title: Kinetic characterization and molecular docking of a novel, potent, and selective slow-binding inhibitor of human cathepsin L.
abstract: A novel small molecule thiocarbazate (PubChem SID 26681509), a potent inhibitor of human cathepsin L (EC 3.4.22.15) with an IC(50) of 56 nM, was developed after a 57,821-compound screen of the National Institutes of Health Molecular Libraries Small Molecule Repository. After a 4-h preincubation with cathepsin L, this compound became even more potent, demonstrating an IC(50) of 1.0 nM. The thiocarbazate was determined to be a slow-binding and slowly reversible competitive inhibitor. Through a transient kinetic analysis for single-step reversibility, inhibition rate constants were k(on) = 24,000 M(-1)s(-1) and k(off) = 2.2 x 10(-5) s(-1) (K(i) = 0.89 nM). Molecular docking studies were undertaken using the experimentally derived X-ray crystal structure of papain/CLIK-148 (1cvz. pdb). These studies revealed critical hydrogen bonding patterns of the thiocarbazate with key active site residues in papain. The thiocarbazate displayed 7- to 151-fold greater selectivity toward cathepsin L than papain and cathepsins B, K, V, and S with no activity against cathepsin G. The inhibitor demonstrated a lack of toxicity in human aortic endothelial cells and zebrafish. In addition, the thiocarbazate inhibited in vitro propagation of malaria parasite Plasmodium falciparum with an IC(50) of 15.4 microM and inhibited Leishmania major with an IC(50) of 12.5 microM.
authors.affiliation: Penn Center for Molecular Discovery, University of Pennsylvania, 1024 Vagelos Laboratories, Philadelphia, PA 19104-6383, USA.
authors.forename: Parag P
authors.initials: PP
authors.lastname: Shah
authors.forename: Michael C
authors.initials: MC
authors.lastname: Myers
authors.forename: Mary Pat
authors.initials: MP
authors.lastname: Beavers
authors.forename: Jeremy E
authors.initials: JE
authors.lastname: Purvis
authors.forename: Huiyan
authors.initials: H
authors.lastname: Jing
authors.forename: Heather J
authors.initials: HJ
authors.lastname: Grieser
authors.forename: Elizabeth R
authors.initials: ER
authors.lastname: Sharlow
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Napper
authors.forename: Donna M
authors.initials: DM
authors.lastname: Huryn
authors.forename: Barry S
authors.initials: BS
authors.lastname: Cooperman
authors.forename: Amos B
authors.initials: AB
authors.lastname: Smith
authors.forename: Scott L
authors.initials: SL
authors.lastname: Diamond
mesh_terms: D000818:Animals; D001011:Aorta / Q000166:cytology; D001665:Binding Sites; D056668:Cathepsin L; D002403:Cathepsins / Q000032:analysis / Q000037:antagonists & inhibitors*; D002478:Cells, Cultured; D018360:Crystallography, X-Ray; D003546:Cysteine Endopeptidases / Q000032:analysis; D015853:Cysteine Proteinase Inhibitors / Q000737:chemistry* / Q000378:metabolism*; D042783:Endothelial Cells / Q000187:drug effects; D004730:Endothelium, Vascular / Q000166:cytology; D006801:Humans; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D020128:Inhibitory Concentration 50; D007700:Kinetics; D018320:Leishmania major / Q000187:drug effects; D008956:Models, Chemical; D015394:Molecular Structure; D010206:Papain / Q000737:chemistry; D010963:Plasmodium falciparum / Q000187:drug effects; D011485:Protein Binding; D012680:Sensitivity and Specificity
chemical_list: D015853:Cysteine Proteinase Inhibitors; D002403:Cathepsins; D003546:Cysteine Endopeptidases; C534281:CTSL protein, human; D056668:Cathepsin L; D010206:Papain