HINT 2.30 Manual: Chapter 5S

Usage and Strategy


Objectives

This chapter describes the basic steps you should follow to use the SYBYL version of HINT. It contains two sections related to the application of HINT: an overview of the HINT strategy and several specific tutorials that cover most of the commonly used features of HINT.

After studying the descriptive material in the HINT Strategy section and performing the later tutorials you should comfortable with the following operations of HINT:

  1. Partitioning both small molecules and biological macromolecules.
  2. Tabulating InterMolecular and IntraMolecular interactions.
  3. Mapping hydropathic surfaces and interactions.
  4. Using HINT fields and parameters in CoMFA.

Methodology

First we will outlines the basic steps involved in a HINT calculation. Commands provided in HINT are discussed in general terms in the order in which they are used in a typical calculation. Also included are suggestions about when certain parameter values should or should not be used. For a more detailed discussion of each command, refer to the Graphical Interface chapter which has a detailed description of each parameter.

The second portion presents general scenarios where using HINT would be appropriate. Much of this information is background material for the HINT tutorials, so it is recommended that you read this section before starting the tutorial lessons.

Basic Steps for a HINT Calculation

To summarize the basic steps involved in the HINT calculation, the process consists of six steps:

  1. Create and modify the input molecule(s).

  2. Partition the molecule(s).

  3. Set up calculation parameters.

  4. Run the calculation.

  5. Analyze the results.


Typical HINT Scenarios

The preceding section described how to setup and run some HINT calculations without particular regard to the problem being solved. This section describes several common types of interaction calculations for which HINT is appropriate and the strategies used to obtain the desired results. This is not intended as an exhaustive list of the uses of HINT, but rather as an introduction to some underlying principles that can be extended to many other types of applications.

Examination of Hydropathic Field around Molecule

One of the most common uses of HINT is to calculate the hydropathic potential field around a small molecule or macromolecule, and display this result as three-dimensional contours. This provides qualitative information that may be used to explain the interaction of the molecule with other molecules, or suggest a rationale for the observed structure of the molecule (i.e., intramolecular non-covalent forces). The most detailed information would be obtained by parallel runs using the Hydrophobic/Polar and Acid/Base Grid Types, which can be contoured together to display the hydrophobic, acidic, and basic regions of the molecule. The preferred HINT Distance_ Function for Molecule maps is one using the exponential hydropathic term and no steric term.

Prediction of Hydropathic Field for Complementary Species

HINT can be used to predict the Hydropathic Field for a Complementary species. When the structure of a receptor is known it is useful to qualitatively identify the hydropathic structural features of the ideal Complementary molecule (termed the "Key"). With this information it may be possible to construct a molecule with those features, that would be presumed to be the "best" substrate for the receptor site. Likewise, with a known drug, a "Lock" map can be constructed that may reveal the hydropathic structural features of an unknown receptor.

A special parameter in the HintMap Complement command, Asymmetry Factor, controls the directionality of the complementary hydropathic density. With no directionality the density indicates little preference for frontside vs. backside interactions. Using an Asymmetry Factor of 1.0 directs the Lock or Key density along bond axes to be consistent with frontside non-covalent interaction.)

Tabulation/Visualization of InterMolecular Interactions

The best visualization of InterMolecular interactions is obtained by using two HINT runs. One to calculate the Hydrophobic interactions and the second to calculate the Polar interactions. Both runs will be calculated over the same grid space, and can be contoured and displayed simultaneously. Interpretation of the maps is aided by the preparation of a HintTable for the same InterMolecular interaction. This, in essence, will give you a legend to the maps.

The preferred HINT Distance_Function for interaction maps is one which includes both the exponential Hydropathic term and the Steric term. We have found a Steric/Hydro Scaler of 50.0 to be satisfactory in its balance of the two terms. Note that the majority of quantitatively large negative interactions are due to steric violations where the two interacting atoms are too close to each other.

Analysis of a Series of Substrates

If you have a series of molecules known or suspected to bind at the same receptor HINT provides tools for analysis of these data. If the receptor structure is known, you can perform InterMolecular (Binding) HintTable calculations for each substrate with the receptor. The resulting HINT interaction constants may be then correlated with known binding constants for the substrate/receptor binding to construct a calibration curve for the system. HINT has been shown in several cases to order predicted vs. actual binding constants. It is particularly convenient to use the HINTScore option in the molecular spreadsheet if you organized your ligands that way in Sybyl. The next obvious step, once a calibration curve is available, is to predict the binding constants for new molecules. It is important to note the large number of potential uncertainties in this approach. Each atom-atom interaction contributes to the total interaction constant; and each atom-atom microbinding constant is significantly dependent on the distance between the atoms, and by inference, the quality of the molecular model construction.

Secondly, you can examine a series of substrates using the CoMFA technique in the SYBYL QSAR module. HINT adds functionality to CoMFA by providing a hydropathic field to supplement the basic steric and electrostatic CoMFA fields. A second entry point to HINT has been provided in the SYBYL Molecular Spreadsheet to use the HINT calculation of LogP for the QSAR.

Hydropathic Studies of Site-Directed Mutations

Both the Molecule and Interaction HintMaps can be useful tools for investigating the effects of site-directed protein mutations. The Difference command in the HintMap submenu will take the difference (subtract or add) between two contour maps. One strategy would be to compare the Hydropathic maps for "native" and "mutant" Molecules to determine the effect of the mutation on Hydropathic structure. This could reveal, for instance, whether there is an increase in hydrophobicity at the active site due to the mutation.

If the mutation involves structural features implicated in substrate binding, at a subunit interface or in protein folding, difference maps from InterMolecular or IntraMolecular interaction calculations may be useful tools to gain a qualitative understanding of the effect of the mutation on the non-covalent forces at the molecular interface.