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Journal of Virology, October 2001, p. 9502-9508, Vol. 75, No. 19
0022-538X/01/$04.00+0 DOI: 10.1128/JVI.75.19.9502-9508.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Viral Evolution in Response to the Broad-Based
Retroviral Protease Inhibitor TL-3
Bernd
Bühler,1
Ying-Chuan
Lin,2
Garrett
Morris,2
Arthur J.
Olson,2
Chi-Huey
Wong,3
Douglas D.
Richman,4,5
John H.
Elder,2 and
Bruce E.
Torbett1,*
Departments of Molecular and Experimental
Medicine,1 Molecular
Biology,2 and
Chemistry,3 The Scripps Research
Institute, La Jolla, California 92037; Departments of
Pathology and Medicine, University of California, San Diego, La
Jolla, California 920934; and San Diego
VA Healthcare System, San Diego, California
921615
Received 26 February 2001/Accepted 23 June 2001
 |
ABSTRACT |
TL-3 is a protease inhibitor developed using the feline
immunodeficiency virus protease as a model. It has been shown to
efficiently inhibit replication of human, simian, and feline
immunodeficiency viruses and therefore has broad-based activity. We now
demonstrate that TL-3 efficiently inhibits the replication of 6 of 12 isolates with confirmed resistance mutations to known protease
inhibitors. To dissect the spectrum of molecular changes in protease
and viral properties associated with resistance to TL-3, a panel of
chronological in vitro escape variants was generated. We have
virologically and biochemically characterized mutants with one (V82A),
three (M46I/F53L/V82A), or six (L24I/M46I/F53L/L63P/V77I/V82A) changes in the protease and structurally modeled the protease mutant containing six changes. Virus containing six changes was found to be 17-fold more
resistant to TL-3 in cell culture than was wild-type virus but
maintained similar in vitro replication kinetics compared to the
wild-type virus. Analyses of enzyme activity of protease variants with
one, three, and six changes indicated that these enzymes, compared to
wild-type protease, retained 40, 47, and 61% activity, respectively.
These results suggest that deficient protease enzymatic activity is
sufficient for function, and the observed protease restoration might
imply a selective advantage, at least in vitro, for increased protease activity.
 |
INTRODUCTION |
Highly active antiretroviral therapy
(HAART) with reverse transcriptase inhibitors in combination with
protease inhibitors has proven to suppress human immunodeficiency virus
type 1 (HIV-1) replication to undetectable levels in patients
(11, 12, 17). HIV-1 variants frequently evolve that
escape HAART by developing resistance to the inhibitors used (4,
15, 19, 28, 40, 42). Of patients first treated with a single
drug regimen and then going onto HAART, as many as 40% have a viral
rebound within the first 3 years, and this number is likely to be
higher outside of controlled studies (20, 35). Moreover,
transmission of drug-resistant HIV has been observed and is likely to
increase with more patients on combination therapy (25,
38). Thus, there is a need to fully understand the sequence of
molecular changes to HIV concomitant with development of resistance to
protease inhibitors. In turn, this knowledge should facilitate the
development of new inhibitors with activities against drug-resistant isolates.
The protease structure of feline immunodeficiency virus (FIV) was used
as a model for the development of a series of protease inhibitors with
broad efficacy (21). This strategy is based on our
observation that various potent HIV inhibitors are less-efficient inhibitors of FIV protease by a factor of more than 100 (21). Moreover, although HIV and FIV protease have only
23% amino acid identity, the active-site structures are almost
superimposable (39). We therefore reasoned that by
designing inhibitors of proteases with a similar alpha-carbon structure
and diverse substrate specificities, such as FIV protease, the
resulting inhibitors may be effective against drug-resistant HIVs as
well. Our first studies documented that one of these protease
inhibitors, TL-3, was truly a broad-based inhibitor as shown by its
ability to efficiently inhibit in vitro replication of human, simian,
and feline immunodeficiency viruses in the micromolar range
(21).
We report here on the antiviral activity of TL-3 on clinical isolates
from patients failing potent antiretroviral therapy and viruses
engineered to be drug resistant. We demonstrate that TL-3 was active
against 6 of 12 isolates tested. Common to isolates resistant to TL-3
was a V82A mutation in combination with additional mutations.
Generation of TL-3 escape variants in culture documented that an
initial V82A mutation was required and was followed by subsequent
protease mutations. Biochemical analysis of protease from
TL-3-resistant viruses with three and six mutations demonstrated a
progressive decrease of affinity (higher
Km) for substrate and increased
turnover (kcat). The secondary
mutations resulted in the maintenance of an acceptable catalytic
efficiency,
kcat/Km, and therefore, an effective mutant protease. Comparison of wild-type- and TL-3-resistant protease structural models, derived by energy minimization, offer a sterically plausible explanation for the loss of
potency to TL-3 in the protease with six mutations. The protease
mutations contributed to diminished protease-TL-3 affinity while
maintaining a catalytically efficient enzyme possibly due to the
mutations in the flap domain. These secondary mutations are necessary
for the generation of a fit virus and the broadening of
cross-resistance. It is anticipated that the panel of well-defined TL-3-resistant viral isolates may prove useful for the understanding and design of inhibitors less susceptible to resistance development.
 |
MATERIALS AND METHODS |
Cells and viruses.
The MT-2 cell line was obtained through
the AIDS Research and Reference Program. The R8 virus was a kind gift
of D. Trono (University of Geneva, Geneva, Switzerland)
(10). Primary HIV isolates were obtained from the
peripheral blood mononuclear cells (PBMC) of patients failing
antiretroviral therapy with regimens containing the protease inhibitors
as identified in Fig. 1. All PBMC samples
were obtained from patients treated at the University of California at
San Diego Medical Center or at the San Diego VA Health Care Facility.
Patient PBMC were activated with phytohemagglutinin (PHA) and
interleukin-2 (IL-2) and cocultivated with PBMC from seronegative
donors, and HIV stocks were prepared by low-level passage.

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FIG. 1.
TL-3 cross-resistance to and amino acid sequence of
protease inhibitor-resistant HIV-1 isolates and isolates obtained from
patients failing antiretroviral therapy. The numbered protease
consensus amino acid sequence is shown. Bold arrows indicate amino
acids associated with resistance when present with other mutations, and
amino acids in boldface are active-site mutations. Viral isolates, in
the first column, starting with B, C, or D, were obtained from patients
experiencing a viral rebound during treatment with the protease
inhibitor(s) indicated in the second column. Inhibitors: I, indinavir;
N, nelfinavir; S, saquinavir; R, ritonavir. The Z886 isolate was
resistant to SC52151. Relative susceptibility to TL-3 is expressed as
the relative IC50 compared to the control virus, R8, and
values shown are the means from two independent experiments.
Significant resistance was defined as a >4-fold-higher
IC50 compared to R8.
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Resistance to TL-3.
To determine TL-3 susceptibility of the
isolates, 106 PHA-stimulated PBMC were exposed to
5,000 to 50,000 50% tissue culture infective dose(s)
(TCID50) for 3 h, washed, and plated in
duplicate at 20,000 cells per well in 96-well culture plates in the
presence of various concentrations of TL-3 in complete RPMI 1640, and
20 U of IL-2/ml (29). Three-day supernatants were used to
determine p24 antigen production (30). The drug
concentration resulting in 50% inhibition (IC50)
was determined by comparison to the drug-free cultures. The relative
resistance was determined by comparing the IC50
value to that of the wild-type R8 virus.
Generation of TL-3-resistant HIV mutants.
Viral mutants
resistant to TL-3 were generated by cultivating R8 wild-type virus at
an initial concentration of 35 nM TL-3 in MT-2 cells grown in complete
medium (29). When viral growth had resulted in abundant
syncytium formation, usually days 4 to 10, one-half of the viral
supernatant was passaged to uninfected MT-2 cells containing a higher
TL-3 concentration. Culture medium was exchanged with fresh medium
containing TL-3 at the desired concentration every 3 days to maintain
selective pressure. The remaining supernatant was stored in aliquots at
80°C for further analysis or as a backup if virus did not grow at
the higher TL-3 concentration.
Sequence analysis of protease from selected passages.
The
protease gene was amplified from proviral DNA present in infected cells
by using primers PR1s (5'-GCCGATAGACAAGGAACTGT) and PR2AS
(5'-TTCCTGGCTTTAATTTTACTG). The PCR products were cloned into pCR2.1 (Invitrogen) or gel purified for direct sequencing.
Cloning and purification of HIV proteases.
The entire
protease gene of wild-type and TL-3 resistant viruses were cloned for
protein expression and the protein was expressed, purified, and
verified, as previously described (21).
Protease assay.
Proteolytic activity and cleavage
efficiencies (percent cleavage) and the Km
and Vmax values were determined as
previously described (21, 24, 36). TL-3
IC50 was as reported previously (24).
Molecular modeling of protease structure.
Modeling of TL-3
with the wild-type and TL-3-resistant 6x mutant HIV-1 protease was
performed using the AMBER force field as implemented in the Discover 3 module of InsightII version 98.0 (MSI). All atoms were allowed to move,
and energy minimization was performed for 500 iterations of conjugate
gradients with both wild-type and the 6x mutant viruses. The starting
structure of the HIV-1 protease inhibitor, TL-3, complexed with the
wild-type form of HIV-1 protease was taken from the crystal structure
(Protein Data Bank accession code 3TLH) (23). The presumed
structure of the 6x mutant of HIV-1 protease was constructed by using
homology modeling, based on wild-type HIV-1 protease complexed with
TL-3 (Protein Data Bank accession code 3TLH). The side chains in both
chains were mutated as follows: L24I, M46I, F53L, L63P, V77I, and V82A.
Simulations began with the same backbone conformations of the crystal
structure 3TLH. Since only one monomer of HIV-1 protease was seen in
the asymmetric unit cell, the dimer was constructed by applying the
appropriate transformation. This asymmetric unit cell also contained
only one half of the TL-3 inhibitor, which is in itself a symmetric
molecule. The resulting two halves of the TL-3 inhibitor were connected
by a single bond. One of the two catalytic aspartic acid side chains
was protonated, while the other was treated as charged. In both cases,
water-301 and the four water molecules that bind adjacent to positions
R8 and R8' were also included.
 |
RESULTS AND DISCUSSION |
Some protease inhibitor-resistant patient isolates are
susceptible to TL-3.
We have shown that the protease inhibitor
TL-3 was active against wild-type HIV and FIV and drug-resistant
proteases containing G48V and V82F mutations (22). To
further define the inhibitory activity of TL-3 on drug-resistant viral
isolates, we tested a panel of 11 primary viral isolates obtained from
individuals that failed treatment with regimens containing the protease
inhibitors indicated in Fig. 1. No cross-resistant assessment of viral
isolates to currently approved protease inhibitors was performed. In
Fig. 1, the viral isolates, information on the patient's drug regime, and the protease gene sequence are shown. Protease sequence
determination allowed the verification of mutations associated with
inhibitor resistance. Two molecular clones with known mutations and
well-documented cross-resistance to most inhibitors (clone Z605-2
[L10R, M46I, L63P, V82T, and I84V] and clone Z952-7 [M46I and
I84V], respectively) (3, 27) and one isolate, Z886,
selected in vitro for resistance to SC-52151, were also tested
(9). Nine of the eleven patient isolates have protease
mutations at D30, G48, V82, I84, and/or L90, all of which are mutations
associated with clinical resistance to protease inhibitors (4,
32, 34). Two isolates, D507-4 (V77I and I93L) and D507-7 (M36I),
were found to contain only mutations generally considered as secondary,
rather than primary active-site mutations. Thus, these isolates were
not considered resistant to approved protease inhibitors.
IC50 was determined for each isolate by measuring
viral p24 levels on day 3 over a concentration range of 10 to 1,250 nM
TL-3 in PHA- and IL-2-stimulated and infected PBMC. Figure 1 shows the
relative IC50 values of all isolates compared to
the control virus, R8. Six of the isolates were found to have a
>4-fold relative resistance, and five of these TL-3-resistant isolates
shared a V82A/T mutation (Fig. 1). Nonetheless, the V82A change in
itself does not lead to significant resistance, as evidenced by the
D726-5 isolate with only the G48V and V82A active-site mutations and threefold relative resistance. The V82A/T mutation is commonly found in
isolates from patients who failed ritonavir or indinavir therapy
(4, 28, 34, 37). Besides the mutation at position 82, an
I54V mutation was observed in the three isolates with the highest TL-3
resistance, a combination found in 27% of highly cross-resistant
isolates (13). Of the three laboratory-derived resistant
isolates, only one was found to be >4-fold resistant. In general, the
predominant mutation associated with resistance to TL-3 in five of six
isolates was a change at V82 to either an A or a T in combination with
additional mutations. A V82A change in itself did not lead to
high-level resistance to TL-3, since the D726-5 isolate had a threefold
increase in resistance only. However, the sample size is too small to
determine which mutation initially confers resistance and which
combination of mutations is involved in increasing the resistance to
TL-3.
TL-3-resistant virus.
To determine chronological changes in
the protease gene conferring TL-3 resistance, R8 virus was passaged in
MT-2 cells in the presence of increasing concentrations of the drug. R8
was initially grown in the presence of 35 nM TL-3, which is
approximately the IC50, and the concentration was
gradually increased to 46 µM during 56 passages over a 5-month
period. At concentrations greater than 46 µM, TL-3 begins to
precipitate out of the solution, therefore defining the TL-3
concentration limit. Susceptibility to TL-3 was determined every five
to seven passages during the 5-month selection period. Figure
2 documents the relative resistance of
isolates from passages 21, 31, 37, 44, and 56 compared to the wild-type
R8 virus. The relative resistance increased by passage 56 to 17-fold.

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FIG. 2.
Amino acid sequences of proteases from TL-3 escape
mutants resistant to TL-3 at passages (P) 21, 31, 37, 44, and 56. The
fraction of clones containing non-wild-type R8 protease sequences is
indicated in the rightmost column. The sequence of the R8 virus is
shown in the top row. Identity with R8 at individual amino acid
positions is indicated by dashes. Superscripts: a, not
applicable (NA) since the PCR product was sequenced directly;
b, position 53 was ambiguous at passage 56, but clonal
analysis demonstrated two independent mutations to L (codons CTT and
TTG).
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The proviral protease genes from passages 21, 31, 37, 44, and 56 were
cloned from each viral stock and sequenced. For the later passages 44 and 56, the amplified protease region was directly sequenced to
determine the predominant mutations in the virus stock. Wild-type
sequence was seen at passage 21 in the majority of clones, although two
clones were found to have an S-to-N mutation at the
P2 position of the p6*-protease cleavage site,
and one clone demonstrated an additional mutation at position 35 (Fig. 2). By passage 31, resistance increased twofold over that of the wild-type virus. All of the six clones sequenced had a V82A
substitution, a position associated with the S1 and S3 pocket in the
active site of the enzyme and often found to be mutated in
drug-resistant viral isolates (8, 30). At passage 37, two
additional mutations, M46I and F53L, were observed in five of six
clones isolated. These additional mutations were associated with a
tripling of resistance to TL-3 relative to resistance of the single
V82A mutant observed at P31. By passage 44, a V77I mutation was
apparent in all clones, but TL-3 resistance had increased very little.
Interestingly, this mutation was already present in one of six clones
at P37. At passage 56 two more mutations, L24I and L63P, were observed and were associated with a doubling of resistance to TL-3 compared to
the 4x mutant from passage 44. Thus, prolonged cultivation of HIV-1 in
TL-3 results in a sequential increase of drug resistance, which is
paralleled by acquisition of mutations in the protease gene.
It has been reported that some mutations in the protease gene result in
a reduced viral replicative ability in vitro (5, 14, 27).
The analysis of TL-3-resistant viruses with one, three, and six
protease gene mutations (i.e., 1x, 3x, and 6x, respectively)
were tested using MT-2 cells for alterations in viral replication. MT-2
cells were infected at a multiplicity of infection of 0.001, and viral
replication was monitored for 7 days by determining the p24
content. Although viral isolates varied in their protease gene
mutations, their replication rates, as judged by p24 increase over
time, were indistinguishable (data not shown). Impairment of viral
fitness is hypothesized to be a result of defective processing of the
structural proteins or the cassette encoded by pol (6,
7, 26, 41). It has been reported that HIV carrying the V82A
mutation in combination with M46I causes impaired growth kinetics
(42). However, in some studies with viruses with mutant
proteases the growth kinetics were found to be similar to those of
wild-type viruses (16). Although the V82A mutation
impaired purified protease activity, it is estimated that protease
activity must fall below 10% of that of wide-type protease activity to
disrupt the production of infectious viral particles (18, 27, 31,
33). Therefore, TL-3 mutant protease activity may not be
rate-limiting for viral replication at a level of 40% activity of the
wild-type in the case of the V82A mutation. Alternately, the simple
comparisons of in vitro replication, rather than a competitive analysis
of viral fitness of TL-3-resistant mutants versus wild-type virus, may
have underestimated the true extent of loss of viral fitness in
TL-3-resistant isolates (27). Although gag/pol
cleavage site mutations that could allow more efficient cleavage by the
mutated protease were not observed (data not shown), we cannot rule out the possibility that additional mutations outside of the protease gene
may be present in TL-3-resistant viruses that compensate for defective
protease function (1, 42).
The catalytic activity of protease from TL-3-resistant virus is
reduced.
To quantify biochemical changes in the protease activity
of TL-3 selected mutants, purified wild-type and 1x (passage 31), 3x
(passage 37), and 6x (passage 56) mutant proteases were tested for
relative enzymatic activity using a fluorogenic substrate (21) and a 16-amino-acid peptide representing the
matrix-capsid (MA-CA) cleavage site. The results for the affinity
(Km), the turnover rate
(kcat), and the catalytic efficiency
(i.e.,
kcat/Km) for the fluorogenic substrate and the percent cleavage of the MA-CA
peptide are presented in Table 1. The
Km for the fluorogenic substrate increased
from 45 to 73 µM with the V82A position change in the protease,
whereas the kcat dropped from 2.73 to
1.74 s
1. Thus, the resulting
kcat/Km
for the V82A mutation was only 40% of the wild-type catalytic
efficiency (0.060 to 0.024 s
1
µM
1). With subsequent mutations in the
protease, the Km increased even further
but was compensated for by an increase in the catalytic activity to
levels higher than that of wild-type protease. This results in a net
increase of the catalytic efficiency of the 3x and 6x mutants to 47 and
62%, respectively, of the wild-type levels. These findings are
paralleled by results obtained from analyzing the cleavage of the MA-CA
peptide (Table 1). After 30 min of incubation of the MA-CA peptide with
a constant amount of V82A mutant protease, only 18% of the peptide was
cleaved. In contrast, the wild-type enzyme cleaved 31% of the peptide
under identical assay conditions. With increasing mutations, the
protease completely regained enzyme activity for this substrate, with
32% of the peptide being cleaved by the 6x mutant in the equivalent
time interval. Thus, evaluation of enzymatic activity using two
different substrates demonstrated that the initial V82A mutation
decreased enzymatic activity, but this activity was restored with
subsequent mutations.
TL-3-resistant mutants are cross-resistant.
The mutant
protease from the 3x mutant (passage 37) was found to be 11-fold and
that of the 6x mutant (passage 56) was found to be 30-fold resistant to
TL-3 compared to wild-type protease (Table
2). The 3x mutant protease was
cross-resistant to saquinavir (5-fold), ritonavir (7-fold), and
nelfinavir (4-fold) and by passage 56 the resulting 6x mutant protease
demonstrated increased resistance to saquinavir (9-fold), ritonavir
(14-fold), and nelfinavir (8-fold) compared to the wild-type protease.
Given the primary V82A active site mutation seen after TL-3 passage, a
mutation commonly found in the development of resistance to ritonavir,
it is not surprising that some cross-resistance to ritonavir was
evident. Our earlier studies suggest that a mutation at V82F impart a
low level of resistance to TL-3 (22). Although the V82A
active-site mutation is not a mutation typically observed during
resistance development to saquinavir and nelfinavir, the generation of
cross-resistance with the acquisition of secondary mutations is a
characteristic seen in some, but not all, viruses isolated from
patients treated with single protease inhibitors (32). Our
results with TL-3 were not predictable from our earlier studies with
single mutations at G48V and V82F (22) and imply that the
contributions of secondary mutations in the flap and/or interior of the
protease (see below) are critical for enhanced resistance to TL-3 and
cross-resistance.
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TABLE 2.
IC50 values of the wild-type and mutant
proteases to TL-3 and cross-resistance to saquinavir (SQV), ritonavir
(RTV), and nelfinavir (NFV)
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Computer modeling of TL-3 complexed with wild-type and 6x mutant
protease.
It was possible to postulate structural reasons, after
molecular mechanics energy minimization calculations and structural overlays, for the loss in potency of TL-3 when confronted by the changes in the 6x mutant protease (green) compared to the wild-type protease (red) (Fig. 3). Inspection of
the energy-minimized protease-TL-3 complexes revealed alterations in
the packing of residue side chains of the 6x mutant throughout the
structure. The initial V82A mutation, with loss of the larger V side
chain (red) when replaced by the smaller A (green), removed van der
Waals stabilization of the phenyl side chains present in
P1 and P1' of TL-3
(double-headed arrow; the spheres represent the van der Waals radii).
When the F53 side chain was mutated to the smaller, nonaromatic L,
favorable pi-pi contacts with the carboxy-benzyl (Cbz) groups at
P4 and P4' of TL-3 were
lost (double-headed arrow). The L63P mutation results in the loss of a
backbone amido proton. This appears to have a "domino effect" on
the neighboring hydrogen bonding network. In combination with the M46I
mutation, both presumably affect the flap structure. Overall, the flaps
moved outward (arrow) and the backbone of the flaps assumed a more
narrow conformation. In addition, the mutations at L24I and V77I occur
in the interior of the dimeric protease's subunits, and the
introduction of these beta-branched amino acids caused fairly
significant local repacking of the neighboring atoms.

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FIG. 3.
Energy-minimized model of R8 wild-type (red) protease
overlaid with the TL-3 resistant 6x mutant (green) protease. TL-3 is
bound to R8 and mutant proteases. Depicted are the protein backbones
with mutated residues at numbered positions. The double-headed arrows
indicate loss of both the TL-3 P1 interaction (P1' not shown) with V82
upon mutation to the smaller A and the P4-Cbz interaction with the F53
upon mutation to the smaller L. The single-headed arrow points to
distended flaps. The van der Waals radii of the L24I and V77I mutant
side chains, resulting in rearrangement of local packing, are also
shown as red (wild-type) or green (mutant) spheres, respectively.
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Although changes in enzymatic activity based on changes in the flaps
cannot be concluded from energy minimization modeling alone, the
biochemical analysis (Table 1) demonstrates an increase in
kcat consistent with this structural
interpretation. TL-3 selection resulted in protease mutations that
first affected substrate affinity and drastic changes in enzyme
activity were mitigated by increased efficiency of cleavage through
subsequent mutations. Therefore, secondary mutations allowed for
maintenance of an acceptable
kcat/Km, resulting in an effective mutant protease. Taken together, enzymatic results and proposed structural changes offer a sterically plausible explanation for the loss of potency to TL-3 and gain of biochemical function in the 6x mutant.
The demonstration that TL-3 was effective against some, although not
all, drug-resistant viral isolates underscores the potential value of
using FIV protease as a model for HIV protease inhibitor development.
Our chronological panel of well-defined TL-3-resistant HIV isolates
should be useful in helping to understand protease variability and
substrate and inhibitor recognition. Substrates that are very
effectively cleaved by HIV protease have been shown to be useful as
models for designing tight binding inhibitors (2).
Recently, a phage library was used to display potential substrates to
compare FIV and HIV protease substrate specificities (Z. Q. Beck,
Y.-C. Lin, and J. H. Elder, unpublished data). This method
should prove useful for investigating the substrate specificity and
cleavage efficacy of our panel of TL-3-resistant proteases and allow a
rapid selection of substrates that can then be employed as templates to
generate efficacious inhibitors for evaluation. It is anticipated that
that our findings will help to define structural parameters to aid in
the development of broad-based inhibitors less susceptible to evasion
by mutations within protease.
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ACKNOWLEDGMENTS |
We gratefully acknowledge the laboratory assistance of Kent A. Smith, Giano P. Panzarella, Hugh B. Perkin, and Danica L. Lerner.
This study was supported by NIH grants DK49886 (B.E.T.), P01GM48870
(J.H.E., A.J.O., and C.-H.W.), and AI27670, AI38585, AI43638, and
AI29164 (D.D.R.) and by the Research Center for AIDS and HIV Infection
of the San Diego Veterans Affairs Healthcare System. TL-3 was
synthesized and supplied under a contract operated by the Division of
AIDS, National Institute of Allergy and Infectious Diseases, National
Institutes of Health.
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FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Molecular and Experimental Medicine, L-55, The Scripps Research
Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037. Phone:
(858) 784-9123. Fax: (858) 784-2121. E-mail:
betorbet{at}scripps.edu.
Publication 13925-MEM from The Scripps Research Institute.
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REFERENCES |
| 1.
|
Bally, F.,
R. Martinez,
S. Peters,
P. Sudre, and A. Telenti.
2000.
Polymorphism of HIV type 1 gag p7/p1 and p1/p6 cleavage sites: clinical significance and implications for resistance to protease inhibitors.
AIDS Res. Hum. Retrovir.
16:1209-1213[CrossRef][Medline].
|
| 2.
|
Beck, Z. Q.,
L. Hervio,
P. E. Dawson,
J. H. Elder, and E. L. Madison.
2000.
Identification of efficiently cleaved substrates for HIV-1 protease using a phage display library and use in inhibitor development.
Virology
274:391-401[CrossRef][Medline].
|
| 3.
|
Chen, Z.,
Y. Li,
H. B. Schock,
D. Hall,
E. Chen, and L. C. Kuo.
1995.
Three-dimensional structure of a mutant HIV-1 protease displaying cross-resistance to all protease inhibitors in clinical trials.
J. Biol. Chem.
270:21433-21436[Abstract/Free Full Text].
|
| 4.
|
Condra, J. H.,
W. A. Schleif,
O. M. Blahy,
L. J. Gabryelski,
D. J. Graham,
J. C. Quintero,
A. Rhodes,
H. L. Robbins,
E. Roth,
M. Shivaprakash,
D. Titus,
T. Yang,
H. Teppler,
K. E. Squires,
P. J. Deutsh, and E. A. Emini.
1995.
In vivo emergence of HIV-1 variants resistant to multiple protease inhibitors.
Nature
374:569-571[CrossRef][Medline].
|
| 5.
|
Croteau, G.,
L. Doyon,
D. Thibeault,
G. McKercher,
L. Pilote, and D. Lamarre.
1997.
Impaired fitness of human immunodeficiency virus type 1 variants with high-level resistance to protease inhibitors.
J. Virol.
71:1089-1096[Abstract].
|
| 6.
|
de la Carriere, L. C.,
S. Paulous,
F. Clavel, and F. Mammano.
1999.
Effects of human immunodeficiency virus type 1 resistance to protease inhibitors on reverse transcriptase processing, activity, and drug sensitivity.
J. Virol.
73:3455-3459[Abstract/Free Full Text].
|
| 7.
|
Doyon, L.,
G. Croteau,
D. Thibeault,
F. Poulin,
L. Pilote, and D. Lamarre.
1996.
Second locus involved in human immunodeficiency virus type 1 resistance to protease inhibitors.
J. Virol.
70:3763-3769[Abstract].
|
| 8.
|
Eastman, P. S.,
J. Mittler,
R. Kelso,
C. Gee,
E. Boyer,
J. Kolberg,
M. Urdea,
J. M. Leonard,
D. W. Norbeck,
H. Mo, and M. Markowitz.
1998.
Genotypic changes in human immunodeficiency virus type 1 associated with loss of suppression of plasma viral RNA levels in subjects treated with ritonavir (Norvir) monotherapy.
J. Virol.
72:5154-5164[Abstract/Free Full Text].
|
| 9.
|
Fischl, M. A.,
D. D. Richman,
C. Flexner,
M. F. Para,
R. Haubrich,
A. Karim,
P. Yeramian,
J. Holden-Wiltse, and P. M. Meehan.
1997.
Phase I/II study of the toxicity, pharmacokinetics, and activity of the HIV protease inhibitor SC-52151.
J. Acquir. Immune Defic. Syndr. Hum. Retrovirol.
15:28-34[Medline].
|
| 10.
|
Gallay, P.,
V. Stitt,
C. Mundy,
M. Oettinger, and D. Trono.
1996.
Role of the karyopherin pathway in human immunodeficiency virus type 1 nuclear import.
J. Virol.
70:1027-1032[Abstract].
|
| 11.
|
Gulick, R. M.,
J. W. Mellors,
D. Havlir,
J. J. Eron,
C. Gonzalez,
D. McMahon,
D. D. Richman,
F. T. Valentine,
L. Jonas,
A. Meibohm,
E. A. Emini, and J. A. Chodakewitz.
1997.
Treatment with indinavir, zidovudine, and lamivudine in adults with human immunodeficiency virus infection and prior antiretroviral therapy.
N. Engl. J. Med.
337:734-739[Abstract/Free Full Text].
|
| 12.
|
Hammer, S. M.,
K. E. Squires,
M. D. Hughes,
J. M. Grimes,
L. M. Demeter,
J. S. Currier,
J. J. Eron, Jr.,
J. E. Feinberg,
H. H. Balfour, Jr.,
L. R. Deyton,
J. A. Chodakewitz, and M. A. Fischl.
1997.
A controlled trial of two nucleoside analogues plus indinavir in persons with human immunodeficiency virus infection and CD4 cell counts of 200 per cubic millimeter or less. AIDS Clinical Trials Group 320 Study Team.
N. Engl. J. Med.
337:725-733[Abstract/Free Full Text].
|
| 13.
|
Hertogs, K.,
S. Bloor,
S. D. Kemp,
C. Van den Eynde,
T. M. Alcorn,
R. Pauwels,
M. Van Houtte,
S. Staszewski,
V. Miller, and B. A. Larder.
2000.
Phenotypic and genotypic analysis of clinical HIV-1 isolates reveals extensive protease inhibitor cross-resistance: a survey of over 6000 samples.
AIDS
14:1203-1210[CrossRef][Medline].
|
| 14.
|
Ho, D. D.,
T. Toyoshima,
H. Mo,
D. J. Kempf,
D. Norbeck,
C. M. Chen,
N. E. Wideburg,
S. K. Burt,
J. W. Erickson, and M. K. Singh.
1994.
Characterization of human immunodeficiency virus type 1 variants with increased resistance to a C2-symmetric protease inhibitor.
J. Virol.
68:2016-2020[Abstract/Free Full Text].
|
| 15.
|
Jacobsen, H.,
M. Hanggi,
M. Ott,
I. B. Duncan,
S. Owen,
M. Andreoni,
S. Vella, and J. Mous.
1996.
In vivo resistance to a human immunodeficiency virus type 1 proteinase inhibitor: mutations, kinetics, and frequencies.
J. Infect. Dis.
173:1379-1387[Medline].
|
| 16.
|
Jacobsen, H.,
K. Yasargil,
D. L. Winslow,
J. C. Craig,
A. Krohn,
I. B. Duncan, and J. Mous.
1995.
Characterization of human immunodeficiency virus type 1 mutants with decreased sensitivity to proteinase inhibitor Ro 31-8959.
Virology
206:527-534[CrossRef][Medline].
|
| 17.
|
Kirk, O.,
T. L. Katzenstein,
J. Gerstoft,
L. Mathiesen,
H. Nielsen,
C. Pedersen, and J. D. Lundgren.
1999.
Combination therapy containing ritonavir plus saquinavir has superior short-term antiretroviral efficacy: a randomized trial.
AIDS
13:F9-F16[CrossRef][Medline].
|
| 18.
|
Konvalinka, J.,
M. A. Litterst,
R. Welker,
H. Kottler,
F. Rippmann,
A. M. Heuser, and H. G. Krausslich.
1995.
An active-site mutation in the human immunodeficiency virus type 1 proteinase (PR) causes reduced PR activity and loss of PR-mediated cytotoxicity without apparent effect on virus maturation and infectivity.
J. Virol.
69:7180-7186[Abstract].
|
| 19.
|
Lawrence, J.,
J. Schapiro,
M. Winters,
J. Montoya,
A. Zolopa,
R. Pesano,
B. Efron,
D. Winslow, and T. C. Merigan.
1999.
Clinical resistance patterns and responses to two sequential protease inhibitor regimens in saquinavir and reverse transcriptase inhibitor-experienced persons.
J. Infect. Dis.
179:1356-1364[CrossRef][Medline].
|
| 20.
|
Ledergerber, B.,
M. Egger,
M. Opravil,
A. Telenti,
B. Hirschel,
M. Battegay,
P. Vernazza,
P. Sudre,
M. Flepp,
H. Furrer,
P. Francioli, and R. Weber.
1999.
Clinical progression and virological failure on highly active antiretroviral therapy in HIV-1 patients: a prospective cohort study. Swiss HIV Cohort Study.
Lancet
353:863-868[CrossRef][Medline].
|
| 21.
|
Lee, T.,
G. S. Laco,
B. E. Torbett,
H. S. Fox,
D. L. Lerner,
J. H. Elder, and C. H. Wong.
1998.
Analysis of the S3 and S3' subsite specificities of feline immunodeficiency virus (FIV) protease: development of a broad-based protease inhibitor efficacious against FIV, SIV, and HIV in vitro and ex vivo.
Proc. Natl. Acad. Sci. USA
95:939-944[Abstract/Free Full Text].
|
| 22.
|
Lee, T.,
V.-D. Le,
D. Lim,
Y.-C. Lin,
G. M. Morris,
A. L. Wong,
A. J. Olson,
J. H. Elder, and C. H. Wong.
1999.
Development of a new type of protease inhibitors, efficacious against FIV and HIV variants.
J. Am. Chem. Soc.
121:1145-1155[CrossRef].
|
| 23.
|
Li, M.,
G. M. Morris,
T. Lee,
G. S. Laco,
C. H. Wong,
A. J. Olson,
J. H. Elder,
A. Wlodawer, and A. Gustchina.
2000.
Structural studies of FIV and HIV-1 proteases complexed with an efficient inhibitor of FIV protease.
Proteins
38:29-40[CrossRef][Medline].
|
| 24.
|
Lin, Y. C.,
Z. Beck,
T. Lee,
V. D. Le,
G. M. Morris,
A. J. Olson,
C. H. Wong, and J. H. Elder.
2000.
Alteration of substrate and inhibitor specificity of feline immunodeficiency virus protease.
J. Virol.
74:4710-4720[Abstract/Free Full Text].
|
| 25.
|
Little, S. J.,
E. S. Daar,
R. T. D'Aquila,
P. H. Keiser,
E. Connick,
J. M. Whitcomb,
N. S. Hellmann,
C. J. Petropoulos,
L. Sutton,
J. A. Pitt,
E. S. Rosenberg,
R. A. Koup,
B. D. Walker, and D. D. Richman.
1999.
Reduced antiretroviral drug susceptibility among patients with primary HIV infection.
JAMA
282:1142-1149[Abstract/Free Full Text].
|
| 26.
|
Mammano, F.,
C. Petit, and F. Clavel.
1998.
Resistance-associated loss of viral fitness in human immunodeficiency virus type 1: phenotypic analysis of protease and gag coevolution in protease inhibitor-treated patients.
J. Virol.
72:7632-7637[Abstract/Free Full Text].
|
| 27.
|
Martinez-Picado, J.,
A. V. Savara,
L. Sutton, and R. T. D'Aquila.
1999.
Replicative fitness of protease inhibitor-resistant mutants of human immunodeficiency virus type 1.
J. Virol.
73:3744-3752[Abstract/Free Full Text].
|
| 28.
|
Molla, A.,
M. Korneyeva,
Q. Gao,
S. Vasavanonda,
P. J. Schipper,
H. M. Mo,
M. Markowitz,
T. Chernyavskiy,
P. Niu,
N. Lyons,
A. Hsu,
G. R. Granneman,
D. D. Ho,
C. A. Boucher,
J. M. Leonard,
D. W. Norbeck, and D. J. Kempf.
1996.
Ordered accumulation of mutations in HIV protease confers resistance to ritonavir.
Nat. Med.
2:760-766[CrossRef][Medline].
|
| 29.
|
Mosier, D. E.,
R. J. Gulizia,
P. D. MacIsaac,
B. E. Torbett, and J. A. Levy.
1993.
Rapid loss of CD4+ T cells in human-PBL-SCID mice by noncytopathic HIV isolates.
Science
260:689-692[Abstract/Free Full Text].
|
| 30.
|
Patick, A. K.,
R. Rose,
J. Greytok,
C. M. Bechtold,
M. A. Hermsmeier,
P. T. Chen,
J. C. Barrish,
R. Zahler,
R. J. Colonno, and P. F. Lin.
1995.
Characterization of a human immunodeficiency virus type 1 variant with reduced sensitivity to an aminodiol protease inhibitor.
J. Virol.
69:2148-2152[Abstract].
|
| 31.
|
Rose, J. R.,
L. M. Babe, and C. S. Craik.
1995.
Defining the level of human immunodeficiency virus type 1 (HIV-1) protease activity required for HIV-1 particle maturation and infectivity.
J. Virol.
69:2751-2758[Abstract].
|
| 32.
|
Schinazi, R. F.,
B. A. Larder, and J. W. Mellors.
1997.
Mutations in the retroviral genes associated with drug resistance.
Antiviral News
5:129-142.
|
| 33.
|
Schock, H. B.,
V. M. Garsky, and L. C. Kuo.
1996.
Mutational anatomy of an HIV-1 protease variant conferring cross-resistance to protease inhibitors in clinical trials. Compensatory modulations of binding and activity.
J. Biol. Chem.
271:31957-31963[Abstract/Free Full Text].
|
| 34.
|
Shafer, R. W.,
P. Hsu,
A. K. Patick,
C. Craig, and V. Brendel.
1999.
Identification of biased amino acid substitution patterns in human immunodeficiency virus type 1 isolates from patients treated with protease inhibitors.
J. Virol.
73:6197-6202[Abstract/Free Full Text].
|
| 35.
|
Staszewski, S.,
V. Miller,
C. Sabin,
A. Carlebach,
A. M. Berger,
E. Weidmann,
E. B. Helm,
A. Hill, and A. Phillips.
1999.
Virological response to protease inhibitor therapy in an HIV clinic cohort.
AIDS
13:367-373[CrossRef][Medline].
|
| 36.
|
Toth, M. V., and G. R. Marshall.
1990.
A simple, continuous fluorometric assay for HIV protease.
Int. J. Peptide Protein Res.
36:544-550[Medline].
|
| 37.
|
Turriziani, O.,
G. Antonelli,
H. Jacobsen,
J. Mous,
E. Riva,
M. Pistello, and F. Dianzani.
1994.
Identification of an amino acid substitution involved in the reduction of sensitivity of HIV-1 to an inhibitor of viral proteinase.
Acta Virol.
38:297-298[Medline].
|
| 38.
|
Wegner, S. A.,
S. K. Brodine,
J. R. Mascola,
S. A. Tasker,
R. A. Shaffer,
M. J. Starkey,
A. Barile,
G. J. Martin,
N. Aronson,
W. W. Emmons,
K. Stephan,
S. Bloor,
J. Vingerhoets,
K. Hertogs, and B. Larder.
2000.
Prevalence of genotypic and phenotypic resistance to anti-retroviral drugs in a cohort of therapy-naive HIV-1 infected US military personnel.
AIDS
14:1009-1015[CrossRef][Medline].
|
| 39.
|
Wlodawer, A.,
A. Gustchina,
L. Reshetnikova,
J. Lubkowski,
A. Zdanov,
K. Y. Hui,
E. L. Angleton,
W. G. Farmerie,
M. M. Goodenow,
D. Bhatt, et al.
1995.
Structure of an inhibitor complex of the proteinase from feline immunodeficiency virus.
Nat. Struct. Biol.
2:480-488[CrossRef][Medline].
|
| 40.
|
Young, B.,
S. Johnson,
M. Bahktiari,
D. Shugarts,
R. K. Young,
M. Allen,
R. R. Ramey II, and D. R. Kuritzkes.
1998.
Resistance mutations in protease and reverse transcriptase genes of human immunodeficiency virus type 1 isolates from patients with combination antiretroviral therapy failure.
J. Infect. Dis.
178:1497-1501[CrossRef][Medline].
|
| 41.
|
Zennou, V.,
F. Mammano,
S. Paulous,
D. Mathez, and F. Clavel.
1998.
Loss of viral fitness associated with multiple Gag and Gag-Pol processing defects in human immunodeficiency virus type 1 variants selected for resistance to protease inhibitors in vivo.
J. Virol.
72:3300-3306[Abstract/Free Full Text].
|
| 42.
|
Zhang, Y. M.,
H. Imamichi,
T. Imamichi,
H. C. Lane,
J. Falloon,
M. B. Vasudevachari, and N. P. Salzman.
1997.
Drug resistance during indinavir therapy is caused by mutations in the protease gene and in its Gag substrate cleavage sites.
J. Virol.
71:6662-6670[Abstract].
|
Journal of Virology, October 2001, p. 9502-9508, Vol. 75, No. 19
0022-538X/01/$04.00+0 DOI: 10.1128/JVI.75.19.9502-9508.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
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