From genome to drug lead: identification of a small-molecule inhibitor of the SARS virus

Abstract

Virtual screening, a fast, computational approach to identify drug leads [Perola, E.; Xu, K.; Kollmeyer, T. M.; Kaufmann, S. H.; Prendergast, F. G. J. Med. Chem.2000, 43, 401; Miller, M. A. Nat. Rev. Drug Disc.2002, 1 220], is limited by a known challenge in crystallographically determining flexible regions of proteins. This approach has not been able to identify active inhibitors of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) using solely the crystal structures of a SARS-CoV cysteine proteinase with a flexible loop in the active site [Yang, H. T.; Yang, M. J.; Ding, Y.; Liu, Y. W.; Lou, Z. Y. Proc. Natl. Acad. Sci. U.S.A.2003, 100, 13190; Jenwitheesuk, E.; Samudrala, R. Bioorg. Med. Chem. Lett.2003, 13, 3989; Rajnarayanan, R. V.; Dakshanamurthy, S.; Pattabiraman, N. Biochem. Biophys. Res. Commun.2004, 321, 370; Du, Q.; Wang, S.; Wei, D.; Sirois, S.; Chou, K. Anal. Biochem.2005, 337, 262; Du, Q.; Wang, S.; Zhu, Y.; Wei, D.; Guo, H. Peptides2004, 25, 1857; Lee, V.; Wittayanarakul, K.; Remsungenen, T.; Parasuk, V.; Sompornpisut, P. Science (Asia)2003, 29, 181; Toney, J.; Navas-Martin, S.; Weiss, S.; Koeller, A. J. Med. Chem.2004, 47, 1079; Zhang, X. W.; Yap, Y. L. Bioorg. Med. Chem.2004, 12, 2517]. This article demonstrates a genome-to-drug-lead approach that uses terascale computing to model flexible regions of proteins, thus permitting the utilization of genetic information to identify drug leads expeditiously. A small-molecule inhibitor of SARS-CoV, exhibiting an effective concentration (EC50) of 23 microM in cell-based assays, was identified through virtual screening against a computer-predicted model of the cysteine proteinase. Screening against two crystal structures of the same proteinase failed to identify the 23-microM inhibitor. This study suggests that terascale computing can complement crystallography, broaden the scope of virtual screening, and accelerate the development of therapeutics to treat emerging infectious diseases such as SARS and Bird Flu.

Graphical abstract

Figure 1

CS11 in complex with the active site of CCP. (Top) Chemical structures and protonation states of small-molecule inhibitors (CS11 and CS14) of severe acute respiratory syndrome coronavirus chymotrypsin-like cysteine proteinase (CCP); (middle) key intermolecular interactions of CS11 with the active-site residues of CCP; (bottom) overlay of CS11 with a reported substrate fragment (ATVRLQ^p1A^p1′) bound in the active site of CCP (PDB codes: 1P76 and 2AJ5).

Figure 2

Comparison of the backbone conformations in the flexible loop (residues 45–48) of SARS-CoV CCP. Backbones (CA, C, and N) of the flexible loop (residues 45–48) in the active site of severe acute respiratory syndrome coronavirus chymotrypsin-like cysteine proteinase (CCP) in the overlaid models of the 2.0-ns computer model (magenta, PDB code: 1P76), the 4.0-ns computer model (red, PDB code: 2AJ5), the crystal structure in the bound state (blue, PDB code: 1UK4), and the crystal structure in the unbound state (cyan, PDB code: 1UK2).

Figure 3

Comparison of residue conformations in the flexible loop (residues 45–48) of CCP. Residues in the flexible loop of severe acute respiratory syndrome coronavirus chymotrypsin-like cysteine proteinase (CCP) in the 4.0-ns computer model (top, PDB code: 2AJ5), the crystal structure in the bound state (middle, PDB code: 1UK4), and the overlay of the two (bottom).