Identification of noncovalent proteasome inhibitors with high selectivity for chymotrypsin-like activity by a multistep structure-based virtual screening.
Noncovalent proteasome inhibitors introduce an alternative mechanism of inhibition to that of covalent inhibitors, e.g. carfilzomib, used in cancer therapy. A multistep hierarchical structure-based virtual screening (SBVS) of the 65,375 NCI lead-like compound library led to the identification of two compounds (9 and 28) which noncovalently inhibited the chymotrypsin-like (ChT-L) activity (Ki = 2.18 and 2.12 μM, respectively) with little or no effects on the other two major proteasome proteolytic activities, trypsin-like (T-L) and post-glutamyl peptide hydrolase (PGPH) activities. A subsequent hierarchical similarity search over the full NCI database with the most active tripeptide-based inhibitor 9 resulted in the discovery of the β5/β6-specific tripeptide derivative 38 that noncovalently binds the ChT-L site (Ki = 0.42 μM). The solution structure of 9 and 38 was solved by (1)H NMR spectroscopy and the binding mode of the inhibitors was elucidated by docking experiments using the yeast 20S proteasome. Compound 38 (IC50 = 26.7 μM) is slightly more potent than 9 (IC50 = 34.3 μM) at inhibiting survival of dexamethasone-resistant (MM.1R) human multiple myeloma cells. The identified ligand thus provides valuable insights for the future structure-based design of subtype-specific proteasome inhibitors.
Department of Pharmacy, "Drug Discovery" Laboratory, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy.
Carmen
C
Di Giovanni
Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Annunziata, 98168 Messina, Italy.
Roberta
R
Ettari
Department of Pharmacy, "Drug Discovery" Laboratory, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy.
Serena
S
Sarno
Department of Biomedical Sciences, Dentistry, and Morpho-functional Sciences, University of Messina, Via C. Valeria, 98125 Messina, Italy.
Archimede
A
Rotondo
Department of Clinical and Experimental Medicine, University of Messina, Via C. Valeria, 98125 Messina, Italy.
Alessandra
A
Bitto
Department of Clinical and Experimental Medicine, University of Messina, Via C. Valeria, 98125 Messina, Italy.
Francesco
F
Squadrito
Department of Biomedical Sciences, Dentistry, and Morpho-functional Sciences, University of Messina, Via C. Valeria, 98125 Messina, Italy.
Domenica
D
Altavilla
Institute of Pharmacy and Biochemistry, University of Mainz, Staudinger Weg 5, 55099 Mainz, Germany.
Tanja
T
Schirmeister
Department of Pharmacy, "Drug Discovery" Laboratory, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy.
Ettore
E
Novellino
Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Annunziata, 98168 Messina, Italy.
Silvana
S
Grasso
Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Annunziata, 98168 Messina, Italy.
Maria
M
Zappalà
Department of Pharmacy, "Drug Discovery" Laboratory, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy. Electronic address: antonio.lavecchia@unina.it.
Antonio
A
Lavecchia
D045744:Cell Line, Tumor; D049109:Cell Proliferation; D002918:Chymotrypsin / Q000378:metabolism*; D004353:Drug Evaluation, Preclinical; D006801:Humans; D062105:Molecular Docking Simulation; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism; D061988:Proteasome Inhibitors / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*; D011487:Protein Conformation; D059748:Proteolysis / Q000187:drug effects; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D014584:User-Computer Interface
D061988:Proteasome Inhibitors; D002918:Chymotrypsin; D046988:Proteasome Endopeptidase Complex
Docking studies; Non-covalent; Peptide scaffold; Proteasome inhibitors; Virtual screening