Shashidhar N. Rao

7 – Modeling Drug–Receptor Interactions

This chapter presents numerous examples which show that molecular modeling contribute in measurable ways to the drug discovery process. Many of the compounds in which molecular modeling has played a critical role in the discovery and optimization are well into human clinical trials and are nearing the market place. This is especially true in cases where explicit crystallographic or NMR structures of the drug target are available. A number of other new technologies have also started to contribute to drug discovery. Drugs are unlikely to be found directly from screening. Leads need to be optimized and while combinatorial chemistry can help optimize a lead; design will retain an essential role in optimization. Furthermore, the types of chemistries available from combinatorial libraries will be somewhat limited for the foreseeable future. The techniques of molecular modeling and combinatorial chemistry may complement one another. Computer-aided drug design has been most successful when an explicit 3D structure of the biomolecular target is available. Crystallization and structure determination of soluble proteins have almost become routine. Furthermore, sequences arising from the human genome project coupled with homology modeling will provide models for many of the remaining soluble receptors. Even with an explicit receptor structure, it is still difficult to predict precisely what modifications to a ligand will enhance affinity or to predict what novel structures selected from a database will bind to the receptor with high affinity.

Nucleophilic Opening of N-Carboalkoxy-2,3-anhydro-1-deoxymannojirimycin. A Useful Method for the Syntheses of 2-, 3- and 2,3-Disubstituted 1-Deoxynojirimycin Analogs

Abstract A useful methodology for the synthesis of a number of 2-, 3- and 2,3-disubstituted deoxynojirimycin analogs is reported. It has been found that the epoxides in stereoselectively synthesized N-carboalkoxy-2,3-anhydro-1-deoxymannojirimycins (4 and 5) react with N-, S- and F- nucleophiles to give a mixture of gluco and altro products. The 3-azido altro compound (12b) yields the desired gluco derivative (40) by oxidation, in situ epimerization at C-3, followed by stereoselective reduction of the carbonyl group. The azido intermediate (12a) affords the 2,3-diazido gluco compound (51) by double inversion at C-3. Attempts have been made to understand the factors contributing to the opening of epoxides (4, 5 and 9) by different nucleophiles.

Conformational Studies on Deoxyribonucleosides of C6-Substituted Pyrimidines

Abstract Conformational energy calculations have been presented on 6-methyl-2′-deoxyuridine using molecular mechanics and conformational analysis. The results are presented in terms of isoenergy contours in the conformational space of the glycosidic (χ) and C4′-C5′ (γ) bonds torsions, for three commonly found furanose geometry, C2′ endo, C3′ endo and O1′endo. The χ-γ interrelationships are very similar to those previously calculated for unmodified nucleosides and nucleotides.

Conformational Studies on Nucleosides with Furanose Ring Modifications. 1.

Abstract Conformational energy calculations have been presented on adenine and thymine nucleosides in which the furanose ring is replaced by 2′,3′-dideoxy-2′,3′-didehydrofuran using molecular mechanics and conformational analysis. Conformational energies have been evaluated using the MM2 and AMBER94 force field parameters at two different dielectric constants. The results are presented in terms of isoenergy contours in the conformational space of the glycosidic (χ) and C4′-C5′ (γ) bonds torsions. In general, the χ-γ interrelationships exhibit similarities with the corresponding plots for unmodified nucleosides and nucleotides, reported previously. Consistency of the calculated preferred conformations with the X-ray data is sensitive to the force field employed.

NMR spectroscopy and conformational analysis of 3-deoxy-3-C-(hydroxymethyl)-1,2:5,6-di-O-isopropylidene-α-d-allofuranose

Abstract Homonuclear and heteronuclear 1- and 2-dimensional NMR techniques have been used to establish stereochemical and conformational relationships in the hydroxymethyl furanoside 2 . Concurrent with the NMR studies, theoretical calculations were performed on this compound using computer-assisted model building (MacroModel) and molecular mechanics (MM2). From the NOE and J -coupling constraints obtained from NMR experiments, refined structures for this compound in two different solvents have been identified and optimized. The “solvent effects” observed in the NMR spectra for 2 are interpreted in terms of the differences in the requirements for intramolecular electrostatic stabilization in the two solvents.

Drug Modeling at Cell Membrane Receptors: The Concept of Pseudoreceptors

Explicit molecular design of small molecules intended to target a macromolecule generally utilizes one of two computational approaches: receptor fitting or receptor mapping. A comprehensive strategy for the design of potent, selective and novel ligands for cell-bound receptors combines the two by means of pseudoreceptor modeling. Definition of a refined pharmacophore model is the first step. We describe a new and rigorous method (APOLLO) to accomplish this task. A subsequent step involves construction of a pseudoreceptor - an explict molecular binding pocket - for the bioactive conformation of a series of ligands with high affinity for a particular receptor subtype. Finally, free energy perturbation with solvent is used to calculate relative ligand binding: ΔG(rel)/Ki(rel). These principles are illustrated for a subset of NMDA agonists and antagonists. We conclude by reflecting on the future prospects of modeling for providing deeper understanding of the interaction between ligand and receptor.

NMR spectroscopy and conformational analysis of substituted 1,2:5,6-di-O-isopropylidene-α-d-allofuranose derivatives

Abstract We have utilized contemporary multidimensional NMR techniques to establish stereochemical and conformational relationships in two cyano-containing furanoses. Concurrently, theoretical calculations were performed on these two compounds using computer-assisted model building (MacroModel) and molecular mechanics (MM2). From the NOE and J -coupling constraints obtained from NMR experiments coupled with the results of our theoretical calculations, refined structures for these compounds have been identified and optimized. This study further highlights the significance of combining the results of NMR investigations concurrently with computational approaches in the elucidation of molecular structure in solution.

Conformations of Cyclobut-A and Cyclobut-G: Structural Resemblance to Nucleosides and Incorporation into Double Helical DNA

Conformational energy calculations have been carried out on two modified nucleosides Cyclobut-A and Cyclobut-G using the methods of molecular mechanics (MM2) obtainable in the computational software MacroModel. Conformations were generated as a function of the torsion angles equivalent to the glycosidic and backbone torsions in deoxyribonucleotides. The structural resemblance of the energy minimized models of the modified nucleosides to their corresponding deoxyribonucleosides has been investigated. It is found that conformations which lie within 3 kcal/mole of the global minimum do resemble the overall shape and volume of the B-DNA nucleoside. Following this result, two deoxypentanucleotides d(GCGCG).d(CGCGC) and d(ATATA).d(TATAT) were model built incorporating cyclobut-G and cyclobut-A, respectively. These were then energy refined using the molecular mechanics package AMBER. The resultant structures demonstrate that cyclobut-A and cyclobut-G can be easily accommodated in double helical polynucleotides with minimal overall distortions.