Hypoxia-inducible factor-1 (HIF-1) plays an essential role in tumor development and progression by regulating genes that are vital for proliferation, glycolysis, angiogenesis, and metastasis. To identify strategies of targeting the HIF-1 pathway, we screened a siRNA library against the entire druggable genome and a small-molecule library consisting of 691,200 compounds using a HIF-1 reporter cell line. Although the siRNA library screen failed to reveal any druggable targets, the small-molecule library screen identified a class of alkyliminophenylacetate compounds that inhibit hypoxia-induced HIF-1 reporter activity at single-digit nanomolar concentrations. These compounds were found to inhibit hypoxia but not deferoxamine-induced HIF-1␣ protein stabilization. Further analysis indicated that the alkyliminophenylacetate compounds likely inhibit the HIF-1 pathway through blocking the hypoxia-induced mitochondrial reactive oxygen species (ROS) production. Strikingly, all of the nonalkyliminophenylacetate HIF-1 inhibitors identified from the small-molecule library screen were also found to target mitochondria like the alkyliminophenylacetate compounds. The exclusive enrichment of mitochondria inhibitors from a library of >600,000 diverse compounds by using the HIF-1 reporter assay highlights the essential role of mitochondria in HIF-1 regulation. These results also suggest that targeting mitochondrial ROS production might be a highly effective way of blocking HIF-1 activity in tumors.hypoxia-inducible factor ͉ hypoxia ͉ reactive oxygen species ͉ siRNA ͉ RNAi H ypoxia-inducible factor-1 (HIF-1) is the master regulator of cellular responses to low oxygen (1-3). It consists of a constitutively expressed  subunit and an oxygen-regulated ␣ subunit. The proline hydroxylase domain-containing proteins (PHDs) were originally thought to be the main oxygen sensor that mediates oxygen-dependent HIF-1␣ degradation. Under aerobic conditions, PHDs hydroxylate HIF-1␣ at key proline residues by using oxygen as a substrate, which ultimately causes polyubiquitination and degradation of HIF-1␣ through an E3 ubiquitin ligase complex containing the von Hippel-Lindau protein (4, 5). Because oxygen is required for PHD-mediated hydroxylation, the low oxygen level under hypoxic conditions prevents HIF-1␣ hydroxylation, which subsequently leads to the stabilization of HIF-1␣. However, several recent studies demonstrate that the hypoxia-induced production of reactive oxygen species (ROS) in mitochondria is both necessary and sufficient for hypoxia-dependent HIF-1␣ accumulation, suggesting that mitochondria may act as an oxygen sensor for HIF-1␣ regulation by generating ROS under hypoxic conditions (6-9).HIF-1 has emerged as an attractive target for cancer therapy in the last several years. The requirement of HIF-1 for tumor growth has been examined by abrogating the HIF-1 pathway in tumors by using RNAi, small molecule inhibitors, or genetic alterations. Although the degree of tumor responses to HIF-1 inhibition varies among studies, the major...