Substrate-based inhibitors of HIV-1 protease

Enantioselective vinylogous aldol reaction of acylphosphonates with 3-alkylidene oxindoles

A simple strategy for yielding chiral tertiary α-hydroxy phosphonates that integrates two highly biologically relevant scaffolds namely 3-alkylidene-2-oxindoles and phosphonates has been described. The hydrogen bonding ability of the bifunctional thiourea catalyst allows simultaneous dual activation of a vinylogous oxindole nucleophile and an acylphosphonate electrophile, affording hydroxyphosphonato-3-alkylidene-2-oxindoles as aldol adducts in high yields (up to 92%) with excellent stereocontrol (up to 99% ee).

Resolution of Racemic α-Hydroxyphosphonates: Bi(OTf)3-Catalyzed Stereoselective Esterification of α-Hydroxyphosphonates with (+)-Dibenzoyl-l-tartaric Anhydride

A practical and efficient method has been developed for the preparation of optically active α-hydroxyphosphonates through resolution of the racemates. Treatment of racemic diethyl 1-hydroxy-1-phenylmethylphosphonate (1) with (+)-dibenzoyl-L-tartaric anhydride gave two diastereomeric esters 2 and 3 in the presence of bismuth triflate (15 mol %) in an 86:14 ratio. The two diastereomeric esters were separated by simple column chromatography, and the structure for the major diastereomer was determined by X-ray crystallographic analysis. Simple hydrolysis of the isolated major diastereomer in the usual manner afforded (R)-O,O-diethyl-1-[hydroxyl(phenyl)methyl] phosphonate 1. The advantages of the present method are that the operation is simple and easy to handle, along with rapid and good yield preparations of both enantiomers of the racemic α-phosphonates 1. Diastereoselective reactions of various racemic α-hydroxyphosphonates with d-Bz-L-TA in the presence of Bi(OTf)₃ are also described.

An n→π* Interaction in the Bound Substrate of Aspartic Proteases Replicates the Oxyanion Hole

Aspartic proteases regulate many biological processes and are prominent targets for therapeutic intervention. Structural studies have captured intermediates along the reaction pathway, including the Michaelis complex and tetrahedral intermediate. Using a Ramachandran analysis of these structures, we discovered that residues occupying the P1 and P1' positions (which flank the scissile peptide bond) adopt the dihedral angle of an inverse γ-turn and polyproline type-II helix, respectively. Computational analyses reveal that the polyproline type-II helix engenders an n→π* interaction in which the oxygen of the scissile peptide bond is the donor. This interaction stabilizes the negative charge that develops in the tetrahedral intermediate, much like the oxyanion hole of serine proteases. The inverse γ-turn serves to twist the scissile peptide bond, vacating the carbonyl π* orbital and facilitating its hydration. These previously unappreciated interactions entail a form of substrate-assisted catalysis and offer opportunities for drug design.

Organocatalytic decarboxylative aldol reaction of β-ketoacids with α-ketophosphonates en route to the enantioselective synthesis of tertiary α-hydroxyphosphonates

γ-Aroyl tertiary α-hydroxyphosphonates with a chiral quaternary centre were synthesized via a facile organocatalyzed decarboxylative aldol reaction between β-ketoacids and α-ketophosphonates.

Asymmetric synthesis of chloroisothreonine derivatives via syn-stereoselective Mannich-type additions across N-sulfinyl-α-chloroimines

Mannich-type reactions across N-sulfinyl-α-chloroaldimines resulted in syn-stereoselective synthesis of chloroisothreonine derivatives as excellent building blocks.

Chiral biphenylamide derivative: an efficient organocatalyst for the enantioselective synthesis of alpha-hydroxy phosphonates

The aldol reactions of alpha-keto phosphonates and aldehydes were facilitated by an axially chiral biphenylprolinamide under mild conditions, affording the synthetically and pharmaceutically useful products in high yields and excellent enantioselectivities.

Highly Enantioselective Aerobic Oxidation of α-Hydroxyphosphonates Catalyzed by Chiral Vanadyl(V) Methoxides Bearing N-Salicylidene-α-aminocarboxylates

An unprecedented vanadyl(V) methoxide complex 4 derived from 3,5-dibromo-N-salicylidene-l-tert-leucinate enables highly enantioselective aerobic oxidations of alpha-hydroxyphosphonates at ambient temperature with selectivity factors ranging from 3 to >99.

Structure-based design of achiral, nonpeptidic hydroxybenzamide as a novel P2/P2' replacement for the symmetry-based HIV protease inhibitors

A combination of structure-activity studies, kinetic analysis, X-ray crystallographic analysis, and modeling were employed in the design of a novel series of HIV-1 protease (HIV PR) inhibitors. The crystal structure of a complex of HIV PR with SRSS-2,5-bis[N-(tert-butyloxycarbonyl)amino]-3,4-dihydroxy-1, 6-diphenylhexane (1) delineated a crucial water-mediated hydrogen bond between the tert-butyloxy group of the inhibitor and the amide hydrogen of Asp29 of the enzyme. Achiral, nonpeptidic 2-hydroxyphenylacetamide and 3-hydroxybenzamide groups were modeled as novel P2/P2' ligands to replace the crystallographic water molecules and to provide direct interactions with the NH groups of the Asp29/129 residues. Indeed, the symmetry-based inhibitors 7 and 19, possessing 3-hydroxy and 3-aminobenzamide, respectively, as a P2/P2' ligand, were potent inhibitors of HIV PR. The benzamides were superior in potency to the phenylacetamides and have four fewer rotatable bonds. An X-ray crystal structure of the HIV PR/7 complex at 2.1 A resolution revealed an asymmetric mode of binding, in which the 3-hydroxy group of the benzamide ring makes the predicted interaction with the backbone NH of Asp29 on one side of the active site only. An unexpected hydrogen bond with the Gly148 carbonyl group, resulting from rotation of the aromatic ring out of the amide plane, was observed on the other side. The inhibitory potencies of the benzamide compounds were found to be sensitive to the nature and position of substituents on the benzamide ring, and can be rationalized on the basis of the structure of the HIV PR/7 complex. These results partly confirm our initial hypothesis and suggest that optimal inhibitor designs should satisfy a requirement for providing polar interactions with Asp29 NH, and should minimize the conformational entropy loss on binding by reducing the number of freely rotatable bonds in inhibitors.

HIV-1 protease inhibitors: ketomethylene isosteres with unusually high affinity compared with hydroxyethylene isostere analogs

HIV protease is a member of the aspartic proteinase family of proteolytic enzymes which include pepsin and renin. In contrast to the enhanced affinity seen with renin and pepsin upon conversion of the transition-state isostere, ketomethylene, to the hydroxyethylene, a set of HIV protease inhibitors showed a reduction in affinity. This implies that interactions with the active site of other segments of the inhibitor than those of the transition-state analog must predominate in the case of HIV protease, and that observations made on mammalian aspartic proteinases do not necessarily apply to viral aspartic proteinases.

Recent advances in drug design methods: where will they lead?

Drug design methods have made significant new advances over the last ten years, mainly in the areas of molecular modelling. In more recent times important developments in theory have led to a different type of modelling becoming possible, the so-called de novo or automated design algorithms. In this new method the programs perform much of the chemist's thinking, in finding appropriately sized chemical groups to fit into a target site. However this is a combinatoric problem which has no general analytical solution; it is ripe for optimization. Other advances, such as combinatorial chemical synthesis and screening, will dramatically influence the search for new lead structures for target sites, which at present are poorly understood. Already these methods are being applied to peptide libraries. Peptides do not make good drug compounds because of their poor bioavailability; further, their flexibility reduces their affinity. In some cases peptide backbones can be removed and replaced with rigid non-peptide scaffolds.