Suresh Babu Mekapati

On the Role of Polarizability in Chemical−Biological Interactions

This report considers the importance of electronic effects in their role in the QSAR of chemical-biological interactions. The problem of accounting for polarizability effects in ligand-substrate interactions is discussed in terms of molecular polarizability (MR) and NVE (number of valence electrons) using additive values for valence electrons. The two approaches give essentially the same result in examples of frog nerve toxicity and examples of nerve toxicity with rabbits and cockroaches. The point is made that no matter how one approaches QSAR, electronic interactions must be considered if we are to begin to develop a science of chemical-biological interactions.

QSAR: then and now.

In this review, the evolution of QSAR is traced from the insightful observations of Crum-Brown and Frazier to Hammetts critical equations and finally Hanschs seminal contributions on hydrophobicity and modelling of biological activity based on extrathermodynamic principles. Todays QSAR models can stand alone, augment other graphical approaches or be examined in tandem with equations of a similar mechanistic genre to truly reveal the power of the paradigm. This review will focus on the three standard classifications routinely used in QSAR analysis electronic, hydrophobic, and steric, as well as topological indices. Electronic parameters will focus on Hammett sigma constants and their numerous variations. Dipole moments, hydrogen bond descriptors and quantum chemical indices as well as applications of their utilization will be described. The hydrophobicity parameter will be examined by tracing its early history, its operational definition and its determination by either experimental methods or computational calculations. Steric parameters, which run the gamut from size to shape, will be described by Tafts, Hancocks, Chartons, Fujitas, Verloops and Simons contributions. Topological effects, delineated by connectivity indices, kappa shape and electrotopological indices of Kier and Hall are also described. Examples of QSAR models incorporating most of these parameters are reviewed. In cases where the 95% confidence intervals of variables are available, they are listed in parentheses. A brief Comparative QSAR analysis of non-nucleoside reverse transcriptase inhibitors (NNRTIs) is outlined and various models obtained by different groups examining 4, 5, 6, 7-tetrahydro-5-methylimidazo [4, 5,1-j,k][1,4] benzodiazepin-2(1H)-ones (TIBO) and 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)-thymine (HEPT) derivatives are compared for mechanistic insight that could be useful in the process of inhibitor design.

QSAR of Cytochrome P450

The cytochrome P450 class of enzymes is an extremely important and complex group. It has a significant place in ADME (adsorption, distribution, metabolism, elimination) that those developing new drugs must be concerned with. While there are various ways in which organic compounds can undergo metabolic attack, P450 is probably the most important. Recently, Lewis (2000) reviewed his extensive studies on P450 and efforts to use QSAR to gain a deeper understanding on this important class of enzymes. We have also been interested in the QSAR of P450 enzymes, but much has appeared since our last review (Hansch and Zhang, 1993).

HIV-1 Protease Inhibitors: A Comparative QSAR Analysis

An excellent example in the field of rational drug design is the discovery and development of more than a dozen drugs for the treatment of AIDS. The major targets for the development of new chemotherapeutic agents are Reverse Transcriptase and Protease, the enzymes encoded by HIV-1. The introduction of HIV-1 protease (HIV-1 PR) inhibitors, in particular, has drastically decreased the mortality and morbidity associated with AIDS. The inhibition of this enzyme results in production of immature and noninfectious virions. In the present review, a comparative quantitative structure activity relationship (QSAR) study of various peptidomimetic and non-peptidomimetic molecules investigated for their inhibitory activity has been reported. Among the various physicochemical properties studied, hydrophobicity, steric and electronic interactions are found to play important role in binding to the receptor.

Allosteric interactions and QSAR: On the role of ligand hydrophobicity

A study of a very large database of QSAR (9100) has uncovered a few unusual examples where as one increases the hydrophobicity of the members of a set of congeners, activity decreases until at a certain point, activity begins to increase. Obviously a change in mechanism is involved. The only way we have found to rationalize this unusual event is by a change in the structure of the receptor. We have found this to occur with hemoglobin, a substance first used to define allosteric reactions.

On the parametrization of the toxicity of organic chemicals to Tetrahymena pyriformis. The problem of establishing a uniform activity

In this report we illustrate the importance of making an effort to ensure that all of the dependent variables in a QSAR are associated with one mechanism of action. If this cannot be established, it will not be possible to compare the QSAR with others acting on different biological systems. That is, such information cannot be used to develop a science of chemical-biological interactions. A study of the action of a large set of phenols acting on Tetrahymena pyriformis made by Cronin and Schultz is analyzed to illustrate the problem.

QSAR of apoptosis induction in various cancer cells.

In continuing our QSAR study of apoptosis, we consider in this report the action of phenolic compounds on Ramos cells (non-Hodgkins B-cell lymphoma): the effect of O-8-thapsigargin analogues on human prostate cancer cells, Tsu-Pr-1 and the induction of apoptosis of a complex set of congeners on human fibrosarcoma cells HT 1080. The human prostate cancer cells activity is very similar to that of the Ramos cells. While the QSAR for the fibrosarcoma cells resembles that of our earlier study with L1210 leukemia cells. The two different types of QSAR suggest at least two quite different types of receptors for the induction of apoptosis.

Searching for allosteric effects via QSAR. Part II

Allosteric interactions have in the past been established by means of X-ray crystallography or careful study of a single molecule at a variety of concentrations. Here we report a method for using QSAR to establish a change in reaction mechanism by establishing an inversion point. That is, as polarizability of a member of a congeneric set of compounds is increased (as measured by CMR), activity at first decreases until, at the inversion, activity turns around and increases. Out of 23 examples, 14 have inversion points of 10+/-1. This includes a wide variety of receptors such as thrombin, 5-HT, dopamine, and tyrosine kinase acting with a variety of ligands.

Comparative QSAR studies on bibenzimidazoles and terbenzimidazoles inhibiting topoisomerase I

Terbenzimidazoles that inhibit topoisomerase are of interest as anticancer drugs. We have reviewed the literature and have developed 13 quantitative structure-activity relationships (QSARs) on cleaving DNA or inhibiting the growth of tumor cell cultures. The results are correlated with octanol/water partition coefficients or molecular refractivity. Suggestions have been made for the development of improved derivatives.

Mechanism-based QSAR approach to the study of the toxicity of endocrine active substances*

Mechanism-based QSAR models for interactions between various ligands and the estrogenic receptor are developed by using well-developed physicochemical parameters. Common features of these QSARs are identified, and deficiencies in some datasets are highlighted. The relative binding affinities of various substituted hexestrols to estrogen receptors are examined in terms of their steric, electronic, and hydrophobic attributes. Different QSARs for hexestrols and tamoxifens reveal that steric effects are of overriding importance in variations of binding affinity. In the few cases where a large number of diverse substituents are located on aromatic rings, electronic effects emerge and suggest that electron-donating groups enhance binding to the receptor while hydrophobicity plays a marginal role in decreasing binding affinity. With substituted phenols bearing alkyl-type substituents and substituted hydroxy-biphenyls, the binding is strictly dependent on hydrophobicity and size. These QSAR models are described in detail and examined together to illustrate the utility of lateral validation in mechanistic interpretation.