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

Petr Cígler ^1,3 , Milan Koíek ¹, Pavlína ezáová ^2, 4, Jíí Brynda ², Zbyszek Otwinowski ⁴, Jana Pokorná ¹, Jaromír Pleek ⁵, Bohumír Grüner ⁵, Lucie Doleková-Mareová ¹, Martin Máa ¹, Juraj Sedláek ², Jochen Bodem ⁶, Hans-Georg Kräusslich ⁶, Vladimír Král ^3,  and Jan Konvalinka ^1, 7

¹Institutes of ^*Organic Chemistry and Biochemistry and

²Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo námstí 2, 166 10 Prague 6, Czech Republic

³Department of Analytical Chemistry, Institute of Chemical Technology, Technicka 5, 166 28 Prague 6, Czech Republic

⁴Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8816

⁵Institute of Inorganic Chemistry, Academy of Sciences of the Czech Republic, Area of Research Institutes 1001, 250 68 Husinec-Rez near Prague, Czech Republic;

⁶Department of Virology, University of Heidelberg, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany;

⁷Department of Biochemistry, Faculty of Natural Science, Charles University, Hlavova 2030, Prague 2, 128 43 Czech Republic

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.