complicated molecules.Thus, fragment-like molecules are unique tools to identify novel targets and probe uncharted biological target space. Our preliminary data in Sotorasib resistant cell models indicates the ability of this screen to identify fragments with enhanced activity in the resistant cells compared to drug sensitive parent. In addition, using a group of functionalized 20 fragments, we demonstrate in the KRASG12C mutant H1792 cell the ability to identify targets of these fragments using chemical proteomics. Aim 1 will test the hypothesis that we can identify fragments that have enhanced activity in the Sotorasib resistant cells compared to untreated drug sensitive cells. We will leverage additional cell line models of Sotorasib resistance, and use non-KRASG12C mutant lung cancer models and non-tumor lung epithelial cells to enhance selectivity. Aim 2 we will test the hypothesis that targets that drive the resistant phenotype can be identified by chemoproteomics. We will assess targets in our 20 functionalized fragment library as well as assess targets identified in our larger fragment screening. By using this approach that enables probing a significantly larger biological target space, we expect to identify unique targets for KRASG12C inhibitor resistant cells. At the same time, our approach will identify chemical leads engaging these targets for future dedicated drug discovery projects.