Virtual screening for finding natural inhibitor against cathepsin-L for SARS therapy
First Online: 29 September 2006 Received: 25 April 2006 Accepted: 08 August 2006 DOI:
10.1007/s00726-006-0403-1 Cite this article as: Wang, S., Du, Q., Zhao, K. et al. Amino Acids (2007) 33: 129. doi:10.1007/s00726-006-0403-1 Summary.
Recently Simmons et al. reported a new mechanism for SARS virus entry into target cells, where MDL28170 was identified as an efficient inhibitor of CTSL-meditated substrate cleavage with IC
50 of 2.5 nmol/l. Based on the molecule fingerprint searching method, 11 natural molecules were found in the Traditional Chinese Medicines Database (TCMD). Molecular simulation indicates that the MOL376 (a compound derived from a Chinese medicine herb with the therapeutic efficacy on the human body such as relieving cough, removing the phlegm, and relieving asthma) has not only the highest binding energy with the receptor but also the good match in geometric conformation. It was observed through docking studies that the van der Waals interactions made substantial contributions to the affinity, and that the receptor active pocket was too large for MDL21870 but more suitable for MOL736. Accordingly, MOL736 might possibly become a promising lead compound for CTSL inhibition for SARS therapy. Keywords: Severe acute respiratory syndrome (SARS) – MDL28170 – KZ7088 – Molecular simulation – Docking – Structural bioinformatics References Anand, K, Ziebuhr, J, Wadhwani, P, Mesters, JR, Hilgenfeld, R 2003 Coronavirus main proteinase (3CL(pro)) structure: Basis for design of anti-SARS drugs Science 300 1763 1767 PubMed CrossRef Bron, RD, Martin, YC 1996 Use of structure-activity data to compare structure-based clustering: methods and descriptors for use in compound selection J Chem Info Comput Sci 36 572 584 CrossRef Chou, KC 2004a Review: Structural bioinformatics and its impact to biomedical science Curr Med Chem 11 2105 2134 Chou, KC 2004b Modelling extracellular domains of GABA-A receptors: subtypes 1, 2, 3, and 5 Biochem Biophys Res Commun 316 636 642 CrossRef Chou, KC 2004c Insights from modelling three-dimensional structures of the human potassium and sodium channels J Proteome Res 3 856 861 CrossRef Chou, KC 2004d Insights from modelling the tertiary structure of BACE2 J Proteome Res 3 1069 1072 CrossRef Chou, KC 2004e Insights from modelling the 3D structure of the extracellular domain of alpha7 nicotinic acetylcholine receptor Biochem Biophys Res Commun 319 433 438 CrossRef Chou, KC 2005a Coupling interaction between thromboxane A2 receptor and alpha-13 subunit of guanine nucleotide-binding protein J Proteome Res 4 1681 1686 CrossRef Chou, KC 2005b Modeling the tertiary structure of human cathepsin-E Biochem Biophys Res Commun 331 56 60 CrossRef Chou, KC, Howe, WJ 2002 Prediction of the tertiary structure of the beta-secretase zymogen Biochem Biophys Res Commun 292 702 708 PubMed CrossRef Chou, KC, Watenpaugh, KD, Heinrikson, RL 1999 A Model of the complex between cyclin-dependent kinase 5(Cdk5) and the activation domain of neuronal Cdk5 activator Biochem Biophys Res Commun 259 420 428 PubMed CrossRef Chou, KC, Tomasselli, AG, Heinrikson, RL 2000 Prediction of the tertiary structure of a caspase-9/inhibitor complex FEBS Lett 470 249 256 PubMed CrossRef Chou, KC, Wei, DQ, Zhong, WZ 2003 Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. Biochem Biophys Res Commun 308 148 151 PubMed CrossRef Du, QS, Wang, SQ, Jiang, ZQ, Gao, WN, Li, Y, Wei, DQ, Chou, KC 2005 Application of Bioinformatics in search for cleavable peptides of SARS CoV Mpro and chemical modification of octapeptides Med Chem 1 209 213 PubMed CrossRef Ewing, TJ, Makino, S, Skillman, AG, Kuntz, ID 2001 Dock 4.0: search strategies for automated molecular docking of flexible molecule databases J Comput Aided Mol Des 15 411 428 PubMed CrossRef Graham, S, Dhaval, NG, Andrew, JR, Jacqueline, DR, Scott, LD, Paul, B 2005 Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry Proc Natl Acad Sci OSA 102 11876 11881 CrossRef Guan, Y, Zheng, BJ, He, YQ, Liu, XL, Zhuang, ZX, Cheung, CL, Luo, SW, Li, PH, Zhang, LJ, Guan, YJ, et al. 2003 Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China Science 302 276 278 PubMed CrossRef Guncar, G, Pungercic, G, Klemencic, I, Turk, V, Turk, D 1999 Crystal structure of Mhc class II associated P41 II fragment bound to cathepsin L reveals the structural basis for differentiation between cathepsins L and S EMBO J 18 793 803 PubMed CrossRef Jeffrey, H, Diana, Q, Zhong, ZY, Barbara, C 1995 Inhibition of /I-amyloid formation identifies proteolytic precursors and SubceUular site of catabolism Neuron 14 651 659 CrossRef Kakegawa, H 1993 Particapation of cathepsin L in bone resorption FEBS Lett 321 247 250 PubMed CrossRef
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