High‐resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure‐based design of ribonucleolytic inhibitors

• Published in: Protein science 2003-11, Vol.12 (11), p.2559-2574
• Main Authors: Leonidas, Demetres D., Chavali, Gayatri B., Oikonomakos, Nikos G., Chrysina, Evangelia D., Kosmopoulou, Magda N., Vlassi, Metaxia, Frankling, Claire, Acharya, K. Ravi
• Format: Article
• Language: English
• Subjects: 2′‐deoxyuridine 3′‐pyrophosphate (P′→5′) adenosine; 3′,5′‐ADP, adenosine‐3′,5′‐diphosphate, 2′,5′‐ADP, adenosine‐2′,5′‐diphosphate, 5′‐ADP, adenosine‐5′‐diphosphate, pdUppA‐3′‐p, 5′‐phospho‐2′‐deoxyuridine 3‐pyrophosphate (P′→5′) adenosine 3′‐phosphate; Adenosine Diphosphate - analogs & derivatives; Adenosine Diphosphate - chemistry; Ang, angiogenin; angiogenin; Animals; Binding Sites; Blood Proteins - antagonists & inhibitors; Blood Proteins - chemistry; Blood Proteins - metabolism; Cattle; Crystallography, X-Ray; Drug Design; dUppA‐3′‐p; ECP, eosinophil cationic protein; EDN, eosinophil derived neurotoxin; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - metabolism; eosinophil cationic protein; Eosinophil Granule Proteins; Eosinophil-Derived Neurotoxin; Humans; Hydrogen Bonding; Models, Molecular; PEG, poly(ethylene glycol); ppA‐2′‐p, 5′‐diphosphoadenosine 2′‐phosphate; ppA‐3′‐p, 5′‐diphosphoadenosine 3′‐phosphate; Protein Binding; Protein Conformation; Ribonuclease A inhibitors; Ribonuclease, Pancreatic - antagonists & inhibitors; Ribonuclease, Pancreatic - chemistry; Ribonuclease, Pancreatic - metabolism; Ribonucleases - antagonists & inhibitors; Ribonucleases - chemistry; Ribonucleases - metabolism; RNase A, bovine pancreatic Ribonuclease A; structure‐aided drug design; Uracil Nucleotides - chemistry; Uracil Nucleotides - metabolism
• ISSN: 0961-8368; 1469-896X
• DOI: 10.1110/ps.03196603

The crystal structures of bovine pancreatic ribonuclease A (RNase A) in complex with 3′,5′‐ADP, 2′,5′‐ADP, 5′‐ADP, U‐2′‐p and U‐3′‐p have been determined at high resolution. The structures reveal that each inhibitor binds differently in the RNase A active site by anchoring a phosphate group in subsite P1. The most potent inhibitor of all five, 5′‐ADP (Ki = 1.2 μM), adopts a syn conformation (in contrast to 3′,5′‐ADP and 2′,5′‐ADP, which adopt an anti), and it is the β‐ rather than the α‐phosphate group that binds to P1. 3′,5′‐ADP binds with the 5′‐phosphate group in P1 and the adenosine in the B2 pocket. Two different binding modes are observed in the two RNase A molecules of the asymmetric unit for 2′,5′‐ADP. This inhibitor binds with either the 3′ or the 5′ phosphate groups in subsite P1, and in each case, the adenosine binds in two different positions within the B2 subsite. The two uridilyl inhibitors bind similarly with the uridine moiety in the B1 subsite but the placement of a different phosphate group in P1 (2′ versus 3′) has significant implications on their potency against RNase A. Comparative structural analysis of the RNase A, eosinophil‐derived neurotoxin (EDN), eosinophil cationic protein (ECP), and human angiogenin (Ang) complexes with these and other phosphonucleotide inhibitors provides a wealth of information for structure‐based design of inhibitors specific for each RNase. These inhibitors could be developed to therapeutic agents that could control the biological activities of EDN, ECP, and ANG, which play key roles in human pathologies.