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

摘要 近年来的一个重大突破是靶向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的突变。sotorasib和adagrasib的缓解率均为 在KRASG12C突变型肺癌中几乎占40%。尽管取得了这一进展，但仍然存在两个主要问题， 地址.首先，相当一部分患者的肿瘤没有消退。第二，答案是 短暂的，随着耐药性的出现导致肿瘤进展。虽然基因组机制 虽然已经确定了驱动获得性耐药性的基因，但相当大的一组肿瘤缺乏明显的基因组机制， 并且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 概括非基因组抗性机制的模型，以（i）鉴定与以下相关的此类靶标： 耐药性和（ii）开发先导化合物，以服务于未来的药物发现工作。为了确定这两个新目标 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。片段样探针 与较大的、更多修饰的药物样分子相比具有明显的优势，因为它们（i）较小的尺寸， (ii)更简单的结构，可以接合目标结合位点，这些位点是更发达和更复杂的细胞无法接近的。 因此，片段样分子是鉴定新靶点和探测未知生物学特性的独特工具。 目标空间我们在Sotorasib耐药细胞模型中的初步数据表明，该筛选能够识别 与药物敏感亲本相比，在抗性细胞中具有增强活性的片段。此外，使用 一组功能化的20个片段，我们在KRASG12C突变体H1792细胞中证明了鉴定 利用化学蛋白质组学研究这些片段的靶点。目标1将检验我们能够识别 与未处理的药物敏感细胞相比，在Sotorasib抗性细胞中具有增强活性的片段。 我们将利用Sotorasib耐药的其他细胞系模型，并使用非KRASG12C突变型肺癌 模型和非肿瘤肺上皮细胞，以提高选择性。目标2：我们将检验以下假设： 可以通过化学蛋白质组学来鉴定。我们将在20年内评估目标 功能化片段文库以及评估在我们的较大片段筛选中鉴定的靶标。通过使用 这种方法，使探测一个显着更大的生物目标空间，我们希望确定独特的 KRASG12C抑制剂抗性细胞的靶点。与此同时，我们的方法将确定化学线索， 这些目标是未来专门的药物发现项目。

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.