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Bacheler L, Jeffrey S, Hanna G, D'Aquila R, Wallace L, Logue K, Cordova B, Hertogs K, Larder B, Buckery R, Baker D, Gallagher K, Scarnati H, Tritch R, Rizzo C. Genotypic correlates of phenotypic resistance to efavirenz in virus isolates from patients failing nonnucleoside reverse transcriptase inhibitor therapy. J Virol 2001; 75:4999-5008. [PMID: 11333879 PMCID: PMC114903 DOI: 10.1128/jvi.75.11.4999-5008.2001] [Citation(s) in RCA: 175] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Efavirenz (also known as DMP 266 or SUSTIVA) is a potent nonnucleoside inhibitor of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) activity and of HIV-1 replication in vitro and in vivo. Most patients on efavirenz-containing regimens have sustained antiviral responses; however, rebounds in plasma viral load have been observed in some patients in association with the emergence of mutant strains of HIV-1. Virus isolates from the peripheral blood mononuclear cells (PBMCs) of patients with such treatment failures, as well as recombinant viruses incorporating viral sequences derived from patient plasma, show reduced in vitro susceptibility to efavirenz in association with mutations in the RT gene encoding K103N, Y188L, or G190S/E substitutions. Patterns of RT gene mutations and in vitro susceptibility were similar in plasma virus and in viruses isolated from PBMCs. Variant strains of HIV-1 constructed by site-directed mutagenesis confirmed the role of K103N, G190S, and Y188L substitutions in reduced susceptibility to efavirenz. Further, certain secondary mutations (V106I, V108I, Y181C, Y188H, P225H, and F227L) conferred little resistance to efavirenz as single mutations but enhanced the level of resistance of viruses carrying these mutations in combination with K103N or Y188L. Viruses with K103N or Y188L mutations, regardless of the initial selecting nonnucleoside RT inhibitor (NNRTI), exhibited cross-resistance to all of the presently available NNRTIs (efavirenz, nevirapine, and delavirdine). Some virus isolates from nevirapine or delavirdine treatment failures that lacked K103N or Y188L mutations remained susceptible to efavirenz in vitro, although the clinical significance of this finding is presently unclear.
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Affiliation(s)
- L Bacheler
- DuPont Pharmaceuticals Company, Wilmington, Delaware 19880-0336, USA.
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Martinez-Picado J, Sutton L, De Pasquale MP, Savara AV, D'Aquila RT. Human immunodeficiency virus type 1 cloning vectors for antiretroviral resistance testing. J Clin Microbiol 1999; 37:2943-51. [PMID: 10449480 PMCID: PMC85420 DOI: 10.1128/jcm.37.9.2943-2951.1999] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Better detection of minority human immunodeficiency virus type 1 (HIV-1) populations containing gene mutations may improve the usefulness of antiretroviral resistance testing for clinical management. Molecular cloning of HIV-1 PCR products which might improve minority detection can be slow and difficult, and commercially available recombinant virus assays test drug susceptibility of virus pools. We describe novel plasmids and simple methods for rapid cloning of HIV-1 PCR products from patient specimens and their application to generate infectious recombinant virus clones for virus phenotyping and genotyping. Eight plasmids with differing deletions of sequences encoding HIV-1 protease, reverse transcriptase, or Gag p7/p1 and Gag p1/p6 cleavage sites were constructed for cloning HIV-1 PCR products. A simple HIV-1 sequence-specific uracil deglycosylase-mediated cloning method with the vectors and primers designed here was more rapid than standard ligase-mediated cloning. Pooled and molecularly cloned infectious recombinant viruses were generated with these vectors. Replicative viral fitness and drug susceptibility phenotypes of cloned infectious viruses containing patient specimen-derived sequences were measured. Clonal resistance genotyping analyses were also performed from virus isolates, plasma HIV-1 RNA, and infected cell DNA. Sequencing of a limited number of molecular clones detected minorities of resistant virus not identified in the pooled population PCR product sequence and linkage of minority mutations.
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Carrillo A, Stewart KD, Sham HL, Norbeck DW, Kohlbrenner WE, Leonard JM, Kempf DJ, Molla A. In vitro selection and characterization of human immunodeficiency virus type 1 variants with increased resistance to ABT-378, a novel protease inhibitor. J Virol 1998; 72:7532-41. [PMID: 9696850 PMCID: PMC109995 DOI: 10.1128/jvi.72.9.7532-7541.1998] [Citation(s) in RCA: 131] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABT-378, a new human immunodeficiency virus type 1 (HIV-1) protease inhibitor which is significantly more active than ritonavir in cell culture, is currently under investigation for the treatment of AIDS. Development of viral resistance to ABT-378 in vitro was studied by serial passage of HIV-1 (pNL4-3) in MT-4 cells. Selection of viral variants with increasing concentrations of ABT-378 revealed a sequential appearance of mutations in the protease gene: I84V-L10F-M46I-T91S-V32I-I47V. Further selection at a 3.0 microM inhibitor concentration resulted in an additional change at residue 47 (V47A), as well as reversion at residue 32 back to the wild-type sequence. The 50% effective concentration of ABT-378 against passaged virus containing these additional changes was 338-fold higher than that against wild-type virus. In addition to changes in the protease gene, sequence analysis of passaged virus revealed mutations in the p1/p6 (P1' residue Leu to Phe) and p7/p1 (P2 residue Ala to Val) gag proteolytic processing sites. The p1/p6 mutation appeared in several clones derived from early passages and was present in all clones obtained from passage P11 (0.42 microM ABT-378) onward. The p7/p1 mutation appeared very late during the selection process and was strongly associated with the emergence of the additional change at residue 47 (V47A) and the reversion at residue 32 back to the wild-type sequence. Furthermore, this p7/p1 mutation was present in all clones obtained from passage P17 (3.0 microM ABT-378) onward and always occurred in conjunction with the p1/p6 mutation. Full-length molecular clones containing protease mutations observed very late during the selection process were constructed and found to be viable only in the presence of both the p7/p1 and p1/p6 cleavage-site mutations. This suggests that mutation of these gag proteolytic cleavage sites is required for the growth of highly resistant HIV-1 selected by ABT-378 and supports recent work demonstrating that mutations in the p7/p1/p6 region play an important role in conferring resistance to protease inhibitors (L. Doyon et al., J. Virol. 70:3763-3769, 1996; Y. M. Zhang et al., J. Virol. 71:6662-6670, 1997).
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Affiliation(s)
- A Carrillo
- Pharmaceutical Products Division, Abbott Laboratories, Abbott Park, Illinois 60064, USA.
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De Lucca GV, Kim UT, Liang J, Cordova B, Klabe RM, Garber S, Bacheler LT, Lam GN, Wright MR, Logue KA, Erickson-Viitanen S, Ko SS, Trainor GL. Nonsymmetric P2/P2' cyclic urea HIV protease inhibitors. Structure-activity relationship, bioavailability, and resistance profile of monoindazole-substituted P2 analogues. J Med Chem 1998; 41:2411-23. [PMID: 9632373 DOI: 10.1021/jm980103g] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Using the structural information gathered from the X-ray structures of various cyclic urea/HIVPR complexes, we designed and synthesized many nonsymmetrical P2/P2'-substituted cyclic urea analogues. Our efforts concentrated on using an indazole as one of the P2 substituents since this group imparted enzyme (Ki) potency as well as translation into excellent antiviral (IC90) potency. The second P2 substituent was used to adjust the physical and chemical properties in order to maximize oral bioavailability. Using this approach several very potent (IC90 11 nM) and orally bioavailable (F% 93-100%) compounds were discovered (21, 22). However, the resistance profiles of these compounds were inadequate, especially against the double (I84V/V82F) and ritonavir-selected mutant viruses. Further modification of the second P2 substituent in order to increase H-bonding interactions with the backbone atoms of residues Asp 29, Asp 30, and Gly 48 led to analogues with much better resistance profiles. However, these larger analogues were incompatible with the apparent molecular weight requirements for good oral bioavailability of the cyclic urea class of HIVPR inhibitors (MW < 610).
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Affiliation(s)
- G V De Lucca
- Dupont Merck Pharmaceutical Company, Experimental Station, P.O. Box 80500, Wilmington, Delaware 19880-0500, USA.
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Hodge CN, Lam PYS, Eyermann CJ, Jadhav PK, Ru Y, Fernandez CH, De Lucca GV, Chang CH, Kaltenbach RF, Holler ER, Woerner F, Daneker WF, Emmett G, Calabrese JC, Aldrich PE. Calculated and Experimental Low-Energy Conformations of Cyclic Urea HIV Protease Inhibitors. J Am Chem Soc 1998. [DOI: 10.1021/ja972357h] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- C. Nicholas Hodge
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Patrick Y. S. Lam
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Charles J. Eyermann
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Prabhakar K. Jadhav
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Y. Ru
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Christina H. Fernandez
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - George V. De Lucca
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Chong-Hwan Chang
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Robert F. Kaltenbach
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Edward R. Holler
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Francis Woerner
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Wayne F. Daneker
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - George Emmett
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Joseph C. Calabrese
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Paul E. Aldrich
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
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Rayner MM, Cordova B, Jackson DA. Population dynamics studies of wild-type and drug-resistant mutant HIV in mixed infections. Virology 1997; 236:85-94. [PMID: 9299620 DOI: 10.1006/viro.1997.8620] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have studied the population dynamics in response to selective drug pressure of mixtures of wild-type and mutant HIV viruses exposed to either an inhibitor of the viral protease or a nonnucleoside allosteric inhibitor of the viral reverse transcriptase. In order to quantitate mutant virus present in a mixed population, we developed a selective plaque assay, which appears to be generally applicable to population dynamics studies where the viruses in question differ in the sensitivity to a given drug by at least 10-fold. In this assay system, the titer of virus in a mixture is measured in the absence and presence of a concentration of a specific inhibitor known to suppress virus replication by 99%. Virus detected in the presence of inhibitor corresponds to mutant virus, whereas detection in the absence of drug results in quantitation of the total virion population. Wild-type virus is then estimated by difference. Utilizing this system we studied the fate of mixtures of wild-type and the protease-resistant mutant variant I84V in the presence and absence of the cyclic urea HIV protease inhibitor, DMP 450. We also examined the dynamics of mixtures of wild-type and the resistant mutant variant, L100I, in the presence and absence of the drug DMP 266. In both systems we demonstrated that in the absence of drug, mutant virus is at a selective disadvantage for growth compared to wild-type, whereas in the presence of a specific inhibitor, mutant virus exhibits the selective growth advantage over wild-type virus. Better understanding of HIV population dynamics may allow the development of superior inhibitors and the careful application of combination therapy in the clinical setting.
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Affiliation(s)
- M M Rayner
- Molecular Biology Department, The DuPont Merck Pharmaceutical Company, Wilmington, Delaware 19880, USA
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Hodge CN, Aldrich PE, Bacheler LT, Chang CH, Eyermann CJ, Garber S, Grubb M, Jackson DA, Jadhav PK, Korant B, Lam PY, Maurin MB, Meek JL, Otto MJ, Rayner MM, Reid C, Sharpe TR, Shum L, Winslow DL, Erickson-Viitanen S. Improved cyclic urea inhibitors of the HIV-1 protease: synthesis, potency, resistance profile, human pharmacokinetics and X-ray crystal structure of DMP 450. CHEMISTRY & BIOLOGY 1996; 3:301-14. [PMID: 8807858 DOI: 10.1016/s1074-5521(96)90110-6] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
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.
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Affiliation(s)
- C N Hodge
- Department of Chemical Sciences, DuPont Merck Pharmaceutical Co., Wilmington, DE 19880, USA.
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