HIV protease as an inhibitor target for the treatment of AIDS

Screening for production of proteinase inhibitors by Antarctic Streptomycetes

Three out of 17 Streptomycetes strains - Streptomyces sp. 35 LBG09, Streptomyces sp. 36 LBG09, and Streptomyces sp. 39 LBG09, were selected based on the high production of proteinase inhibitors with trypsin serine proteinase activity. The strains were isolated from soil samples taken from the area around the Bulgarian station on Livingston Island, Antarctica. Biosynthesis of proteinase inhibitors by the promising strains started at different stages of their development but was generally not associated with the growth of the producers. Peak levels were reached in the stationary phase (96-120 h) of their cultivation. Inducing effects on strain development, biomass accumulation, and proteinase inhibitor biosynthesis were based on the composition of the nutrient medium: the polypeptones contained in Taguchi medium and glucose as a carbon source. The most productive out of the three strains was Streptomyces sp. 36 LBG09. Its maximum inhibitory activity was reached at 96 h in culturing media modified by three different carbon sources. The active proteinase inhibitor biosynthesis proceeded at pH values between 6.8 and 8.6 and the dynamics of production depended on the type of carbon source. Peak levels of extracellular protein and dry biomass were reached at 120 h in the stationary growth phase. The residual sugars were minimal at the end of the process when using soluble starch as a carbon source, and maximal when glucose was used.

Potent and Orally Bioavailable HIV-1 Proteinase Inhibitors Containing the 2-aminobenzylstatine Moiety

In order to design HIV proteinase inhibitors which combine antiviral potency in HIV-infected cells with good oral bioavailability, new derivatives of 2-aminobenzylstatine containing HIV-1 proteinase inhibitors were synthesized. Compounds showing the desired profile emerged from a series of modifications at the P3′ moiety of the parent inhibitor [1], and are characterized by the presence of hydroxy or methoxy substituents at the C-terminal benzylamide. The most potent congeners, compounds [15] and [19], were evaluated in more detail and proved inhibitory to HIV-1 replication in primary T4 lymphocytes with EC90 = 2.2 and 2.7 nM, respectively. They also exhibited adequate oral bioavailability in the range of [13] to 42% in mice and rats. Thus, further investigation of this type of HIV proteinase inhibitor seems warranted.

HIV protease inhibitors in gut barrier dysfunction and liver injury

The development of HIV protease inhibitors (HIV PIs) has been one of the most significant advances of the past two decades in controlling HIV infection. HIV PIs have been used successfully in highly active anti-retroviral therapy (HAART) for HIV infection, which is currently the most effective treatment available. Incorporation of HIV PIs in HAART causes profound and sustained suppression of viral replication, significantly reduces the morbidity and mortality of HIV infection, and prolongs the lifespan of HIV patients. However, in the era of HAART, drug-induced gastrointestinal (GI) side effects and hepatotoxicity have emerged as important potential complications of HIV therapy, particularly those regimens containing HIV PIs. In this mini-review, we highlight the current understanding of the mechanisms of HIV PI-associated GI and liver injury.

Understanding HIV-1 protease autoprocessing for novel therapeutic development

In the infected cell, HIV-1 protease (PR) is initially synthesized as part of the GagPol polyprotein. PR autoprocessing is a virus-specific process by which the PR domain embedded in the precursor catalyzes proteolytic reactions responsible for liberation of free mature PRs, which then recognize and cleave at least ten different peptide sequences in the Gag and GagPol polyproteins. Despite extensive structure and function studies of the mature PRs as well as the successful development of ten US FDA-approved catalytic-site inhibitors, the precursor autoprocessing mechanism remains an intriguing yet-to-be-solved puzzle. This article discusses current understanding of the autoprocessing mechanism, in an effort to prompt the development of novel anti-HIV drugs that selectively target precursor autoprocessing.

Secolignans, neolignans and phenylpropanoids from Daphne feddei and their biological activities

Two new secolignans and one new neolignan, named feddeiphenols A-C (1-3), together with eight known compounds (4-11), were isolated from the leaves and stems of Daphne feddei. Their structures were established on the base of spectroscopic methods, mainly extensive NMR, UV spectroscopy, and MS spectrometry. Compounds 1-11 were tested for their anti-human immunodeficiency virus (HIV)-1 activity and cytotoxicity. The results revealed that compounds 1, 2, 3, 7, and 9 showed therapeutic index (TI) values above 30, respectively, and the other compounds also showed weak anti-HIV-1 activity. Compound 1 showed modest cytotoxic activity. The other compounds also showed weak cytotoxic activity.

Flexible catalytic site conformations implicated in modulation of HIV-1 protease autoprocessing reactions

BACKGROUND

The HIV-1 protease is initially synthesized as part of the Gag-Pol polyprotein in the infected cell. Protease autoprocessing, by which the protease domain embedded in the precursor catalyzes essential cleavage reactions, leads to liberation of the free mature protease at the late stage of the replication cycle. To examine autoprocessing reactions in transfected mammalian cells, we previously described an assay using a fusion precursor consisting of the mature protease (PR) along with its upstream transframe region (p6*) sandwiched between GST and a small peptide epitope.

RESULTS

In this report, we studied two autoprocessing cleavage reactions, one between p6* and PR (the proximal site) and the other in the N-terminal region of p6* (the distal site) catalyzed by the embedded protease, using our cell-based assay. A fusion precursor carrying the NL4-3 derived protease cleaved both sites, whereas a precursor with a pseudo wild type protease preferentially autoprocessed the proximal site. Mutagenesis analysis demonstrated that several residues outside the active site (Q7, L33, N37, L63, C67 and H69) contributed to the differential substrate specificity. Furthermore, the cleavage reaction at the proximal site mediated by the embedded protease in precursors carrying different protease sequences or C-terminal fusion peptides displayed varied sensitivity to inhibition by darunavir, a catalytic site inhibitor. On the other hand, polypeptides such as a GCN4 motif, GFP, or hsp70 fused to the N-terminus of p6* had a minimal effect on darunavir inhibition of either cleavage reaction.

CONCLUSIONS

Taken together, our data suggest that several non-active site residues and the C-terminal flanking peptides regulate embedded protease activity through modulation of the catalytic site conformation. The cell-based assay provides a sensitive tool to study protease autoprocessing reactions in mammalian cells.

Looking at the proteases from a simple perspective

Proteases have received enormous interest from the research and medical communities because of their significant roles in several human diseases. Some examples include the involvement of thrombin in thrombosis, HIV-1 protease in Acquired Immune Deficiency Syndrome, cruzain in Trypanosoma cruzi infection, and membrane-type 1 matrix metalloproteinase in tumor invasion and metastasis. Many efforts has been undertaken to design effective inhibitors featuring potent inhibitory activity, specificity, and metabolic stability to those proteases involved in such pathologies. Protease inhibitors usually target the active site, but some of them act by other inhibitory mechanisms. The understanding of the structure-function relationships of proteases and inhibitors has an impact on new inhibitor drugs designing. In this paper, the structures of four proteases (thrombin, HIV-protease, cruzain, and a matrix metalloproteinase) are briefly reviewed, and used as examples of the importance of proteases for the development of new treatment strategies, leading to a longer and healthier life.

Formal Total Synthesis of the Potent Renin Inhibitor Aliskiren: Application of a SmI2-Promoted Acyl-like Radical Coupling

A formal total synthesis of the potent renin inhibitor aliskiren is disclosed exploiting an alternative coupling strategy recently developed by this laboratory for the preparation of the hydroxyethylene isostere-based class of protease inhibitors. The thioester derivative of the amino acid representing the C5-C9 fragment of the aliskiren carbon skeleton underwent a carbon chain extension via a SmI2-promoted radical addition to n-butyl acrylate. Introduction of the C3-isopropyl group with the correct relative configuration was accomplished via stereoselective reduction of the obtained ketone with concomitant lactonization, followed by an aldol reaction with acetone. Further functional group and protecting group manipulation culminated in a formal total synthesis of aliskiren in 10 steps from the corresponding fully protected non-natural amino acid.

HIV protease inhibitors: synthesis and activity of N-aryl-N'-hydroxyalkyl hydrazide pseudopeptides

We describe the synthesis and activities of a series of pseudopeptides containing an N-aryl-N'-hydroxyalkyl hydrazide core structure to inhibit human immunodeficiency virus protease and viral replication. Of the series, compound Hmb-Leu-N(Bzl)-N(CH2-CH-OH)-rPro-Boc (24) displayed the greatest inhibitory potency (IC50 < 1 microM) and exhibited enzymatic resistance and stability in vitro.

2-Pyrone natural products and mimetics: isolation, characterisation and biological activity

The review summarises natural products containing the 2-pyrone moiety. An emphasis has been placed upon the biological activity associated with 2-pyrones, particularly with respect to potential therapeutic or anti-microbial agents. Where appropriate, non-natural 2-pyrone analogues are discussed, particularly those derived from natural product lead compounds.

Topological models for the prediction of HIV-protease inhibitory activity of tetrahydropyrimidin-2-ones

Relationship between the topological indices and HIV-protease inhibitory activity of tetrahydropyrimidine-2-ones has been investigated. Three topological indices, Wiener's index--a distance based topological descriptor, Zagreb group parameter--an adjacency based topological descriptor and eccentric connectivity index--an adjacency-cum-distance based topological descriptor were used for the present investigations. A dataset comprising of 80 substituted tetrahydropyrimidine-2-one analogues was selected for the present studies. The values of the Wiener's index, Zagreb group parameter and eccentric connectivity index for each of the 80 compounds comprising the dataset were computed using an in-house computer program. The dataset was divided randomly into training and test sets. Resultant data was analyzed and suitable models were developed after identifying the active ranges in the training set. Subsequently, a biological activity was assigned to each of the compound involved in the test set using these models, which was then compared with the reported HIV-protease inhibitory activity. Accuracy of prediction using these models was found to vary from a minimum of approximately 86% to a maximum of approximately 88%.

QSAR modelling of HIV-1 reverse transcriptase inhibition by benzoxazinones using a combination of P_VSA and pharmacophore feature descriptors

In pursuit of better anti-HIV drugs, a quantitative structure-activity relationship analysis using a novel set of 2D descriptors was performed on a series of HIV-1 reverse transcriptase inhibitory benzoxazinones. The QSAR models derived from the above mentioned descriptors were found to be statistically significant and exhibited superior predictive power. The results of the study justify the application of the descriptors for exploring the binding mode of the benzoxazinones to the enzyme.

Inhibition of phosphate transport in rat heart mitochondria by 3'-azido-3'-deoxythymidine due to stimulation of superoxide anion mitochondrial production

In order to gain some insight into the mechanism by which 3'-azido-3'-deoxythymidine (AZT) damages mitochondria, we investigated whether externally added AZT can stimulate reactive oxygen species (ROS) production by rat heart mitochondria (RHM). An increase in superoxide anion ((O(2)(.-)) production was measured in RHM added with AZT, by using a photometrically method which allows an early O(2)(.-) detection by following the absorbance increase at 550 nm due to the ferricytochrome c reduction. Such an increase was found to be prevented from externally added superoxide dismutase. The stimulation of O(2)(.-) mitochondrial production induced by AZT was found to occur under conditions in which mitochondrial oxygen consumption was prevented by both inhibitors of electron flow and ATP synthesis. Since ROS can cause mitochondrial carrier impairment, we investigated whether AZT can affect mitochondrial permeability in virtue of its capability to stimulate ROS production. In this regard, we studied the transport of phosphate (P(i)), by measuring the mitochondrial shrinkage that takes place as a result of P(i) uptake by RHM previously swollen in a calcium acetate medium. As a result of the AZT-dependent O(2)(.-) production, uncompetitive inhibition of the rate of P(i) transport in RHM was found (K(i) of about 10 microM), consistently, such an inhibition was found to prevent by certain known ROS scavengers, i.e. superoxide dismutase, the antioxidant Vitamin C and reduced gluthatione.

Synthesis of prodrug candidates: conjugates of amino acid with nucleoside boranophosphate

[structure: see text] Preparation of antiviral and anticancer prodrug candidates, P-tyrosinyl(P-O)-5'-P-nucleosidyl boranophosphates, is described. One-pot synthesis via a phosphoramidite method resulted in the title compounds with good yields. The P-boranophosphate diastereomers were separated by RP-HPLC, and their structures were confirmed by 1H and 31P NMR spectroscopy and MS analysis.

HIV-1 protease inhibitors containing an N-Hydroxyamino acid core structure

Two series of peptidomimetics containing an N-hydroxyamino acid core structure were prepared by mixed solution solid-phase synthesis and tested for inhibitory activity against the human immunodeficiency virus (HIV-1) protease (Pr) and the virus in cell culture. In general, N-hydroxy Gly containing pseudopeptides displayed modest HIV Pr inhibition (IC50 > or = 930 nM). In the N-hydroxy Phe derivatives, Fmoc-Phe-psi[CO-N(OH)]-Phe-Pro-NHtBu was the best inhibitor of the series (IC50 = 144nM) showing satisfactory inhibition of HIV replication in cell culture (ED50 = 98 nM) and remarkable stability against cell culture and plasma enzymes.

Synthesis and biological evaluation of prodrug-type anti-HIV agents: ester conjugates of carboxylic acid-containing dipeptide HIV protease inhibitors and a reverse transcriptase inhibitor

On the basis of substrate transition-state mimic concept of HIV protease, a series of small-sized dipeptide inhibitors containing hydrophilic carboxyl group were designed and synthesized. These dipeptide inhibitors showed good HIV protease inhibitory activity, but their anti-HIV activity was poor. The low antiviral activities of these inhibitors were probably due to their inadequate cell membrane permeability caused by the presence of a free carboxylic acid in the inhibitors. Based on the prodrug concept as well as the combination of two different classes of anti-HIV agents, conjugates of HIV protease inhibitors with a nucleoside reverse transcriptase inhibitor were synthesized. Some of these conjugates exhibited excellent antiviral activity compared with that of individual inhibitors. The synergistic enhancement of anti-HIV activities of these conjugates may be due to their ability to penetrate into the target cell and subsequent regeneration of two different classes of anti-HIV agents in the cytoplasm.

Syntheses of FDA Approved HIV Protease Inhibitors

The treatment of HIV and AIDS was revolutionized by the introduction of peptidomimetic aspartyl protease inhibitors. One of the major limitations of this type of therapy is that higher therapeutic doses are necessary because of the presence of 'peptide-like' features in the drugs. Therefore, adequate supplies and cost effective syntheses of these drugs are of utmost importance. To date, there are six protease inhibitors approved by the United States Food and Drug Administration (FDA) for the treatment of HIV and AIDS. This review focuses on the published syntheses of currently FDA approved HIV protease inhibitor drugs, their isosteres and ligands.

In search of an enzyme: the beta-secretase of Alzheimer's disease is an aspartic proteinase

The deposition of beta-amyloid (Abeta) in the brain is a neuropathological feature of Alzheimer's disease. Abeta is cleaved from its precursor protein (APP) by processing at its N and C termini by enzymes known as beta- and gamma-secretases,respectively. The identity of these enzymes has been elusive but the search for the N-terminal secretase might have ended recently with the almost simultaneous publication by five major laboratories claiming a transmembrane aspartic proteinase to be the long sought after beta-secretase. Even at this early stage of its characterization, this aspartic proteinase fulfils many of the key criteria necessary for beta-secretase. The race is now on to develop inhibitors that could prove effective in halting the progression of Alzheimer's disease.

Structural and biochemical studies of retroviral proteases

Retroviral proteases form a unique subclass of the family of aspartic proteases. These homodimeric enzymes from a number of viral sources have by now been extensively characterized, both structurally and biochemically. The importance of such knowledge to the development of new drugs against AIDS has been, to a large extent, the driving force behind this progress. High-resolution structures are now available for enzymes from human immunodeficiency virus types 1 and 2, simian immunodeficiency virus, feline immunodeficiency virus, Rous sarcoma virus, and equine infectious anemia virus. In this review, structural and biochemical data for retroviral proteases are compared in order to analyze the similarities and differences between the enzymes from different sources and to enhance our understanding of their properties.

Conformational homogeneity in molecular recognition by proteolytic enzymes

Crystal structures for several hundred protease-inhibitor complexes have been analysed and their superimpositions have been used to demonstrate a universal relationship between inhibitor/substrate conformation and molecular recognition by all aspartic, serine, cysteine and metallo proteases. Proteases universally recognize an extended beta strand conformation in all their peptidic (and non-peptidic) inhibitors and substrate analogues without significant exceptions. This conformational homogeneity is illustrated here for a subset of 180 protease-inhibitor structures which are displayed as (a) structural overlays of multiple inhibitors for each of eight aspartic, eight serine, six metallo and five cysteine proteases; (b) single inhibitors each bound to different proteases; and (c) Ramachandran plots of peptide or pseudo-peptide dihedral angle pairs which demonstrate beta strands (Phi -54 degrees to -173 degrees, Psi 24 degrees to 174 degrees ) like those normally found paired in proteins as beta sheets. However, unlike beta sheets, alpha and 3(10) helices, beta and gamma turns, where the folded main chain amide components are intramolecularly hydrogen bonded and thus unavailable for interaction with proteins, an inhibitor/substrate in an isolated beta strand conformation provides maximum exposure of its hydrogen bonding donors/acceptors and side chain components to a putative protease receptor. This analysis highlights the advantages of a strand conformation over other elements of secondary structure for protease recognition and may lead to generic strategies for inhibitor design.

Role of pharmacokinetics in the discovery and development of indinavir

The discovery of indinavir is a successful example in which pharmacokinetic and metabolic information were incorporated into drug design. The use of animal and in vitro human metabolic data in predicting the oral bioavailability and hepatic clearance in humans was critical in selecting indinavir as a drug candidate for development. In its development stage, pharmacokinetics continued to play an important role in identifying the key properties of indinavir in vivo, which allowed the characterization and prediction of the time course of drug action under physiological and pathological conditions. This review describes the role of pharmacokinetics and drug metabolism in the discovery and development of indinavir.

Transferrin trojan horses as a rational approach for the biological delivery of therapeutic peptide domains

One novel approach for the biological delivery of peptide drugs is to incorporate the sequence of the peptide into the structure of a natural transport protein, such as human serum transferrin. To examine whether this is feasible, a peptide sequence cleavable by the human immunodeficiency virus type 1 protease (VSQNYPIVL) was inserted into various regions of human serum transferrin, and the resultant proteins were tested for function. Experimentally, molecular modeling was used to identify five candidate insertion sites in surface exposed loops of human serum transferrin that were distant from biologically active domains. These insertions were cloned using polymerase chain reaction mutagenesis, and the proteins were expressed using a baculovirus expression vector system. Analysis of the mutant proteins provided a number of important findings: (a) they retained native human serum transferrin function, (b) the inserted peptide sequence was surface exposed, and most importantly, (c) two of these mutants could be cleaved by human immunodeficiency virus-1 protease. In conclusion, this investigation has validated the use of human serum transferrin as a carrier protein for functional peptide domains introduced into its structure using protein engineering. These findings will be useful for developing a novel class of therapeutic agents for a broad spectrum of diseases.

Quantitative structure-activity relationships of some HIV-protease inhibitors

A quantitative structure-activity relationship (QSAR) study has been made on different series of cycloalkylpyranones acting as human-immunodeficiency-virus type 1 (HIV-1) protease inhibitors. The results suggest that the enzyme binding affinity of the compounds would be favoured by a cyclooctyl ring, a 3-cyclopropylphenylmethyl substituent at the pyranone ring, and a 4-CN-2-pyridine-, an N-Me-imidazole-, or a 3- or 4-CN-phenyl-sulfonamide group at the meta position of the phenyl ring of the 3-substituent.

Symmetry-based inhibitors of HIV-1 protease. Design, synthesis and preliminary structure-activity studies of acylated 2,3-diamino-1-hydroxypropanes and 2,4 diamino-1-hydroxybutanes

Two series of peptidomimetics containing a novel C(2) pseudosymmetrical hydroxyalkyldiamino core structure were prepared from amino acid starting materials and tested for inhibitory activity against the HIV-1 protease (HIV-1 Pr) and the virus in cell culture. In the 2,3-diamino-1-hydroxypropane series, compound 6a, containing P1/P1(I) benzyl and P2/P2(I) Fmoc substituents, displayed modest HIV-1 Pr inhibition (IC(50) = 430 nM). The corresponding 2,4-diamino-1-hydroxybutane derivative (6b) was the best inhibitor of the series (IC(50) = 160 nM). Interestingly, 6a and 6b showed satisfactory inhibition of HIV replication in cell culture (ED(50) = 340 and 110 nM, respectively), a result which suggests good cell membrane penetration by this class of compounds.

Coevolution and subsite decomposition for the design of resistance-evading HIV-1 protease inhibitors

Drug resistance sharply limits the effectiveness of human immunodeficiency virus (HIV) protease inhibitors in acquired immunodeficiency syndrome therapy. In previous work, we presented methods for design of resistance-evading inhibitors using a computational coevolution technique. Here, we report subsite decomposition experiments that examine the relative importance and roles of each subsite in HIV protease, and the constraints on robust inhibitor design that are imposed by possible resistance mutations in each subsite. The results identify several structural features of robust resistance-evading inhibitors for use in drug design, and show their basis in the constraints imposed by the range of allowable mutation in the protease. In particular, the results identify the P3 and P3' sites as being particularly sensitive to protease mutation: inhibitors designed to fill the S3 and S3' sites of the wild-type protease will be susceptible to viral resistance, but inhibitors with side-chains smaller than a phenylalanine residue at P3 and P3', preferably medium-sized amino acids in the range from valine to leucine and isoleucine residues, will be more robust in the face of protease resistance mutation.

Coevolutionary analysis of resistance-evading peptidomimetic inhibitors of HIV-1 protease

We have developed a coevolutionary method for the computational design of HIV-1 protease inhibitors selected for their ability to retain efficacy in the face of protease mutation. For HIV-1 protease, typical drug design techniques are shown to be ineffective for the design of resistance-evading inhibitors: An inhibitor that is a direct analogue of one of the natural substrates will be susceptible to resistance mutation, as will inhibitors designed to fill the active site of the wild-type or a mutant enzyme. Two design principles are demonstrated: (i) For enzymes with broad substrate specificity, such as HIV-1 protease, resistance-evading inhibitors are best designed against the immutable properties of the active site-the properties that must be conserved in any mutant protease to retain the ability to bind and cleave all of the native substrates. (ii) Robust resistance-evading inhibitors can be designed by optimizing activity simultaneously against a large set of mutant enzymes, incorporating as much of the mutational space as possible.

Asymmetric dihydroxylation route to a dipeptide isostere of a protease inhibitor: enantioselective synthesis of the core unit of ritonavir

An enantioselective synthesis of the dipeptide isostere of ritonavir has been accomplished utilizing Sharpless asymmetric hydroxylation as the key step.

A quantitative structure-activity relationship study on some sulfolanes and arylthiomethanes acting as HIV-1 protease inhibitors

A quantitative structure-activity relationship (QSAR) study on some sulfolanes and arylthiomethanes acting as human immunodeficiency virus-1 (HIV-1) protease inhibitors reveals that in the case of sulfolanes an octahydropyrindene ring and a five-membered 3(S)-sulfolane ring with a hydrophobic 2-substituent (cis to 3-substituent) will be crucial for the inhibition activity. The binding of a sulfolane, which is a nonpeptidic molecule, with the enzyme is shown to partly mimic the binding of a peptidic inhibitor. The 2-substituent is found to have strong hydrophobic interaction with the receptor. Similarly, in the case of arylthiomethanes, one of the substituents of the methane is found to have strong hydrophobic interaction with the enzyme, while the aryl substituent (4-hydroxy-6-phenyl-2-oxo-2H-pyran-3-yl) is assumed to be involved in the hydrogen bondings.

Mitochondrial sensitivity to AZT

The possibility of tissue-specific effects regarding mitochondrial sensitivity to AZT was evaluated in this study. When mitochondria isolated from liver, kidney, skeletal and cardiac muscle were oxidizing glutamate, a dose-dependent inhibition by AZT of state 3 respiration was observed; using succinate as substrate the inhibition occurred only in skeletal and cardiac muscle mitochondria. The same results were obtained with FCCP-uncoupled mitochondria. NADH oxidase of intact and disrupted mitochondria, isolated from all four tissues was strongly inhibited. Succinate oxidase activity was inhibited by AZT only in intact mitochondria from skeletal and cardiac muscles, suggesting the involvement of succinate transport systems. Similarly, inhibition by the drug of the hydrolytic activity of H(+)-ATPase was observed only in mitochondria of these tissues. These effects taken together, indicate a tissue/carrier-specific inhibition in vitro, although its precise mechanism requires further research.

Molecular recognition of cyclic urea HIV-1 protease inhibitors

As long as the threat of human immunodeficiency virus (HIV) protease drug resistance still exists, there will be a need for more potent antiretroviral agents. We have therefore determined the crystal structures of HIV-1 protease in complex with six cyclic urea inhibitors: XK216, XK263, DMP323, DMP450, XV638, and SD146, in an attempt to identify 1) the key interactions responsible for their high potency and 2) new interactions that might improve their therapeutic benefit. The structures reveal that the preorganized, C2 symmetric scaffolds of the inhibitors are anchored in the active site of the protease by six hydrogen bonds and that their P1 and P2 substituents participate in extensive van der Waals interactions and hydrogen bonds. Because all of our inhibitors possess benzyl groups at P1 and P1', their relative binding affinities are modulated by the extent of their P2 interactions, e.g. XK216, the least potent inhibitor (Ki (inhibition constant) = 4.70 nM), possesses the smallest P2 and the lowest number of P2-S2 interactions; whereas SD146, the most potent inhibitor (Ki = 0.02 nM), contains a benzimidazolylbenzamide at P2 and participates in fourteen hydrogen bonds and approximately 200 van der Waals interactions. This analysis identifies the strongest interactions between the protease and the inhibitors, suggests ways to improve potency by building into the S2 subsite, and reveals how conformational changes and unique features of the viral protease increase the binding affinity of HIV protease inhibitors.

In vitro selection and characterization of VX-478 resistant HIV-1 variants

VX-478 (141W94), a potent inhibitor of HIV protease, is in late stage clinical trials for the treatment of HIV infection and AIDS. Resistant viruses were raised in vitro by passage of HIV-1IIIB in the presence of increasing concentrations of VX-478 and the related hydroxyethylamino sulfonamide inhibitor VB-11,328. By direct PCR analysis of selected viruses, a number of mutations were identified (L10F, M46I, I47V, I50V and I84V) in the protease gene. These mutations were introduced into recombinant HIV-1 protease and the mutant enzymes assayed against a panel of inhibitors of diverse chemical structure. For VX-478, significant increases in IC90 and Ki were observed for virus or protease, respectively, containing I50V single mutation or an M46I/I47V/I50V triple mutation. The mutant proteases were also characterized for their kinetic competence to process substrates representing cleavage sites of gag-pol viral polypeptide. The kinetic data were interpreted with the aid of molecular modeling to understand the effect of mutations on inhibitor binding and processing of the gag-pol polypeptide to generate infective virions.

Inhibition of HIV-1 protease by water-soluble lignin-like substance from an edible mushroom, Fuscoporia obliqua

Activity that inhibited protease of human immunodeficiency virus type 1 was found in boiling water extracts of an edible mushroom, Fuscoporia obliqua. The active component was identified as a water-soluble lignin derivative of high molecular weight. Other polyphenols of low molecular weight and monomeric components of lignin did not inhibit the protease.

Computational coevolution of antiviral drug resistance

An understanding of antiviral drug resistance is important in the design of effective drugs. Comprehensive features of the interaction between drug designs and resistance mutations are difficult to study experimentally because of the very large numbers of drugs and mutants involved. We describe a computational framework for studying antiviral drug resistance. Data on HIV-1 protease are used to derive an approximate model that predicts interaction of a wide range of mutant forms of the protease with a broad class of protease inhibitors. An algorithm based on competitive coevolution is used to find highly resistant mutant forms of the protease, and effective inhibitors against such mutants, in the context of the model. We use this method to characterize general features of inhibitors that are effective in overcoming resistance, and to study related issues of selection pathways, cross-resistance, and combination therapies.

Human immunodeficiency virus protease inhibitors. From drug design to clinical studies

The discovery of human immunodeficiency virus (HIV) protease inhibitors is an example in which pharmacokinetic evaluation was implemented early in the discovery phase to obtain optimal pharmacological and pharmacokinetic properties. Currently, three HIV protease inhibitors, saquinavir, indinavir and ritonavir are clinically available. As a family, these HIV protease inhibitors are characterized pharmacologically by their ability to inhibit the viral protease enzyme. Pharmacokinetically, they are quite different due to their dissimilarity in physicochemical properties. Bioavailability appears to be limited with saquinavir, but not with indinavir and ritonavir. Although all three drugs are metabolized extensively by cytochrome P-450, saquinavir and indinavir are high clearance drugs while ritonavir is a low clearance drug. Despite their significant differences in elimination clearance, all three HIV proteases are given at high oral doses (600-800 mg) either twice or three times daily. These HIV protease inhibitors show superior therapeutic activity and a more favorable safety profile than those reported for the established reverse transcriptase inhibitors. However, the potential for interactions with other drugs metabolized by the CYP 3A4 isoform appears to be considerable. In addition, repeated administration of enzyme inducers results in a substantial decrease of plasma concentrations of protease inhibitors. Therefore, co-administration of drugs, such as rifampicin and rifabutin, must be avoided. HIV protease inhibitors are promising in the treatment of AIDS. Although they are not a cure, they can significantly inhibit that viral replication and improve the quality of life for people who have HIV infection.

Drug resistance during indinavir therapy is caused by mutations in the protease gene and in its Gag substrate cleavage sites

Two different responses to the therapy were observed in a group of patients receiving the protease inhibitor indinavir. In one, suppression of virus replication occurred and has persisted for 90 weeks (bDNA, < 500 human immunodeficiency virus type 1 [HIV-1] RNA copies/ml). In the second group, a rebound in virus levels in plasma followed the initial sharp decline observed at the start of therapy. This was associated with the emergence of drug-resistant variants. Sequence analysis of the protease gene during the course of therapy revealed that in this second group there was a sequential acquisition of protease mutations at amino acids 46, 82, 54, 71, 89, and 90. In the six patients in this group, there was also an identical mutation in the gag p7/p1 gag protease cleavage site. In three of the patients, this change was seen as early as 6 to 10 weeks after the start of therapy. In one patient, a second mutation occurred at the gag p1/p6 cleavage site, but it appeared 18 weeks after the time of appearance of the p7/p1 mutation. Recombinant HIV-1 variants containing two or three mutations in the protease gene were constructed either with mutations at the p7/p1 cleavage site or with wild-type (WT) gag sequences. When recombinant HIV-1-containing protease mutations at 46 and 82 was grown in MT2 cells, there was a 68% reduction in its rate of replication compared to the WT virus. Introduction of an additional mutation at the gag p7/p1 protease cleavage site compensated for the partially defective protease gene. Similarly, rates of replication of viruses with mutations M46L/I, I54V, and V82A in protease were enhanced both in the presence and in the absence of Indinavir when combined with mutations in the gag p7/p1 and the gag p1/p6 cleavage sites. Optimal rates of virus replication require protease cleavage of precursor polyproteins. A mutation in the cleavage site that enhanced the availability of a protein that was rate limiting for virus maturation would confer on that virus a significant growth advantage and may explain the uniform emergence of viruses with alterations at the p7/p1 cleavage site. This is the first report of the emergence of mutations in the gag p7/p1 protease cleavage sites in patients receiving protease therapy and identifies this change as an important determinant of HIV-1 resistance to protease inhibitors in patient populations.

Quantitative determination of CGP 61755, a protease inhibitor, in plasma and urine by high-performance liquid chromatography and fluorescence detection

A liquid chromatographic assay for the determination of CGP 61755 (I) in plasma and urine is described. A similar method for CGP 53437, another HIV-1 protease inhibitor, has been developed and reported previously. After a deproteinization step, a liquid-liquid extraction is performed. Compound I and the internal standard CGP 55749 (II) are hydrolyzed and the primary amine group derivatized using fluorescamine. Chromatography is achieved by isocratic elution with a mobile phase of 30 mM borax buffer (pH 9)-acetonitrile (58:42, v/v). The derivatives of the compounds I and II fluoresce at 480 nm, on excitation at 395 nm and the retention times under these conditions were approximately 6 and 8 min, respectively. The limit of quantitation (LOQ) which is the lowest concentration of the analyte that can be measured with a coefficient of variation and a deviation from theory of less than 20%, was 15 ng/ml plasma and 20 ng/ml urine. The analyte is stable for at least four months in human plasma and sixteen months in dog plasma samples. Different human plasma sources and three different species (rat, rabbit and dog) were tested and no interference between analyte and plasma constituents was observed.