Synergistic binding of inhibitors to the protease from HIV type 1

Identification of broad-based HIV-1 protease inhibitors from combinatorial libraries

Clinically approved inhibitors of the HIV-1 protease function via a competitive mechanism. A particular vulnerability of competitive inhibitors is their sensitivity to increases in substrate concentration, as may occur during virion assembly, budding and processing into a mature infectious viral particle. Advances in chemical synthesis have led to the development of new high-diversity chemical libraries using rapid in-solution syntheses. These libraries have been shown previously to be effective at disrupting protein-protein and protein-nucleic acid interfaces. We have screened 44000 compounds from such a library to identify inhibitors of the HIV-1 protease. One compound was identified that inhibits wild-type protease, as well as a drug-resistant protease with six mutations. Moreover, analysis of this compound suggests an allosteric non-competitive mechanism of inhibition and may represent a starting point for an additional strategy for anti-retroviral therapy.

Analysis of the combined effect of two linear inhibitors on a single enzyme

Different methods for studying the concurrent effects of two linear inhibitors on a single enzyme have been published, including the fractional product of Webb, the Yonetani-Theorell plot or the method of Chou and Talalay. Recently the use of combination plots has also been advocated for this purpose. We have evaluated the applicability of these methods and found that most of them depend on assumptions about the mechanism of action of the inhibitors. If the mechanism of action is not completely understood, or if some assumptions about the mechanism are unfounded, the parameters obtained may be meaningless. Even if these assumptions are correct, the interaction can be advantageously measured using an alternative representation that does not require a knowledge of the inhibition constants and allows experimental data to be retrieved from the plot. In other cases it is the interpretation of the results rather than the validity of the method that is misleading. A common mistake is to take the exclusivity of the effects of two inhibitors as exclusivity of their binding. We show that this assumption is seldom justified. In any case, it is possible to decide whether the combination of two or more inhibitors is more effective than their individual use by means of isobolographic analysis, even when no information about their mechanism of action is available.

Analysis of the interactions between an enzyme and multiple inhibitors using combination plots

The concurrent effects of two enzyme inhibitors have been analysed previously with the Yonetani-Theorell plot to obtain insight into the interactions between bound inhibitors. This procedure, like many other traditional graphical methods in enzymology, is based on the estimation of intersecting tendencies in a family of lines. In a recent paper from this laboratory [Chan (1995) Biochem. J. 311, 981-985] it was shown that a plot of this nature may sometimes be replaced, with advantage, by a 'combination plot' in which all data points are accommodated in a single line. We have now extended this approach to analyse the effects of multiple inhibitors and have developed combination plots which illustrate the interaction behaviour in an optimal manner. Thus, in these plots, the synergistic or antagonistic nature of the interactions is clearly evident from the slope, which also provides a direct estimate of the interaction coefficient. The analysis is more efficient and consequently requires fewer enzyme assays. This approach is applicable to various special cases, including that in which three inhibitors bind simultaneously to the enzyme.