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Journal of Virology, June 2006, p. 5716-5722, Vol. 80, No. 12
0022-538X/06/$08.00+0 doi:10.1128/JVI.02743-05
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
and
Karl Salzwedel2
Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, Oklahoma City, Oklahoma 73104,1 Panacos Pharmaceuticals, Inc., 209 Perry Parkway, Gaithersburg, Maryland 208772
Received 30 December 2005/ Accepted 23 March 2006
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The central role for Gag and its cleavage product, CA, in viral infectivity has been highlighted recently by the emergence of a potential new class of HIV therapeutic agents, the maturation inhibitors. This new class is typified by the compound 3-O-(3',3'-dimethysuccinyl) betulinic acid, known alternatively as PA-457 (8), DSB (1, 21), or YK-FH312 (6). PA-457 appears to inhibit replication by blocking the very last step in Gag processing, preventing the final product, p24CA, from being liberated by the cleavage of p25CA-p2 (8, 21). The inhibition of only one of the five major cleavage sites in HIV Gag by this compound indicates that it acts not as a traditional enzyme competitive inhibitor but rather likely by direct interaction with the substrate Pr55gag. Evidence to support this unique mechanism of action has come from analyses of resistance mutations that map to the CA-p2 cleavage site (8) and from mutational studies where sensitivity to PA-457 was conferred by the substitution of the cleavage site region sequence from HIV into that of simian immunodeficiency virus (9, 19), which would otherwise be resistant. Uniquely, it appeared that PA-457 activity was dependent not merely upon the cleavage site sequence but also upon the higher-order structure of the molecule, since recombinant Gag protein in solution proved to be resistant to PA-457 in an in vitro processing assay (8).
Utilizing a system whereby the Gag protein is properly assembled into immature particle structures, we have developed an in vitro assay for PA-457 activity, confirmed the requirement for a higher-order Gag structure, and shown the assay to be specific for the active form of the drug. In addition, we have also used this system to evaluate a panel of Gag mutants that have been shown to display a range of resistance in culture assays. Previous analysis of one mutant, A1V, indicated a significantly increased rate of CA-p2 cleavage (9). However, our results from the in vitro analysis indicate that resistance to PA-457 does not precisely correlate with the inherent cleavage rate of the mutant sequence.
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, pDABCh3.I13
, and pDABCh3.M14
were all similarly constructed by subcloning the same SpeI-to-ApaI fragment from pNL4-3/L231C, pNL4-3/
T8, pNL4-3/
I13, and pNL4-3/
M14, respectively. Drugs. PA-457 (PA103001), also known as DSB (21), was dissolved in dimethyl sulfoxide (DMSO) to a concentration of 10 mM. Serial dilutions of this stock in DMSO were made to the appropriate concentration such that the addition of 1 µl to a processing reaction mixture would yield the indicated final drug concentration. Indinavir was similarly dissolved in DMSO and diluted for use.
In vitro production of assembled Gag. Transcription and translation were performed sequentially using the Single Tube Protein System 3 (Novagen) in the presence of [35S]methionine and programmed with the pDABCh series plasmids. Products of these synthesis reactions were analyzed on sucrose gradients. Reaction mixtures (200 µl) were loaded onto 2.2-ml continuous 30 to 55% (wt/wt) sucrose gradients in buffer containing 20 mM Tris (pH 8.0), 100 mM NaCl, 5 mM EDTA, and 0.1% Triton X-100. Gradients were centrifuged in a TLS-55 rotor (Beckman Instruments) for 2 h at 55,000 rpm. Fractions of approximately 200 µl were taken by hand with a Pipetman (Gilson) from the top of the gradient. The pellet was resuspended in 200 µl of 55% (wt/wt) sucrose in gradient buffer. Aliquots (10 µl) of each fraction were dissolved in sodium dodecyl sulfate (SDS) sample buffer and then loaded onto an SDS-10% polyacrylamide gel. After electrophoresis, radioactive bands were visualized on a Perkin-Elmer Cyclone Storage Phosphor system. Peak fractions from the gradient containing assembled Gag were pooled for use in processing experiments. Samples of pooled, assembled Gag and unassembled Gag were then run on SDS-15% polyacrylamide gels and quantitated by phosphorimager analysis to measure radioactive units of Gag per microliter in each sample.
Processing of Gag in vitro. Processing of Gag in vitro was performed similarly to the procedure described previously by Pettit et al. (11). Briefly, equivalent amounts of Gag as measured by phoshorimager analysis (typically approximately 10 µl) were diluted into phosphate-buffered saline (pH 7.4) to a final volume of 50 µl in the presence or absence of drug. A varied amount of recombinant HIV-1 protease (Bachem) was added to each reaction mixture, and processing was allowed to proceed for the times indicated at 30°C. After incubation, a 10-µl aliquot of the reaction mixture was removed, dissolved in SDS-polyacrylamide gel electrophoresis (PAGE) protein loading buffer, and frozen on dry ice. Since the initial cleavage of Gag is so rapid, the "time-zero" aliquot was removed before the addition of the protease. Following the time course experiments, a standardized protocol was established using 0.48 µg of protease for 3 h of incubation. Samples were boiled for 5 min and loaded onto SDS-15% PAGE gels. Fixed and dried gels were then exposed to phosphor plates, and the resulting images were analyzed with OptiQuant software (Perkin-Elmer). For inhibition experiments, radioactivity in the p24 and p25 bands was quantified and adjusted for the number of methionines in each protein. The extent of processing in each reaction was compared to the maximum seen in the control no-drug reaction and then represented as the percentage of that maximum.
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FIG. 1. Schematics of Gag polyprotein precursors used in this study. Shown are the Gag proteins of M-PMV, HIV-1, chimera 4 (Ch4), and chimera 3 (Ch3). The shaded regions are the p12 domain, which contains the internal scaffold domain of M-PMV Gag. Domain designations are given by the convention where protein, "p," or phosphoprotein, "pp," is followed by its apparent molecular weight (in thousands) by SDS-PAGE, i.e., "p12" or "pp24." Letter designations conform to the standardized nomenclature for retroviral proteins where MA is the matrix, CA is the capsid, and NC is the nucleocapsid domain. Numbers above each diagram give the amino acid residue number for the start of each domain or the end of the polyprotein.
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FIG. 2. Generation of assembled substrate for processing experiments. Gag proteins were synthesized in a coupled transcription and translation system and incubated for 24 h to allow assembly to occur. (A) Sucrose gradient analysis of chimera 4 assembly. Assembled Gag was fractionated on a 30 to 55% (wt/wt) sucrose gradient, and aliquots of each fraction were electrophoresed on SDS-10% polyacrylamide gels. Gag is marked by its molecular mass of 65 kDa. An approximately 40-kDa internal initiation product is also indicated. Lanes are marked for fraction numbers starting at the top of the gradient (lane 1) to the pellet (lane P). Lane L is an equal representative fraction of the total before loading onto the gradient. (B) Quantitative representation of the gel data. Radioactivities of Gag and the assembly-incompetent 40-kDa protein were quantified by phosphorimager analysis and are represented as a percentage of the total in lanes 1 to 12, plus P.
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FIG. 3. Processing time course of in vitro-synthesized Gag proteins. HIV and chimera 4 Gag proteins were processed in parallel by recombinant HIV-1 protease. The positions of full-length HIV and chimera 4 Gag proteins are indicated by Pr55gag and Pr65gag, respectively. The final matured p24CA and its immediate precursor, p25CA-p2, are indicated. Apparent molecular mass markers (kilodaltons) are given at the left, and times of incubation are given at the tops of the gels.
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100 µM) of PA-457 had nonspecific global effects on processing by protease at all Gag cleavage sites (data not shown).
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FIG. 4. Processing inhibition by PA-457. HIV and assembled chimera 4 (Ch4) Gag proteins were processed in parallel with increasing concentrations of PA-457. (A) The regions of the gels containing p24 and p25 are shown. The micromolar concentration of PA-457 in each reaction is given above the corresponding gel lanes. (B) Quantitative representation of the gel data normalized to the maximum amount of processing seen in the no-drug control.
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Assembled chimera 4, unassembled chimera 4-M185A, and wild-type HIV Gag proteins were compared in parallel (Fig. 5A). Again, the drug appears to have no effect on HIV Gag and, more significantly, no effect upon unassembled chimera 4-M185A, while the proportion of p24CA cleaved from the assembled chimera 4 was reduced in a dose-dependent manner. Quantitation confirmed that the mutant chimera 4 and wild-type HIV Gag proteins are equivalently unaffected by the drug (Fig. 5B). Thus, the ability of PA-457 to block cleavage of p25CA-p2 correlated with the assembly state of Gag rather than with the presence of p12 in the polyprotein.
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FIG. 5. Comparison of processing inhibition for assembled chimera 4 (Ch4) Gag and unassembled HIV and mutant chimera 4 M185A Gag proteins. (A) Portions of gels showing p24 and p25. The concentration of PA-457 is given at the top. (B) Quantitative representation of gel data. Data were analyzed as described in the legend of Fig. 4.
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FIG. 6. Comparison of processing inhibition by PA-457 and the related compound betulinic acid. (A) Portions of gels showing p24 and p25. The concentration of the drug is given at the top. (B) Quantitative representation of gel data. Data were analyzed as described in the legend of Fig. 4.
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FIG. 7. Comparison of processing inhibition by PA-457 and betulinic acid for chimeras 3 and 4. Gels and data were analyzed as described in the legend of Fig. 4.
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T8,
I13, and
M14 (Fig. 8A). In virus replication assays, the deletion mutants displayed a range of sensitivity to PA-457, with
I13 being sensitive,
T8 being partially resistant, and
M14 being completely resistant (9). In contrast, substitution mutant L231C could not be examined in culture assays since it is defective for particle production (9). This mutant was of particular interest in our analysis of the PA-457 mechanism of action not only because it cannot be assayed in a culture system but also because, in contrast to the resistance mutation A1V, which increases the rate of cleavage, this mutation is known to slow cleavage of p2 from CA in an in vitro processing assay (11).
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FIG. 8. Analysis of CA-p2 region mutants. (A) Diagram showing the amino acid sequence of the cleavage site and p2 with the mutants indicated. The symbol denotes a deletion. (B) Portions of gels from representative experiments showing p24 and p25. The concentrations of PA-457 are given at the top of gel panes. (C) Extent of cleavage achieved by standard reaction conditions in the absence of drug. Error bars indicate standard deviations for three replicate experiments for Ch3. T8; four experiments for Ch3.L231C, Ch3.A1V, and Ch3. M14; and six experiments for Ch3 and Ch3. I13. (D) Quantitative representation of inhibition by PA-457 for each mutant. Error bars are standard deviations for replicates as given in panel C.
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M14 being processed completely to p24CA (Fig. 8C). Ch3.
T8 and Ch3.
I13 were processed to an intermediate extent, while Ch3.L231C was processed at only approximately half the rate of the wt (Fig. 8C).
With respect to their resistance to PA-457 in the in vitro assay, the mutants could be classified into two groups compared to the wt sequence: those that were completely resistant (A1V and
M14) and those that were partially resistant (L231C,
T8, and
I13). These results are in rough agreement with those from the culture assays, again with one significant exception. L231C could be assessed only in vitro, and it was partially resistant to PA-457 even though it was processed more slowly. Thus, it appears that resistance to PA-457 does not strictly correlate with the intrinsic rate of cleavage of the mutant Gag.
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In addition to the assembly state of Gag, the assay proved valuable in assessing the relative extent of resistance to the drug by several mutations both developed through virus culture and created through site-directed mutagenesis. Beyond establishing that the in vitro assay reproduced the resistance seen in cultures with these mutants, it also provided insight into the drug mechanism of action. Most of these mutants significantly increased the inherent rate of cleavage at the CA-p2 junction. One mutant, A1V, changes a residue in the P1' position of the cleavage site itself, but two others,
I13 and
M14, are at the opposite end of p2. How can these two mutations affect cleavage 13 or 14 residues N-terminal to the deletion? The rate of cleavage at the CA-p2 site is apparently regulated by cleavage at the p2-NC site such that blocking cleavage at the downstream site increases the rate at the upstream site by 20-fold (12). Furthermore, the substitution of an isoleucine for the methionine at P1 of the p2-NC cleavage site reduces cleavage there to 35% of that of the wild-type sequence (11). Deletion of M14 results in the placement of I13 at P1 of the p2-NC site, thus partially blocking cleavage and thereby increasing cleavage at CA-p2. How cleavage at p2-NC can affect the rate of cleavage at CA-p2 is not well understood, but this observation provides a plausible argument for the behavior of mutant
M14 as well as mutant
I13, which effectively changes the residue at P2 and which is cleaved more rapidly than the wt. Mutant
T8 also, but less significantly, increases cleavage at CA-p2. Since this deletion is positioned in the center of p2, there is no obvious explanation for its effect upon CA-p2 cleavage other than to say that perhaps it has a modest negative effect on cleavage at p2-NC.
The increase in the cleavage for each of the above-described mutants was roughly proportional to the extent of cleavage in the presence of PA-457, suggesting that the mechanism of resistance is through a more rapid inherent rate at the cleavage site. However, there was one exception. Mutant L231C cleaved only to about 50% of the level of the wt in the absence of the drug, yet it fell into the class of mutants displaying intermediate resistance. This mutant, which could only be tested in our in vitro system due to a defect in particle release, demonstrates that resistance does not correlate precisely with the cleavage rate and provides evidence that would be consistent with a direct drug-Gag interaction model for the mechanism of PA-457.
PA-457 produced a detectable change in the extent of p25CA-p2 cleavage over the range of 0.1 to 10 µM with a 50% inhibitory concentration (IC50) between 1 and 10 µM. These numbers are in apparent contradiction with the previously reported IC50 of approximately 10 nM in tissue culture assays, which is a 100- to 1,000-fold difference. The discrepancy arises from the different endpoints of the assays. The in vitro assay measures the extent of CA-p2 cleavage, while the culture assays measured cell killing as a gauge of virus replication and were therefore an indirect measurement of infectivity. Indeed, if the processing of p25CA-p2 to p24CA is used as an endpoint in the tissue culture system, the activity of PA-457 in cells should be similar to that seen in our in vitro system (9). Since the virus replication IC50 is below the detectable range of activity in the in vitro cleavage assay, the logical conclusion is that the virus is either extremely sensitive to small changes in the rate of processing or that only a very small number of p25CA-p2 molecules is sufficient to poison the virion. Either of these predictions is surprising given that only approximately one-half of the CA protein in a virus particle is assembled into the mature core structure (2, 7). By the first mechanism, one must invoke a rather delicate process of core condensation that requires precise timing to successfully produce an infectious virion. By the second mechanism, two equally plausible theories can be invoked, whereby (i) incorporation of one or more p25CA-p2 molecules can throw core assembly off pathway or (ii) p25CA-p2 cannot coassemble with p24CA into the core but nonetheless poisons an as-yet-cryptic but necessary function of either CA or p2 in infectivity.
As the paper was in final preparation, Zhou et al. (20) reported on the incorporation of PA-457 into immature particles and on an assay using such released particles to reproduce the dose-dependent activity of PA-457 in blocking the processing of p25CA-p2 in vitro. Using 3H-labeled drug and an enzyme-linked immunosorbent assay to quantify CA, those authors estimated the stoichiometry of drug incorporation into particles to be approximately 1:1 with respect to the Gag monomer, while no drug was found within similarly prepared resistant mutant particles. Consistent with these data, our findings provide significant additional evidence for a mechanism of PA-457 whereby the drug interacts directly with the Gag substrate. Moreover, our in vitro assay, by the synthesis of high-specific-activity radiolabeled Gag substrates, provides a more facile approach to a quantitative comparison of additional potential maturation inhibitors and of Gag mutants, including those that may be defective for particle production from cells.
We thank Eric Freed for critical review of the manuscript.
Present address: 19008 Oxcart Place, Gaithersburg, MD 20886. ![]()
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