Prospective identification of biologically active structures by topomer shape similarity searching.

The principle of bioisosterism-similarly shaped molecules are more likely to share biological properties than are other molecules-has long helped to guide drug discovery. An algorithmic implementation of this principle, based on shape comparisons of a single rule-generated "topomer" conformation per molecule, had been found to be the descriptor most consistently predictive of similar biological properties, in retrospective studies, and also to be well-suited for searching large (>10(12)) "virtual libraries" of potential reaction products. Therefore a prospective trial of this shape similarity searching method was carried out, with synthesis of 425 compounds and testing of them for inhibition of binding of angiotensin II (A-II). The 63 compounds that were identified by shape searching as most similar to any of four query structures included all of the seven compounds found to be highly active, with none of the other 362 structures being highly active (p < 0.001). Additional consistent relations (p < 0.05) were found, among all 425 compounds, between the degree of shape similarity to the nearest query structure and the frequency of various levels of observed activity. Known "SAR" (rules specifying structural features required for A-II antagonism) were also regenerated within the biological data for the 63 shape similar structures.

Diversity assessment.

Several themes have been highlighted recently in both conferences and publications: the availability of product-focused and pharmacophore-based methods for the analysis and design of combinatorial libraries; the power of cell-based methods for molecular similarity, diversity and library design applications; methods for 'rational' diverse subset selection (with applicability to library design); the need for specialized optimization programs for the design of combinatorial libraries that maximize the use of common reagents; and the concept of 'drug-likeness' and its importance in the design of combinatorial libraries.

Aminodiol HIV protease inhibitors. Synthesis and structure-activity relationships of P1/P1' compounds: correlation between lipophilicity and cytotoxicity.

A series of novel aminodiol inhibitors of HIV protease based on the lead compound 1 with structural modifications at P1' were synthesized in order to reduce the cytotoxicity of 1. We have observed a high degree of correlation between the lipophilicity and cytotoxicity of this series of inhibitors. It was found that appropriate substitution at the para position of the P1' phenyl group of 1 resulted in the identification of equipotent (both against the enzyme and in cell culture) compounds (10l, 10m, 10n, and 15c) which possess significantly decreased cytotoxicity.

Characterization of a human immunodeficiency virus type 1 variant with reduced sensitivity to an aminodiol protease inhibitor.

Development of viral resistance to the aminodiol human immunodeficiency virus (HIV) protease inhibitor BMS 186,318 was studied by serial passage of HIV type 1 RF in MT-2 cells in the presence of increasing concentrations of compound. After 11 passages, an HIV variant that showed a 15-fold increase in 50% effective dose emerged. This HIV variant displays low-level cross-resistance to the C2 symmetric inhibitor A-77003 but remains sensitive to the protease inhibitors Ro 31-8959 and SC52151. Genetic analysis of the protease gene from a drug-resistant variant revealed an Ala-to-Thr change at amino acid residue 71 (A71T) and a Val-to-Ala change at residue 82 (V82A). To determine the effects of these mutations on protease and virus drug susceptibility, recombinant protease and proviral HIV type 1 clones containing the single mutations A71T and V82A or double mutation A71T/V82A were constructed. Subsequent drug sensitivity assays on the mutant proteases and viruses indicated that the V82A substitution was responsible for most of the resistance observed. Further genotypic analysis of the protease genes from earlier passages of virus indicated that the A71T mutation emerged prior to the V82A change. Finally, the level of resistance did not increase following continued passage in increasing concentrations of drug, and the resistant virus retained its drug susceptibility phenotype 34 days after drug withdrawal.

Aminodiol HIV protease inhibitors. 1. Design, synthesis, and preliminary SAR.

A series of HIV protease inhibitors containing a novel C2 symmetrical "aminodiol" core structure were prepared from amino acid starting materials. The ability of the aminodiols to inhibit HIV replication in cell culture is comparable to their ability to inhibit the isolated enzyme, a result compatible with good cell membrane penetration by this class of compounds. Optimization of the structure-activity in this series led to aminodiol 9a (Ki = 100 nM; ED50 (HIV-1) = 80 nM) containing P1/P1 benzyl and P2/P2 Boc substituents. Compound 9a is a selective inhibitor of HIV protease versus other aspartyl proteases such as human renin, human cathepsin D, and porcine pepsin. In addition, 9a is equipotent against HIV-1 and HIV-2 in cell culture and demonstrates similar activity in infected T-lymphocytes and PBMCs. After i.v. and oral administration in rats, 9a displayed significant oral bioavailability (ca. 40%) and a promising plasma elimination half-life (4 h).

(+-)-Octahydro-2-methyl-trans-5 (1H)-isoquinolone methiodide: a probe that reveals a partial map of the nicotinic receptor's recognition site.

A new, semirigid, nicotinic agonist (+-)-octahydro-2-methyl-trans-5 (1H)-isoquinolone methiodide was synthesized. The disposition of this agonist's nitrogen and carbonyl group conforms well to the prevailing notion of a pharmacophore for the nicotinic receptor. Comparing its structure and electrostatic potential surfaces, we predicted that its activity would be similar to that of carbamylcholine at the frog neuromuscular junction. Instead, the potency of the isoquinolone was only 0.015 times as potent as (+)-carbamylcholine. We conclude, after eliminating other possibilities, that the vicinity of the carbonyl group of an agonist must be planar to fit a confined space within the receptor's recognition site. The isoquinolone is a weak agonist because its methylene group beta to the carbonyl intrudes on this space.

A graphical representation of the electrostatic potential and electric field on a molecular surface.

The graphics program presented, ARCHEM, draws the molecular electrostatic potential (MEP) on a molecular surface color-coded according to the magnitude of the potential. Vectors can be drawn on the surface to show the electric field surrounding the molecule and color-coded according to the magnitude of the field. The electrostatic potential (ESP) calculated from the wave function or from net atomic charges using GAUSSIAN 80 UCSF1.2 can be plotted at points on a shell surrounding the molecule. For the neurotransmitter glycine zwitterion, the MEP is calculated from the wave function and from different point charge models, and the results are represented graphically.

Carbamyl analogues of potent nicotinic agonists: pharmacology and computer-assisted molecular modeling study.

To investigate how the substitution of NH2 for CH3 affects the activity of three, potent, semirigid nicotinic agonists, carbamyl analogues were synthesized. The carbamyl agonists were 1-methyl-4-carbamyl-1,2,3,6-tetrahydropyridine methiodide (1), 1-methyl-4-carbamylpiperidine methiodide (2), and 1-methyl-4-carbamylpiperazine methiodide (3). Their potencies (reciprocals of the equipotent molar ratios) at the frog neuromuscular junction with reference to carbamylcholine were 0.77, 0.052, and 0.15, respectively. The acetyl analogues were more potent by factors of 65, 175, and 17, respectively. Explanations for this variable reduction in activity were sought by using computer-assisted molecular mechanics and calculations of electrostatic potential contours. Bioactive conformations of 1-3 were assigned on the basis of a well-supported pharmacophore and the ground-state conformation of the highly potent (50 times that of carbamylcholine) prototype, isoarecolone methiodide (4). Agonist 3 and its acetyl analogue superimposed closely in their ground-state, bioactive conformations, and the differences in their electrostatic potential contours were the least among the three pairs. Accordingly, their potencies differed the least. Agonists 1 and 2 both showed greater differences (with respect to their acetyl analogues) in their electrostatic potential contours and greater differences in potency. Agonist 2, in addition, could achieve the bioactive conformation only at the expense of 2.8 kcal mol-1, and, correspondingly, its activity relative to its acetyl analogue was lowest of all.

Synthesis, pharmacology, and molecular modeling studies of semirigid, nicotinic agonists.

Eight nicotinic agonists were synthesized, and their potencies were estimated by contracture of the frog rectus abdominis muscle. The most potent, 1-methyl-4-acetyl-1,2,3,6-tetrahydropyridine methiodide (3b), 50 times as potent as carbamylcholine, served as a template for the rest. Although all of the agonists could easily conform to the putative nicotinic pharmacophore, their potencies spanned a nearly 10,000-fold range. This pharmacophore, therefore, may be necessary but deficient. Computer-assisted molecular modeling studies helped to delineate additional factors that may contribute to potency. The factors are (1) the ground-state conformation, (2) superimposability of the hydrogen bond acceptor and the cationic head onto the template, (3) electrostatic potential at the cationic head and at the hydrogen bond acceptor site, and (4) the presence of a methyl group bonded to the carbon atom that bears the hydrogen bond acceptor. A new program, ARCHEM, was used to calculate and to visualize electrostatic potentials at the van der Waals surfaces of the agonists.