For this map you want to define the region of the active site as the grid dimensions. The easiest way to do this now is to read in the known inhibitor, and use it as a template for the Molecule Extents. Go to the File pulldown and select the Read... command. Choose a74704.pdb from the file list. (This molecule should go into Molecular Area M2.) Be sure to select No for Center the Molecule. Otherwise the origin of the coordinate system will not be consistent between the HIV1 and its inhibitor. Turn off the display in molecular area M2 with the Check Box icon under the Tripos logo on the left side of the screen. We will return to this molecule in Step 3, but for now, invoke the Map Complement dialog box with eslc, Hint, HintMap, Complement... from the SYBYL menubar.

First, select the source Molecule... for the Map Complement calculation. It is M1 (HIV1). Next, for the Region Definition... verify that Molecule Extents is the Region and pick M2 (A74704) as the Molecule... to define a region that coincides with the active site of HIV-1.

In the Map Complement dialog box, most of the parameters will be identical to those of the Molecule HintMap command discussed in Lessons 2 and 3. We will set most parameters identical to the choices of Lesson 3. From Grid Types select Hydrophobic/Polar; enter a value of 6.0 for the Cut-Off Radius; and set the Volume Averaging parameter to off.

The major change in setup we will use for this calculation is in the Hint Distance Function. It is especially useful in Complementary Map calculations to use Directionality Vectors to Focus the map density along physically meaningful vectors associated with the molecular structure. In the Distance Function Dialog Box select Hybridized Pi/Lone Pairs for the Directionality Vectors type. The Vector Focus represents how tightly the hydropathic density will adhere to that vector direction; in this case the vector directions are along lone pairs and pi electron pairs for polar atoms. The hydrophobic density is treated as non-directional. Enter a value of 0.50 for the Vector Focus parameter, select exp(-nr) for the Hydropathic Term and set the Steric Term to off. Finally press OK to exit the Distance Function Dialog.

Enter hiv1_co_hp.cnt as the Map File name. This calculation may take in the vicinity of 10 minutes, so run it in Batch. Press OK to initiate the Complement HintMap calculation.

Repeat the map calculation to create a parallel Acid/Base Complement map for HIV1. Use the Map Complement dialog box: select Acid/Base from Grid Types; choose Lewis as the Acid Base Definition; enter hiv1_co_ab.cnt as the Map File name and HintCompMap2 as the Job Name. Make sure all other parameters are the same as before. Press OK.

When both map calculations are complete you may contour the HINT maps for display. Choose Contour... from eslc, Hint, HintMap. Since these two maps were run as NetBatch jobs, in order to contour them we will have to specify their filenames explicitly. In the Map Contour dialog box press the ... button next to the Contour File field to call a Read File dialog box that has been filtered to list only SYBYL .cnt files. First select hiv1_co_hp.cnt to contour the Hydrophobic Complement map. Choose D1 as the Display Area and select a Style appropriate for your computer. Enter 150 for the Contour Value and pick Green for the Contour Color parameter. Press Accept followed by Done to contour the Hydrophobic map. Invoke the Map Contour dialog box a second time to contour the polar (acid and base) complement map. Select hiv1_co_ab.cnt as the Contour File either by typing directly in the text field or by using the Read File dialog box (...). Select Display Area D2. Contour this map with -50 (red) and 50 (blue). The net display of the two contoured maps shows regions of the active site most hospitable to hydrophobic groups and differentiates between two types of Polar regions (Acid-like in red and Base-like in blue) based on Lewis definitions of acids and bases.

One known inhibitor for HIV protease is the A74704 molecule designed, synthesized and analyzed by the Erickson group at Abbott and at the National Cancer Institute. As you recall, we read in this molecule in step 1 of this Lesson in order to use its coordinates to define the active site. Now you will see how well it fits the predictions made by HINT regarding substrate design. (Note that the inhibitor may be asier to interpret if you follow step 2 of Lesson 5.) Use the Check Box icon under the Tripos logo to redisplay M2 (A74704). Color the molecule by atom. You should note how the leucine-like portions of A74704 are enveloped by the hydrophobic green contours of the Complement map, and how many of the polar features of the inhibitor are spatially near analogous regions in the "key" map for HIV. In particular the hydroxyl group of A74704 is enclosed in a red acidic contour.

Inhibitor A74704 and HINT complement map of HIV-1 Protease