Kynostatin (KNI-272), an experimental HIV protease inhibitor, is currently undergoing preclinical testing for the treatment of AIDS. This transition state mimetic tripeptide exhibits extremely low aqueous solubility (4 micrograms/mL) making target concentrations (5-50 mg/mL) for parenteral solution formulations difficult to achieve. The presence of an ionizable (5-isoquinolinyloxy)acetyl moiety makes solubilization via pH adjustment possible, but a solubility > 5 mg/mL requires an adjustment in pH below 2.0, which would be physiologically unacceptable. This study examines and compares two approaches for solubilizing kynostatin: (1) inclusion complex formation at chemically distinct hydrophobic binding sites using (2-hydroxypropyl)-beta-cyclodextrin (HPCD) and a sulfobutyl ether derivative of beta-cyclodextrin (beta-CD-SBE) and (2) a combined strategy utilizing ionization of the isoquinoline moiety coupled with inclusion complex formation at the remaining binding site(s). Macroscopic binding constants determined from solubility profiles as a function of pH and HPCD concentration have been compared with the microscopic binding constant for formation of the isoquinoline-HPCD inclusion complex determined by UV difference spectroscopy to examine the independence of binding domains within KNI-272. As demonstrated in this report, combination strategies tailored to the properties of different domains within the molecule may be highly effective in solubilizing compounds such as poorly soluble peptides.