Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure.

Finding novel leads from which to design drug molecules has traditionally been a matter of screening and serendipity. We present a method for finding a wide assortment of chemical structures that are complementary to the shape of a macromoleculer receptor site whose X-ray crystallographic structure is known. Each of a set of small molecules from the Cambridge Crystallographic Database (Allen; et al. J. Chem. Doc. 1973, 13, 119) is individually docked to the receptor in a number of geometrically permissible orientations with use of the docking algorithm developed by Kuntz et al. (J. Mol. Biol. 1982, 161, 269). The orientations are evaluated for goodness-of-fit, and the best are kept for further examination using the molecular mechanics program AMBER (Weiner; Kollman J. Comput. Chem. 1981, 106, 765). The shape-search algorithm finds known ligands as well as novel molecules that fit the binding site being studied. The highest scoring orientations of known ligands resemble binding modes generated by interactive modeling or determined crystallographically. We describe the application of this procedure to the binding sites of papain and carbonic anhydrase. While the compounds recovered from the Cambridge Crystallographic Database are not, themselves, likely to be inhibitors or substrates of these enzymes, we expect that the structures from such searches will be useful in the design of active compounds.

Design of nonpeptidal ligands for a peptide receptor: cholecystokinin antagonists.

A series of 3-substituted 5-phenyl-1,4-benzodiazepines, nonpeptidal antagonists of the peptide hormone cholecystokinin (CCK), have been synthesized. Designed on the basis of facts regarding CCK, its natural-product antagonist asperlicin (3), and the antianxiety agent diazepam (4), these compounds represent a significant departure from existing CCK antagonists. They also constitute perhaps the first examples of simple, nonpeptidal ligands for a peptide receptor to arise by design rather than by screening. These compounds serve to illuminate the distinction between central and peripheral CCK receptors, as well as to provide orally effective CCK antagonists of potential pharmacological or therapeutic utility. One rationale for their receptor affinity has possible applications in the design of nonpeptidal ligands for other receptors, peptidal as well as nonpeptidal.

An affinity ligand for phospholipase A2 purification.

An alkyl ether analog of phosphatidylcholine was synthesized and used as a ligand to purify acid-extracted phospholipase A2 from bovine ileum smooth muscle by affinity chromatography in the presence of cholate. This ligand contains a primary amino group at the omega-position of the acyl chain in position 1 and so permits direct covalent coupling with the ester group of Affi-Gel-10. An endogenous membrane bound phospholipase A2 has been purified 32-fold in a good yield (70%) employing this ligand in an affinity chromatography step.

Photolabile ligands for opiate receptors.

The 2-nitro-4-azidophenyl(NAP)-D-Ala2-Leu5-Enkephalin derivatives: Try-D-Ala-Gly-Phe-Leu CONCH2CH2NH-NAP (E-NAP-EDA) and Try-D-Ala-Gly-Phe-Leu CONCH2CH2NH-COCH2CH2NHNAP(E-NAP- -Ala-EDA) were synthesized by conventional peptide methods. Their structure was determined by amino acid analysis, ultra violet, visible and infra red spectroscopy. Both peptides were shown a) to bind with high affinity to the opiate receptors of rat brain membranes and b) to inhibit strongly the contractions of electrically stimulated vas deferens and the adenyl cyclase of the NG 108-15 cell membranes. These effects were reversed by the antagonist naloxone. Photoloysis of the rat brain membranes-(E-NAP- -Ala-EDA) complex caused a 20-30% inactivation of the opiate receptors. Inactivation was prevented when the complex was irradiated in the presence of naloxone. The radio-labeled derivatives of these enkephalin analogs may prove useful photochemical labels of the opiate receptor.