The site of attachment in human rhinovirus 14 for antiviral agents that inhibit uncoating.

WIN 51711 and WIN 52084 are structurally related, antiviral compounds that inhibit the replication of rhino (common cold) viruses and related picornaviruses. They prevent the pH-mediated uncoating of the viral RNA. The compounds consist of a 3-methylisoxazole group that inserts itself into the hydrophobic interior of the VP1 beta-barrel, a connecting seven-membered aliphatic chain, and a 4-oxazolinylphenoxy group (OP) that covers the entrance to an ion channel in the floor of the "canyon." Viral disassembly may be inhibited by preventing the collapse of the VP1 hydrophobic pocket or by blocking the flow of ions into the virus interior.

Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors.

Mechanistic information and structure-based design methods have been used to design a series of nonpeptide cyclic ureas that are potent inhibitors of human immunodeficiency virus (HIV) protease and HIV replication. A fundamental feature of these inhibitors is the cyclic urea carbonyl oxygen that mimics the hydrogen-bonding features of a key structural water molecule. The success of the design in both displacing and mimicking the structural water molecule was confirmed by x-ray crystallographic studies. Highly selective, preorganized inhibitors with relatively low molecular weight and high oral bioavailability were synthesized.

Improved cyclic urea inhibitors of the HIV-1 protease: synthesis, potency, resistance profile, human pharmacokinetics and X-ray crystal structure of DMP 450.

BACKGROUND: Effective HIV protease inhibitors must combine potency towards wild-type and mutant variants of HIV with oral bioavailability such that drug levels in relevant tissues continuously exceed that required for inhibition of virus replication. Computer-aided design led to the discovery of cyclic urea inhibitors of the HIV protease. We set out to improve the physical properties and oral bioavailability of these compounds. RESULTS: We have synthesized DMP 450 (bis-methanesulfonic acid salt), a water-soluble cyclic urea compound and a potent inhibitor of HIV replication in cell culture that also inhibits variants of HIV with single amino acid substitutions in the protease. DMP 450 is highly selective for HIV protease, consistent with displacement of the retrovirus-specific structural water molecule. Single doses of 10 mg kg-1 DMP 450 result in plasma levels in man in excess of that required to inhibit wild-type and several mutant HIVs. A plasmid-based, in vivo assay model suggests that maintenance of plasma levels of DMP 450 near the antiviral IC90 suppresses HIV protease activity in the animal. We did identify mutants that are resistant to DMP 450, however; multiple mutations within the protease gene caused a significant reduction in the antiviral response. CONCLUSIONS: DMP 450 is a significant advance within the cyclic urea class of HIV protease inhibitors due to its exceptional oral bioavailability. The data presented here suggest that an optimal cyclic urea will provide clinical benefit in treating AIDS if it combines favorable pharmacokinetics with potent activity against not only single mutants of HIV, but also multiply-mutant variants.

In vitro susceptibility of clinical isolates of HIV-1 to XM323, a non-peptidyl HIV protease inhibitor.

OBJECTIVE: To determine the in vitro susceptibility of primary clinical isolates and laboratory strains of HIV-1 to XM323. METHODS: The AIDS Clinical Trials Group/US Department of Defense p24 antigen-based consensus assay was used to determine in vitro susceptibility of 57 primary clinical isolates and three laboratory strains of HIV-1 to XM323, zidovudine, zalcitabine (ddC), and didanosine (ddI). RESULTS: The concentrations of compound required to inhibit viral p24 antigen production by 50% [median inhibitory concentration (IC50)] for nucleosides were as follows: zidovudine, 0.001-->5 microM; ddC, < 0.01-0.23 microM; ddI, 0.2-->25 microM). Against both nucleoside susceptible and resistant isolates XM323 exhibited potent inhibition with IC50 values of < 0.02-0.27 microM and IC90 values of 0.03-1.17 microM. CONCLUSIONS: XM323 is a potent inhibitor of diverse clinical isolates of HIV-1 in vitro and represents a novel class of non-peptidyl inhibitors of HIV-1 protease.

[[(4,5-Dihydro-2-oxazolyl)phenoxy]alkyl]isoxazoles. Inhibitors of picornavirus uncoating.

A series of [[(4,5-dihydro-2-oxazolyl)phenoxy]alkyl]isoxazoles has been synthesized and evaluated as antipicornavirus agents. The effect of alkyl groups in the 4- and 5-position of the oxazoline ring, as well as the alkyl chain length, on antiviral activity was examined. Compound 14 was evaluated in vivo and was found to significantly reduce mortality at an oral dose of 4 mg/kg in mice infected intracerebrally with poliovirus-2. Compound 14 was also effective in preventing paralysis when administered intraperitoneally to mice infected subcutaneously with a lethal dose of ECHO-9 virus. On the basis of the results of these studies, compound 14 is a strong candidate for clinical evaluation as a systemic agent for the treatment of picornavirus infections.

Enantiomeric effects of homologues of disoxaril on the inhibitory activity against human rhinovirus-14.

X-ray crystallography studies of racemic 5-[7-[4-(4,5-dihydro-4-methyl-2-oxazolyl)phenoxy]heptyl]- 3-methylisoxazole bound to human rhinovirus-14 (HRV-14) indicate selective binding of the S isomer. This result correlates well with the 10-fold greater activity of the S isomer as compared to the R isomer. The enantiomeric effect on activity is explained by a hydrophobic interaction of the methyl group in the case of 2a, with a pocket formed by Leu106 and Ser107. The 4-ethyl, 4-propyl, and 4-butyloxazolinyl homologues were prepared and tested against HRV-14. All of these compounds exhibited a comparable stereochemical effect. In each case, the S isomer displayed greater levels of activity than the R. The results of energetic considerations of the oxazoline ring in an 8-A pocket bound to the HRV-14 binding site suggest that the twist angle between the oxazoline and phenyl rings resulting from hydrophobic interactions of the alkyl substituents could be one of the determining factors for biological activity.

Synthesis and structure-activity studies of some disubstituted phenylisoxazoles against human picornavirus.

A number of 2,6-disubstituted analogues of disoxaril, a broad spectrum antipicornavirus agent, have been prepared and evaluated against several rhinovirus serotypes. A QSAR study revealed that the mean MIC (MIC) against five rhinovirus serotypes correlated well with log P. The 2,6-dichloro analogue, 15, was highly effective in vitro against rhinoviruses with an MIC80 of 0.3 microM, as well as against several enteroviruses, and was also effective in preventing paralysis in mice infected with coxsackievirus A-9.

Structure-activity studies of 5-[[4-(4,5-dihydro-2-oxazolyl) phenoxy]alkyl]-3-methylisoxazoles: inhibitors of picornavirus uncoating.

A series of substituted phenyl analogues of 5-[[4-(4,5-dihydro-2-oxazolyl) phenoxy]alkyl]-3-methylisoxazoles has been synthesized and evaluated in vitro against several human rhinovirus (HRV) serotypes. Substituents in the 2-position greatly enhanced activity when compared to the unsubstituted compound. Many of these compounds exhibited mean MICs (MIC) against five serotypes as low as 0.40 microM. The mean MIC correlated well (r = 0.83) with the MIC80 (the concentration that inhibited 80% of the serotypes tested). A quantitative structure-activity relationship study indicated a strong dependency of MIC on lipophilicity (log P) in combination with inductive effects (sigma m) and bulk factors (MW).

Limited sequence diversity of the HIV type 1 protease gene from clinical isolates and in vitro susceptibility to HIV protease inhibitors.

Proviral DNAs from 3 laboratory strains and 21 clinical isolates of HIV-1 were extracted from infected cells after proteinase K digestion and the protease gene was PCR amplified and sequenced directly by the Sanger method. In vitro susceptibilities of the virus isolates to protease inhibitors were determined by the ACTG/DoD consensus assay. Four different HIV protease inhibitors were tested including P9941, a C2 symmetrical diol (Du Pont-Merck); A80987, an asymmetric mono-ol (Abbott); XM323, a cyclic urea (Du Pont-Merck); and Ro31-8959, an asymmetric hydroxyethylene isostere (Roche). Maximum sequence variation was 10% at both the nucleic and amino acid levels. Purine-purine substitutions were most common. Five noncontiguous regions were conserved across all isolates and corresponded to amino acids 1-9 (amino terminal), 21-32 (catalytic site), 47-56 ("flap" region), 78-88 (substrate-binding region), and 94-99 (carboxy terminal). All clinical isolates demonstrated in vitro susceptibility to the protease inhibitors. There was no significant difference between the susceptibility of the reference strains and the clinical isolates. These data suggest that the variable regions of protease do not contain sites that are important for interactions with the inhibitors tested.

The relationship between the antiviral activity of 5'-amino-5'-deoxythymidine and its incorporation into herpes simplex virus type 1 DNA.

As part of our studies on the molecular basis for the antiherpes activity of 5'-AdThd (5'-amino-5'-deoxythymidine), a study of the HSV-1 DNA synthesized in infected Vero cells exposed to 5'-AdThd was undertaken. Unlike many other antiviral nucleoside analogs, 5'-AdThd did not inhibit HSV-1 DNA synthesis. Analysis of the DNA synthesized in the presence of [14C]5'-AdThd revealed that the analog was incorporated into the viral DNA in a dose-dependent manner and that the degree of incorporation correlated with the antiviral activity as measured by yield reduction assays. Analysis of the 5'-AdThd substituted DNA by centrifugation in neutral and alkaline sucrose gradients revealed no double-stranded breaks but an increase in single-stranded breaks, at very high concentrations of the analog. Analysis of HSV-1-specific RNAs revealed a shift from poly(A+) to poly(A-) RNA. The degree of this shift paralleled the substitution of 5'-AdThd for thymidine in the HSV-1 DNA.

Effects of nucleoside analogues on the expression of herpes simplex type 1-induced proteins.

Exposure of herpes simplex virus type 1 (HSV-1)-infected Vero cells to the nucleoside analogues 5-iodo-5'-amino-2',5'-dideoxyuridine (AIdUrd), 5-iodo-2'-deoxyuridine (IdUrd) or 5'-amino-2',5'-dideoxythymidine (5'-AdThd) resulted in altered expression of HSV-1-induced proteins. Infected cell proteins (ICPs) synthesized in the presence of the nucleoside analogues were compared by sodium dodecyl sulphate (SDS) polyacrylamide gel electrophoresis to ICPs from non-drug-treated cells and it was found that there was no effect on HSV-1-induced alpha proteins but beta and gamma proteins were reduced as much as 60%. There were three exceptions: ICP 35 (Mr = 46,000) and ICP 39 (Mr = 36,000) were not reduced and ICP 36 (Mr = 42,000) was increased during drug treatment. Progeny virions were isolated from drug-treated infected Vero cells and were compared to progeny isolated from control cells with respect to their polypeptide make-up and for their ability to induce HSV-1 proteins in non-drug-treated Vero cells. The progeny virus from drug-treated cells exhibited altered protein patterns on SDS-polyacrylamide gels with respect to control HSV-1. The progeny virions from AIdUrd- or IdUrd- but not from 5'-AdThd-treated cells were defective in their abilities to induce proteins upon subsequent infection of non-drug-treated Vero cells. Two unusual phosphoproteins were detected; one with an apparent molecular weight of 30,000 was induced by progeny virus from AIdUrd-treated cells and another at approximately 69,000 was induced by progeny virus from 5'-AdThd-treated cells.

Production of herpes simplex virus type 1 thymidine kinase in the presence of thymidine analogues.

Treatment of herpes simplex virus type 1 (HSV-1) infected Vero, BHK, BHKtk- and LMtk- cells with 5-iodo-5'-amino-2',5'-dideoxyuridine (AIdUrd) caused increased synthesis of ICP36 and an increase in HSV-1 thymidine kinase (tk) activity at late times of infection. The overproduced ICP36 was identified as the HSV-1 encoded tk protein by immunoprecipitation. Whereas the thymidine analogue 5'-amino-5'-deoxythymidine (AdThd) caused an increase in HSV-1 tk synthesis and activity in wild type Vero and BHK cells, 5-iodo-2'-deoxyuridine (IdUrd) caused a similar increase only in tk- cells (LMtk-, BHKtk-). In vivo and in vitro stabilization studies using a [35S]methionine pulse-chase experiment or heat inactivation studies with purified HSV-1 tk revealed that stabilization of tk by the analogues could not account for the extent of the observed increase. Since overproduction of tk is observed only at late times of infection, it is suggested that the presence of these thymidine analogues in either the viral DNA or the cellular nucleotide pools is responsible for the observed differential effects.

Identification of a clinical isolate of HIV-1 with an isoleucine at position 82 of the protease which retains susceptibility to protease inhibitors.

The HIV-1 protease (PR) is essential for the production of mature virions. As such, it has become a target for the development of anti-HIV chemotherapeutics. Multiple passages of virus in cell culture in the presence of PR inhibitors have resulted in the selection of variants with decreased sensitivity to inhibitors of the PR. The most common alteration observed is a single amino acid change at position 82. This particular position has been well characterized by several laboratories as being important for the susceptibility of the virus to inhibitors of PR function. Mutations which result in the substitution of the wild-type valine with alanine, phenylalanine, threonine or isoleucine at position 82 of the PR have been associated with decreased sensitivity to several PR inhibitors. We describe here a clinical strain of HIV-1 that contains an isoleucine at position 82 of the PR instead of the usual valine. This strain is unique in that it was isolated from a patient that was anti-retroviral naive, and in the past, variants at position 82 of the PR have only been found after treatment of patients or cell culture with PR inhibitors. Moreover, this virus remains sensitive to PR inhibitors of the cyclic urea and C-2 symmetrical diol classes.

Physical and biological consequences of incorporation of antiviral agents into virus DNA.

The molecular basis for the antiviral activity is discussed for a variety of nucleoside compounds approved for clinical use in the U.S.A. (5-iodo-2'-deoxyuridine, 5-trifluoromethyl-2'-deoxyuridine, 9-beta-D-arabinofuranosyladenine, 9-(2-hydroxyethoxymethyl)guanine), or in clinical trial (E-5-(2-bromovinyl)-2'-deoxyuridine, 1-(2-deoxy-2-fluoro-beta-D-arabinosyl)-5-iodocytosine, 1-beta-D-ribofuranosyl-1,2,4-triazole-3-carboxamide), or of specific interest to our laboratory (5-iodo-5'-amino-2',5'-dideoxyuridine, 5'-amino-5'-deoxythymidine). The consequence of incorporation of idoxuridine, the 5'-amino analog of thymidine or the 5'-amino analog of idoxuridine into the DNA of herpes simplex virus type 1 on transcription and translation is emphasized.

Recent developments in antiviral chemotherapy.

As can be seen from the preceding brief discussion, the prospects for new antiviral agents for the treatment of viral diseases ranging in severity from the common cold to AIDS appear promising. The latest advances in technologies such as crystallography, genetic engineering, and monoclonal antibodies are all being applied to the discovery of new ways to inhibit virus-specific processes. In addition, the development of diagnostic tests for viral diseases has proceeded at a rapid pace that should facilitate the proper use of the antivirals when they become available. The one lesson that has been learned in the antiviral field over the past decade is that virus-specific inhibitors do exist, and if an essential virus-specific process or protein can be identified, it is likely that a molecule can be found to inhibit or inactivate it.

The hepatitis B virus M539V polymerase variation responsible for 3TC resistance also confers cross-resistance to other nucleoside analogues.

A variant of hepatitis B virus (HBV) containing a Met-to-Val substitution (M539V) in the YMDD motif of the polymerase nucleoside-binding domain exhibited resistance to the cytosine analogue lamivudine (3TC). To determine if the mutation responsible for the M539V polymerase variant affected the sensitivity of the virus to other nucleoside analogues, we constructed a tetracycline-responsive cell line, HepAD79. This cell line is stably transfected with a cDNA copy of the pregenomic RNA of an HBV genome containing an A-to-G mutation in the first position of the polymerase gene codon 539. This mutation results in a Met-to-Val substitution at amino acid 539 of the polymerase. When grown under the proper conditions, HepAD79 cells produced HBV RNA, contained HBV DNA associated with immature core particles and released core-associated HBV DNA into the medium. The M539V polymerase variant produced in this cell line was approximately 26-fold less sensitive to the antiviral effects of 3TC than wild-type virus. In addition, this variant demonstrated decreased sensitivity to the cytosine analogues FTC and ddC, as well as the thymidine analogue AZT.

A rapid microtiter assay for duck hepatitis virus reverse transcriptase.

The duck hepatitis B virus (DHBV) genome contains a pol gene that codes for the viral polymerase protein. This enzyme, which is essential for the replication of the virus, has multiple activities including an RNA directed DNA polymerase or reverse transcriptase (RT) activity, an RNase H activity, and a DNA-directed DNA polymerase activity. The assay described in this chapter is designed to measure the ability of test compounds to inhibit the RNA-directed DNA polymerase activity of the DHBV pol gene product. The assay is based on research performed in the laboratory of Dr. Christoph Seeger (1) and on the observation that the e stem loop structure in the pregenomic RNA is required for initiation of DNA synthesis (2-4).

Molecular characterization of HIV-2 (ROD) protease following PCR cloning from virus infected H9 cells.

A 450 nucleotide sequence corresponding to the nucleotides 1931-2380 of the viral genome (8) was amplified by polymerase chain reaction (PCR) using template DNA prepared from HIV-2 (ROD) infected H9 cells. The sequence codes for HIV-2 protease and its N-terminal flanking peptide. An identical DNA sequence was obtained from three independent PCR amplifications, which differs from the published sequence of HIV-2 (ROD) in 7 nucleotides scattered throughout the region of the cloned DNA. The cloned DNA was expressed in E. coli cells and resulted in the synthesis of a correctly processed HIV-2 protease, which is enzymatically active. Therefore, none of the seven nucleotide changes, which resulted in two amino acid substitutions, affect the autoproteolytic or trans-cleaving activities of the HIV-2 protease.