From nonpeptide toward noncarbon protease inhibitors: Metallacarboranes as specific and potent inhibitors of HIV protease

Institutes of ^*Organic Chemistry and Biochemistry and ^§Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic; ^†Department of Analytical Chemistry, Institute of Chemical Technology, Technicka 5, 166 28 Prague 6, Czech Republic; ^¶Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816; ^∥Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, Area of Research Institutes 1001, 250 68 Husinec-Rez near Prague, Czech Republic; ^**Department of Virology, University of Heidelberg, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany; and ^‡‡Department of Biochemistry, Faculty of Natural Science, Charles University, Hlavova 2030, Prague 2, 128 43 Czech Republic

Communicated by Josef Michl, University of Colorado, Boulder, CO, August 31, 2005 (received for review June 2, 2005)

Abstract

HIV protease (PR) represents a prime target for rational drug design, and protease inhibitors (PI) are powerful antiviral drugs. Most of the current PIs are pseudopeptide compounds with limited bioavailability and stability, and their use is compromised by high costs, side effects, and development of resistant strains. In our search for novel PI structures, we have identified a group of inorganic compounds, icosahedral metallacarboranes, as candidates for a novel class of nonpeptidic PIs. Here, we report the potent, specific, and selective competitive inhibition of HIV PR by substituted metallacarboranes. The most active compound, sodium hydrogen butylimino bis-8,8-[5-(3-oxa-pentoxy)-3-cobalt bis(1,2-dicarbollide)]di-ate, exhibited a K _i value of 2.2 nM and a submicromolar EC₅₀ in antiviral tests, showed no toxicity in tissue culture, weakly inhibited human cathepsin D and pepsin, and was inactive against trypsin, papain, and amylase. The structure of the parent cobalt bis(1,2-dicarbollide) in complex with HIV PR was determined at 2.15 Å resolution by protein crystallography and represents the first carborane-protein complex structure determined. It shows the following mode of PR inhibition: two molecules of the parent compound bind to the hydrophobic pockets in the flap-proximal region of the S3 and S3′ subsites of PR. We suggest, therefore, that these compounds block flap closure in addition to filling the corresponding binding pockets as conventional PIs. This type of binding and inhibition, chemical and biological stability, low toxicity, and the possibility to introduce various modifications make boron clusters attractive pharmacophores for potent and specific enzyme inhibition.

Footnotes

↵ ‡ P.C., M.K., and P.Ř. contributed equally to this work.
↵ ^††To whom correspondence may be addressed at: Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, 166 28 Prague 6, Czech Republic. E-mail: vladimir.kral{at}vscht.cz. ^§§To whom correspondence may be addressed at: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic. E-mail: konval{at}uochb.cas.cz.
Author contributions: P.C., M.K., V.K., B.G., J. Plešek, and J.K. designed research; P.C., M.K., P.Ř., J. Brynda, J. Pokorná, J. Plešek, B.G., L.D.-M., M.M., J. Bodem, H.-G.K., and V.K. performed research; P.C., Z.O., J. Plešek, B.G., L.D.-M., J. Bodem, H.-G.K., and V.K. contributed new reagents/analytic tools; P.C., M.K., P.Ř., J. Brynda, Z.O., J.S., H.-G.K., V.K., and J.K. analyzed data; and P.C., P.Ř., B.G., H.-G.K., and J.K. wrote the paper.
Abbreviations: MIA, mouse intracisternal A particles; PR, protease; PI, HIV PR inhibitor; PDB, Protein Data Bank.
Data deposition: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.rcsb.org/pdb (PDB ID code 1ZTZ).
Freely available online through the PNAS open access option.