OnconaseTM , a homolog of ribonuclease A (RNase A) with low ribonucleolytic activity, is cytotoxic and has efficacy as a cancer chemotherapeutic. Here variants of RNase A were used to probe the interplay between ribonucleolytic activity and evasion of the cytosolic ribonuclease inhibitor protein (RI) in the cytotoxicity of ribonucleases. K41R/G88R RNase A is a less active catalyst than G88R RNase A but, surprisingly, is more cytotoxic. Like Onconase TM , the K41R/G88R variant has a low affinity for RI, which apparently compensates for its low ribonucleolytic activity. In contrast, K41A/G88R RNase A, which has the same affinity for RI as does the K41R/ G88R variant, is not cytotoxic. The nontoxic K41A/G88R variant is a much less active catalyst than is the toxic K41R/G88R variant. These data indicate that maintaining sufficient ribonucleolytic activity in the presence of RI is a requirement for a homolog or variant of RNase A to be cytotoxic. This principle can guide the design of new chemotherapeutics based on homologs and variants of RNase A.Ribonuclease A (RNase A; EC 3.1.27.5 (1)) was perhaps the most studied enzyme of the twentieth century. Now homologs of RNase A are becoming important new chemotherapeutics (2-4). For example, low levels of bovine seminal ribonuclease (BS-RNase) 1 are cytotoxic (5, 6). More significantly, Onconase TM (ONC), which is isolated from the frog Rana pipiens (7), is currently in Phase III human clinical trials for the treatment of malignant mesothelioma. In addition, ONC inhibits HIV-1 replication in chronically infected human cells (8). Understanding the mechanism of ribonuclease cytotoxicity is vital for the further development of ribonucleases as chemotherapeutics.Ribonuclease-mediated cytotoxicity is known to depend on several factors. Ribonucleases must enter the cell and reach the cytosol, where RNA degradation leads ultimately to cell death (9, 10). Indeed, injecting ribonucleases directly into Xenopus oocytes increases their cytotoxicity (11,12). In the cytosol, ribonucleases encounter the ribonuclease inhibitor protein (RI). RI constitutes Ն0.01% of protein in the cytosol (13,14) and inactivates ribonucleases by forming a tight complex that prevents RNA substrates from entering the active site (Fig. 1A) (15).Ribonucleolytic activity is requisite for the cytotoxicity of BS-RNase and ONC (16,17). Yet despite its relatively high ribonucleolytic activity, RNase A is not cytotoxic (9, 18). The cytotoxicity of BS-RNase and ONC has been attributed to the ability of BS-RNase A and ONC to evade RI (19,20). RI is a potent inhibitor of RNase A with K i near 10 Ϫ14 M (21, 22). In contrast, ONC (estimated K i Ն 10 Ϫ6 M (23)) and BS-RNase (24) escape inhibition by RI.BS-RNase and ONC use different strategies to evade RI. BS-RNase forms a homodimer, which is stabilized by two intersubunit disulfide bridges. This dimeric form has a much lower affinity for RI than does the free monomer (24). ONC evades RI as a monomer. Only 3 of the 24 RNase A residues that contact RI are conserved in ONC...