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1

Pan, Bowen, Sumei Li, Junwei Xiao, Xin Yang, Shouxia Xie, Ying Zhou, Jian Yang et Ying Wei. « Dual Inhibition of HIV-1 and Cathepsin L Proteases by Sarcandra glabra ». Molecules 27, no 17 (29 août 2022) : 5552. http://dx.doi.org/10.3390/molecules27175552.

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The COVID-19 pandemic continues to impose a huge threat on human health due to rapid viral mutations. Thus, it is imperative to develop more potent antivirals with both prophylactic and treatment functions. In this study, we screened for potential antiviral compounds from Sarcandra glabra (SG) against Cathepsin L and HIV-1 proteases. A FRET assay was applied to investigate the inhibitory effects and UPLC-HRMS was employed to identify and quantify the bioactive components. Furthermore, molecular docking was carried out to get a glimpse of the binding of active compounds to the proteases. Our results showed that the SG extracts (SGW, SG30, SG60, and SG85) inhibited HIV-1 protease with an IC50 of 0.003~0.07 mg/mL and Cathepsin L protease with an IC50 of 0.11~0.26 mg/mL. Fourteen compounds were identified along with eight quantified from the SG extracts. Chlorogenic acid, which presented in high content in the extracts (12.7~15.76 µg/mg), possessed the most potent inhibitory activity against HIV-1 protease (IC50 = 0.026 mg/mL) and Cathepsin L protease (inhibition: 40.8% at 0.01 mg/mL). Thus, SG extracts and the active ingredients could potentially be used to prevent/treat viral infections, including SARS-CoV-2, due to their dual-inhibition functions against viral proteases.
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Park, Jung-Ho, Yoshihiro Yamaguchi et Masayori Inouye. « Intramolecular Regulation of the Sequence-Specific mRNA Interferase Activity of MazF Fused to a MazE Fragment with a Linker Cleavable by Specific Proteases ». Applied and Environmental Microbiology 78, no 11 (23 mars 2012) : 3794–99. http://dx.doi.org/10.1128/aem.00364-12.

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ABSTRACTThe genomes of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) consist of single-stranded RNA encoding polyproteins, which are processed to individual functional proteins by virus-encoded specific proteases. These proteases have been used as targets for drug development. Here, instead of targeting these proteases to inhibit viral infection, we utilized the protease activity to activate a toxic protein to prevent viral infection. We engineered the MazE-MazF antitoxin-toxin system ofEscherichia colito fuse a C-terminal 41-residue fragment of antitoxin MazE to the N-terminal end of toxin MazF with a linker having a specific protease cleavage site for either HIV PR (HIV-1 protease), NS3 protease (HCV protease), or factor Xa. These fusion proteins formed a stable dimer (instead of the MazF2-MazE2-MazF2heterohexamer in nature) to inactivate the ACA (sequence)-specific mRNA interferase activity of MazF. When the fusion proteins were incubated with the corresponding proteases, the MazE fragment was cleaved from the fusion proteins, releasing active MazF, which then acted as an ACA-specific mRNA interferase cleaving single-stranded MS2 phage RNA. The intramolecular regulation of MazF toxicity by proteases as demonstrated may provide a novel approach for preventive and therapeutic treatments of infection by HIV-1, HCV, and other single-stranded RNA viruses.
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Capel, Elena, Glòria Martrus, Mariona Parera, Bonaventura Clotet et Miguel Angel Martínez. « Evolution of the human immunodeficiency virus type 1 protease : effects on viral replication capacity and protease robustness ». Journal of General Virology 93, no 12 (1 décembre 2012) : 2625–34. http://dx.doi.org/10.1099/vir.0.045492-0.

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The rapid spread of human immunodeficiency virus type 1 (HIV-1) in humans has been accompanied by continuous extensive genetic diversification of the virus. The aim of this study was to investigate the impact of HIV-1 diversification on HIV-1 replication capacity (RC) and mutational robustness. Thirty-three HIV-1 protease sequences were amplified from three groups of viruses: two naïve sample groups isolated 15 years apart plus a third group of protease inhibitor-(PI) resistant samples. The amplified proteases were recombined with an HXB2 infectious clone and RC was determined in MT-4 cells. RC was also measured in these three groups after random mutagenesis in vitro using error-prone PCR. No significant RC differences were observed between recombinant viruses from either early or recent naïve isolates (P = 0.5729), even though the proteases from the recent isolates had significantly lower sequence conservation scores compared with a subtype B ancestral sequence (P<0.0001). Randomly mutated recombinant viruses from the three groups exhibited significantly lower RC values than the corresponding wild-type viruses (P<0.0001). There was no significant difference regarding viral infectivity reduction between viruses carrying randomly mutated naïve proteases from early or recent sample isolates (P = 0.8035). Interestingly, a significantly greater loss of RC was observed in the PI-resistant protease group (P = 0.0400). These results demonstrate that protease sequence diversification has not affected HIV-1 RC or protease robustness and indicate that proteases carrying PI resistance substitutions are less robust than naïve proteases.
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Martínez, Miguel-Angel, Marta Cabana, Mariona Parera, Arantxa Gutierrez, José A. Esté et Bonaventura Clotet. « A Bacteriophage Lambda-Based Genetic Screen for Characterization of the Activity and Phenotype of the Human Immunodeficiency Virus Type 1 Protease ». Antimicrobial Agents and Chemotherapy 44, no 5 (1 mai 2000) : 1132–39. http://dx.doi.org/10.1128/aac.44.5.1132-1139.2000.

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ABSTRACT Human immunodeficiency virus type 1 (HIV-1) resistance to antiretroviral drugs is the main cause of patient treatment failure. Despite the problems associated with interpretation of HIV-1 resistance testing, resistance monitoring should help in the rational design of initial or rescue antiretroviral therapies. It has previously been shown that the activity of the HIV-1 protease can be monitored by using a bacteriophage lambda-based genetic assay. This genetic screening system is based on the bacteriophage lambda regulatory circuit in which the viral repressor cI is specifically cleaved to initiate the lysogenic to lytic switch. We have adapted this simple lambda-based genetic assay for the analysis of the activities and phenotypes of different HIV-1 proteases. Lambda phages that encode HIV-1 proteases either from laboratory strains (strain HXB2) or from clinical samples are inhibited in a dose-dependent manner by the HIV-1 protease inhibitors indinavir, ritonavir, saquinavir, and nelfinavir. Distinct susceptibilities to different drugs were also detected among phages that encode HIV-1 proteases carrying different resistance mutations, further demonstrating the specificity of this assay. Differences in proteolytic processing activity can also be directly monitored with this genetic screen system since two phage populations compete in culture with each other until one phage outgrows the other. In summary, we present here a simple, safe, and rapid genetic screening system that may be used to predict the activities and phenotypes of HIV-1 proteases in the course of viral infection and antiretroviral therapy. This assay responds appropriately to well-known HIV-1 protease inhibitors and can be used to search for new protease inhibitors.
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McPHEE, Fiona, Patricia S. CALDERA, Guy W. BEMIS, Antony F. McDONAGH, Irwin D. KUNTZ et Charles S. CRAIK. « Bile pigments as HIV-1 protease inhibitors and their effects on HIV-1 viral maturation and infectivity in vitro ». Biochemical Journal 320, no 2 (1 décembre 1996) : 681–86. http://dx.doi.org/10.1042/bj3200681.

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Using recently developed molecular-shape description algorithms, we searched the Available Chemical Directory for known compounds similar in shape to the potent HIV-1 protease inhibitor Merck L-700,417; 15 compounds most similar in shape to the inhibitor were selected for testing in vitro. Four of these inhibited the protease at 100 µM or less and the most active of the four were the naturally occurring pigments biliverdin and bilirubin. Biliverdin and bilirubin inhibited recombinant HIV-1 protease in vitro at pH 7.8 with Ki values of approx. 1 µM, and also inhibited HIV-2 and simian immunodeficiency virus proteases. The related pyrrolic pigments stercobilin, urobilin, biliverdin dimethyl ester and xanthobilirubic acid showed similar inhibitory activity at low micromolar concentrations. Biliverdin, bilirubin and xanthobilirubic acid did not inhibit viral polyprotein processing in cultured cells, but they reduced viral infectivity significantly. At 100 µM, xanthobilirubic acid affected viral assembly, resulting in a 50% decrease in the generation of infectious particles. In contrast, at the same concentrations biliverdin and bilirubin exerted little or no effect on viral assembly but blocked infection of HeLaT4 cells by 50%. These results suggest that bile pigments might be a new class of potential lead compounds for developing protease inhibitors and they raise the question of whether hyperbilirubinaemia can influence the course of HIV infection.
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Raugi, Dana N., Robert A. Smith et Geoffrey S. Gottlieb. « Four Amino Acid Changes in HIV-2 Protease Confer Class-Wide Sensitivity to Protease Inhibitors ». Journal of Virology 90, no 2 (11 novembre 2015) : 1062–69. http://dx.doi.org/10.1128/jvi.01772-15.

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ABSTRACTProtease is essential for retroviral replication, and protease inhibitors (PI) are important for treating HIV infection. HIV-2 exhibits intrinsic resistance to most FDA-approved HIV-1 PI, retaining clinically useful susceptibility only to lopinavir, darunavir, and saquinavir. The mechanisms for this resistance are unclear; although HIV-1 and HIV-2 proteases share just 38 to 49% sequence identity, all critical structural features of proteases are conserved. Structural studies have implicated four amino acids in the ligand-binding pocket (positions 32, 47, 76, and 82). We constructed HIV-2ROD9molecular clones encoding the corresponding wild-type HIV-1 amino acids (I32V, V47I, M76L, and I82V) either individually or together (clone PRΔ4) and compared the phenotypic sensitivities (50% effective concentration [EC50]) of mutant and wild-type viruses to nine FDA-approved PI. Single amino acid replacements I32V, V47I, and M76L increased the susceptibility of HIV-2 to multiple PI, but no single change conferred class-wide sensitivity. In contrast, clone PRΔ4 showed PI susceptibility equivalent to or greater than that of HIV-1 for all PI. We also compared crystallographic structures of wild-type HIV-1 and HIV-2 proteases complexed with amprenavir and darunavir to models of the PRΔ4 enzyme. These models suggest that the amprenavir sensitivity of PRΔ4 is attributable to stabilizing enzyme-inhibitor interactions in the P2 and P2′ pockets of the protease dimer. Together, our results show that the combination of four amino acid changes in HIV-2 protease confer a pattern of PI susceptibility comparable to that of HIV-1, providing a structural rationale for intrinsic HIV-2 PI resistance and resolving long-standing questions regarding the determinants of differential PI susceptibility in HIV-1 and HIV-2.IMPORTANCEProteases are essential for retroviral replication, and HIV-1 and HIV-2 proteases share a great deal of structural similarity. However, only three of nine FDA-approved HIV-1 protease inhibitors (PI) are active against HIV-2. The underlying reasons for intrinsic PI resistance in HIV-2 are not known. We examined the contributions of four amino acids in the ligand-binding pocket of the enzyme that differ between HIV-1 and HIV-2 by constructing HIV-2 clones encoding the corresponding HIV-1 amino acids and testing the PI susceptibilities of the resulting viruses. We found that the HIV-2 clone containing all four changes (PRΔ4) was as susceptible as HIV-1 to all nine PI. We also modeled the PRΔ4 enzyme structure and compared it to existing crystallographic structures of HIV-1 and HIV-2 proteases complexed with amprenavir and darunavir. Our findings demonstrate that four positions in the ligand-binding cleft of protease are the primary cause of HIV-2 PI resistance.
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Álvarez, Enrique, Luis Menéndez-Arias et Luis Carrasco. « The Eukaryotic Translation Initiation Factor 4GI Is Cleaved by Different Retroviral Proteases ». Journal of Virology 77, no 23 (1 décembre 2003) : 12392–400. http://dx.doi.org/10.1128/jvi.77.23.12392-12400.2003.

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ABSTRACT The initiation factor eIF4G plays a central role in the regulation of translation. In picornaviruses, as well as in human immunodeficiency virus type 1 (HIV-1), cleavage of eIF4G by the viral protease leads to inhibition of protein synthesis directed by capped cellular mRNAs. In the present work, cleavage of both eIF4GI and eIF4GII has been analyzed by employing the proteases encoded within the genomes of several members of the family Retroviridae, e.g., Moloney murine leukemia virus (MoMLV), mouse mammary tumor virus, human T-cell leukemia virus type 1, HIV-2, and simian immunodeficiency virus. All of the retroviral proteases examined were able to cleave the initiation factor eIF4GI both in intact cells and in cell-free systems, albeit with different efficiencies. The eIF4GI hydrolysis patterns obtained with HIV-1 and HIV-2 proteases were very similar to each other but rather different from those obtained with MoMLV protease. Both eIF4GI and eIF4GII were cleaved very efficiently by the MoMLV protease. However, eIF4GII was a poor substrate for HIV proteases. Proteolytic cleavage of eIF4G led to a profound inhibition of cap-dependent translation, while protein synthesis driven by mRNAs containing internal ribosome entry site elements remained unaffected or was even stimulated in transfected cells.
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Álvarez, Enrique, Alfredo Castelló, Luis Menéndez-Arias et Luis Carrasco. « HIV protease cleaves poly(A)-binding protein ». Biochemical Journal 396, no 2 (15 mai 2006) : 219–26. http://dx.doi.org/10.1042/bj20060108.

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The PABP [poly(A)-binding protein] is able to interact with the 3′ poly(A) tail of eukaryotic mRNA, promoting its translation. Cleavage of PABP by viral proteases encoded by several picornaviruses and caliciviruses plays a role in the abrogation of cellular protein synthesis. We report that infection of MT-2 cells with HIV-1 leads to efficient proteolysis of PABP. Analysis of PABP integrity was carried out in BHK-21 (baby-hamster kidney) and COS-7 cells upon individual expression of the protease from several members of the Retroviridae family, e.g. MoMLV (Moloney murine leukaemia virus), MMTV (mouse mammary tumour virus), HTLV-I (human T-cell leukaemia virus type I), SIV (simian immunodeficiency virus), HIV-1 and HIV-2. Moreover, protease activity against PABP was tested in a HeLa-cell-free system. Only MMTV, HIV-1 and HIV-2 proteases were able to cleave PABP in the absence of other viral proteins. Purified HIV-1 and HIV-2 proteases cleave PABP1 directly at positions 237 and 477, separating the two first RNA-recognition motifs from the C-terminal domain of PABP. An additional cleavage site located at position 410 was detected for HIV-2 protease. These findings indicate that some retroviruses may share with picornaviruses and caliciviruses the capacity to proteolyse PABP.
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DAVIS, David A., Fonda M. NEWCOMB, Jackob MOSKOVITZ, Paul T. WINGFIELD, Stephen J. STAHL, Joshua KAUFMAN, Henry M. FALES, Rodney L. LEVINE et Robert YARCHOAN. « HIV-2 protease is inactivated after oxidation at the dimer interface and activity can be partly restored with methionine sulphoxide reductase ». Biochemical Journal 346, no 2 (22 février 2000) : 305–11. http://dx.doi.org/10.1042/bj3460305.

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Human immunodeficiency viruses encode a homodimeric protease that is essential for the production of infectious virus. Previous studies have shown that HIV-1 protease is susceptible to oxidative inactivation at the dimer interface at Cys-95, a process that can be reversed both chemically and enzymically. Here we demonstrate a related yet distinct mechanism of reversible inactivation of the HIV-2 protease. Exposure of the HIV-2 protease to H2O2 resulted in conversion of the two methionine residues (Met-76 and Met-95) to methionine sulphoxide as determined by amino acid analysis and mass spectrometry. This oxidation completely inactivated protease activity. However, the activity could be restored (up to 40%) after exposure of the oxidized protease to methionine sulphoxide reductase. This treatment resulted in the reduction of methionine sulphoxide 95 but not methionine sulphoxide 76 to methionine, as determined by peptide mapping/mass spectrometry. We also found that exposure of immature HIV-2 particles to H2O2 led to the inhibition of polyprotein processing in maturing virus particles comparable to that demonstrated for HIV-1 particles. Thus oxidative inactivation of the HIV protease in vitro and in maturing viral particles is not restricted to the type 1 proteases. These studies indicate that two distinct retroviral proteases are susceptible to inactivation after a very minor modification at residue 95 of the dimer interface and suggest that the dimer interface might be a viable target for the development of novel protease inhibitors.
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Sohraby, Farzin, et Hassan Aryapour. « Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by supervised molecular dynamics simulation ». PLOS ONE 16, no 9 (27 septembre 2021) : e0257916. http://dx.doi.org/10.1371/journal.pone.0257916.

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Determining the unbinding pathways of potential small molecule compounds from their target proteins is of great significance for designing efficacious treatment solutions. One of these potential compounds is the approved HIV-1 protease inhibitor, Indinavir, which has a weak effect on the HTLV-1 protease. In this work, by employing the SuMD method, we reconstructed the unbinding pathways of Indinavir from HIV and HTLV-1 proteases to compare and understand the mechanism of the unbinding and to discover the reasons for the lack of inhibitory activity of Indinavir against the HTLV-1 protease. We achieved multiple unbinding events from both HIV and HTLV-1 proteases in which the RMSD values of Indinavir reached over 40 Å. Also, we found that the mobility and fluctuations of the flap region are higher in the HTLV-1 protease, making the drug less stable. We realized that critically positioned aromatic residues such as Trp98/Trp98′ and Phe67/Phe67′ in the HTLV-1 protease could make strong π-Stacking interactions with Indinavir in the unbinding pathway, which are unfavorable for the stability of Indinavir in the active site. The details found in this study can make a reasonable explanation for the lack of inhibitory activity of this drug against HTLV-1 protease. We believe the details discovered in this work can help design more effective and selective inhibitors for the HTLV-1 protease.
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Savarino, Andrea, Roberto Cauda et Antonio Cassone. « Aspartic Proteases ofPlasmodium falciparumas the Target of HIV‐1 Protease Inhibitors ». Journal of Infectious Diseases 191, no 8 (15 avril 2005) : 1381–82. http://dx.doi.org/10.1086/428781.

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Visnegarwala, Fehmida, Daniel M. Musher et A. C. White. « HIV-1 Protease Inhibitors May Interfere with the Ubiquitous Intracellular Proteases ». Annals of Internal Medicine 135, no 9 (6 novembre 2001) : 840. http://dx.doi.org/10.7326/0003-4819-135-9-200111060-00017.

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Yanchunas, Joseph, David R. Langley, Li Tao, Ronald E. Rose, Jacques Friborg, Richard J. Colonno et Michael L. Doyle. « Molecular Basis for Increased Susceptibility of Isolates with Atazanavir Resistance-Conferring Substitution I50L to Other Protease Inhibitors ». Antimicrobial Agents and Chemotherapy 49, no 9 (septembre 2005) : 3825–32. http://dx.doi.org/10.1128/aac.49.9.3825-3832.2005.

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ABSTRACT Protease inhibitors (PIs) are highly effective drugs against the human immunodeficiency virus (HIV), yet long-term therapeutic use is limited by emergence of HIV type 1 (HIV-1) protease substitutions that confer cross-resistance to multiple protease inhibitor drugs. Atazanavir is a highly potent HIV protease inhibitor with a distinct resistance profile that includes effectiveness against most HIV-1 isolates resistant to one or two PIs. The signature resistance substitution for atazanavir is I50L, and it is frequently (53%) accompanied by a compensatory A71V substitution that helps restore viability and increases atazanavir resistance levels. We measured the binding affinities of wild-type (WT) and I50L/A71V HIV-1 proteases to atazanavir and other currently approved PIs (ritonavir, lopinavir, saquinavir, nelfinavir, indinavir, and amprenavir) by isothermal titration calorimetry. Remarkably, we find that all of the PIs have 2- to 10-fold increased affinities for I50L/A71V protease, except for atazanavir. The results are also manifested by thermal stability measures of affinity for WT and I50L/A71V proteases. Additional biophysical and enzyme kinetics experiments show I50L/A71V protease is a stable enzyme with catalytic activity that is slightly reduced (34%) relative to the WT. Computational modeling reveals that the unique resistance phenotype of I50L/A71V protease likely originates from bulky tert-butyl groups at P2 and P2′ (specific to atazanavir) that sterically clash with methyl groups on residue L50. The results of this study provide a molecular understanding of the novel hypersusceptibility of atazanavir-resistant I50L/A71V-containing clinical isolates to other currently approved PIs.
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Eron, Joseph J. « HIV-1 Protease Inhibitors ». Clinical Infectious Diseases 30, Supplement_2 (1 juin 2000) : S160—S170. http://dx.doi.org/10.1086/313853.

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&NA;. « HIV-1 protease inhibitors ». Inpharma Weekly &NA;, no 840 (juin 1992) : 13. http://dx.doi.org/10.2165/00128413-199208400-00018.

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Edwards, Paul. « HIV-1 protease inhibitors ». Drug Discovery Today 6, no 8 (avril 2001) : 437–39. http://dx.doi.org/10.1016/s1359-6446(01)01736-6.

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Deeks, Steven G. « HIV-1 Protease Inhibitors ». JAMA 277, no 2 (8 janvier 1997) : 145. http://dx.doi.org/10.1001/jama.1997.03540260059037.

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Parikh, Sunil, Jiri Gut, Eva Istvan, Daniel E. Goldberg, Diane V. Havlir et Philip J. Rosenthal. « Antimalarial Activity of Human Immunodeficiency Virus Type 1 Protease Inhibitors ». Antimicrobial Agents and Chemotherapy 49, no 7 (juillet 2005) : 2983–85. http://dx.doi.org/10.1128/aac.49.7.2983-2985.2005.

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ABSTRACT Aspartic proteases play key roles in the biology of malaria parasites and human immunodeficiency virus type 1 (HIV-1). We tested the activity of seven HIV-1 protease inhibitors against cultured Plasmodium falciparum. All compounds inhibited the development of parasites at pharmacologically relevant concentrations. The most potent compound, lopinavir, was active against parasites (50% inhibitory concentration [IC50], 0.9 to 2.1 μM) at concentrations well below those achieved by ritonavir-boosted lopinavir therapy. Lopinavir also inhibited the P. falciparum aspartic protease plasmepsin II at a similar concentration (IC50, 2.7 μM). These findings suggest that use of HIV-1 protease inhibitors may offer clinically relevant antimalarial activity.
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Bagossi, Péter, Tamás Sperka, Anita Fehér, János Kádas, Gábor Zahuczky, Gabriella Miklóssy, Péter Boross et József Tözsér. « Amino Acid Preferences for a Critical Substrate Binding Subsite of Retroviral Proteases in Type 1 Cleavage Sites ». Journal of Virology 79, no 7 (1 avril 2005) : 4213–18. http://dx.doi.org/10.1128/jvi.79.7.4213-4218.2005.

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ABSTRACT The specificities of the proteases of 11 retroviruses representing each of the seven genera of the family Retroviridae were studied using a series of oligopeptides with amino acid substitutions in the P2 position of a naturally occurring type 1 cleavage site (Val-Ser-Gln-Asn-Tyr↓Pro-Ile-Val-Gln; the arrow indicates the site of cleavage) in human immunodeficiency virus type 1 (HIV-1). This position was previously found to be one of the most critical in determining the substrate specificity differences of retroviral proteases. Specificities at this position were compared for HIV-1, HIV-2, equine infectious anemia virus, avian myeloblastosis virus, Mason-Pfizer monkey virus, mouse mammary tumor virus, Moloney murine leukemia virus, human T-cell leukemia virus type 1, bovine leukemia virus, human foamy virus, and walleye dermal sarcoma virus proteases. Three types of P2 preferences were observed: a subgroup of proteases preferred small hydrophobic side chains (Ala and Cys), and another subgroup preferred large hydrophobic residues (Ile and Leu), while the protease of HIV-1 preferred an Asn residue. The specificity distinctions among the proteases correlated well with the phylogenetic tree of retroviruses prepared solely based on the protease sequences. Molecular models for all of the proteases studied were built, and they were used to interpret the results. While size complementarities appear to be the main specificity-determining features of the S2 subsite of retroviral proteases, electrostatic contributions may play a role only in the case of HIV proteases. In most cases the P2 residues of naturally occurring type 1 cleavage site sequences of the studied proteases agreed well with the observed P2 preferences.
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Lin, Ying-Chuan, Zachary Beck, Taekyu Lee, Van-Duc Le, Garrett M. Morris, Arthur J. Olson, Chi-Huey Wong et John H. Elder. « Alteration of Substrate and Inhibitor Specificity of Feline Immunodeficiency Virus Protease ». Journal of Virology 74, no 10 (15 mai 2000) : 4710–20. http://dx.doi.org/10.1128/jvi.74.10.4710-4720.2000.

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ABSTRACT Feline immunodeficiency virus (FIV) protease is structurally very similar to human immunodeficiency virus (HIV) protease but exhibits distinct substrate and inhibitor specificities. We performed mutagenesis of subsite residues of FIV protease in order to define interactions that dictate this specificity. The I37V, N55M, M56I, V59I, and Q99V mutants yielded full activity. The I37V, N55M, V59I, and Q99V mutants showed a significant increase in activity against the HIV-1 reverse transcriptase/integrase and P2/nucleocapsid junction peptides compared with wild-type (wt) FIV protease. The I37V, V59I, and Q99V mutants also showed an increase in activity against two rapidly cleaved peptides selected by cleavage of a phage display library with HIV-1 protease. Mutations at Q54K, I98P, and L101I dramatically reduced activity. Mutants containing a I35D or I57G substitution showed no activity against either FIV or HIV substrates. FIV proteases all failed to cut HIV-1 matrix/capsid, P1/P6, P6/protease, and protease/reverse transcriptase junctions, indicating that none of the substitutions were sufficient to change the specificity completely. The I37V, N55M, M56I, V59I, and Q99V mutants, compared with wt FIV protease, all showed inhibitor specificity more similar to that of HIV-1 protease. The data also suggest that FIV protease prefers a hydrophobic P2/P2′ residue like Val over Asn or Glu, which are utilized by HIV-1 protease, and that S2/S2′ might play a critical role in distinguishing FIV and HIV-1 protease by specificity. The findings extend our observations regarding the interactions involved in substrate binding and aid in the development of broad-based inhibitors.
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ASANTE-APPIAH, Ernest, et William W. C. CHAN. « Synergistic binding of inhibitors to the protease from HIV type 1 ». Biochemical Journal 315, no 1 (1 avril 1996) : 113–17. http://dx.doi.org/10.1042/bj3150113.

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Inhibition of the protease in HIV is a potentially useful approach for the treatment of AIDS. In the course of evaluating inhibitors of the HIV-1 protease, we observed a strong synergism between certain inhibitors that might be expected to bind to different sites in this enzyme. The binding affinity of carbobenzyloxyisoleucinylphenylalaninol, for example, is increased 125-fold in the presence of carbobenzyloxyglutaminylisoamylamide. These synergistic effects between inhibitors have specific structural requirements that correlate well with the known substrate preference of the enzyme. The molecular basis for this phenomenon remains to be elucidated but it could involve substrate-induced conformational change as part of the reaction mechanism. Similar effects have been reported previously for several zinc proteases. Thus this work extends the observation to a different class of enzymes and suggests that the phenomenon might be widespread.
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Pettit, Steven C., Sergei Gulnik, Lori Everitt et Andrew H. Kaplan. « The Dimer Interfaces of Protease and Extra-Protease Domains Influence the Activation of Protease and the Specificity of GagPol Cleavage ». Journal of Virology 77, no 1 (1 janvier 2003) : 366–74. http://dx.doi.org/10.1128/jvi.77.1.366-374.2003.

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ABSTRACT Activation of the human immunodeficiency virus type 1 (HIV-1) protease is an essential step in viral replication. As is the case for all retroviral proteases, enzyme activation requires the formation of protease homodimers. However, little is known about the mechanisms by which retroviral proteases become active within their precursors. Using an in vitro expression system, we have examined the determinants of activation efficiency and the order of cleavage site processing for the protease of HIV-1 within the full-length GagPol precursor. Following activation, initial cleavage occurs between the viral p2 and nucleocapsid proteins. This is followed by cleavage of a novel site located in the transframe domain. Mutational analysis of the dimer interface of the protease produced differential effects on activation and specificity. A subset of mutations produced enhanced cleavage at the amino terminus of the protease, suggesting that, in the wild-type precursor, cleavages that liberate the protease are a relatively late event. Replacement of the proline residue at position 1 of the protease dimer interface resulted in altered cleavage of distal sites and suggests that this residue functions as a cis-directed specificity determinant. In summary, our studies indicate that interactions within the protease dimer interface help determine the order of precursor cleavage and contribute to the formation of extended-protease intermediates. Assembly domains within GagPol outside the protease domain also influence enzyme activation.
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Davis, David A., Haydar Bulut, Prabha Shrestha, Hiroaki Mitsuya et Robert Yarchoan. « Regulation of Retroviral and SARS-CoV-2 Protease Dimerization and Activity through Reversible Oxidation ». Antioxidants 11, no 10 (18 octobre 2022) : 2054. http://dx.doi.org/10.3390/antiox11102054.

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Most viruses encode their own proteases to carry out viral maturation and these often require dimerization for activity. Studies on human immunodeficiency virus type 1 (HIV-1), type 2 (HIV-2) and human T-cell leukemia virus (HTLV-1) proteases have shown that the activity of these proteases can be reversibly regulated by cysteine (Cys) glutathionylation and/or methionine oxidation (for HIV-2). These modifications lead to inhibition of protease dimerization and therefore loss of activity. These changes are reversible with the cellular enzymes, glutaredoxin or methionine sulfoxide reductase. Perhaps more importantly, as a result, the maturation of retroviral particles can also be regulated through reversible oxidation and this has been demonstrated for HIV-1, HIV-2, Mason-Pfizer monkey virus (M-PMV) and murine leukemia virus (MLV). More recently, our group has learned that SARS-CoV-2 main protease (Mpro) dimerization and activity can also be regulated through reversible glutathionylation of Cys300. Overall, these studies reveal a conserved way for viruses to regulate viral polyprotein processing particularly during oxidative stress and reveal novel targets for the development of inhibitors of dimerization and activity of these important viral enzyme targets.
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24

Dekhtyar, Tatyana, Teresa I. Ng, Liangjun Lu, Sherie Masse, David A. DeGoey, William J. Flosi, David J. Grampovnik, Larry L. Klein, Dale J. Kempf et Akhteruzzaman Molla. « Characterization of a Novel Human Immunodeficiency Virus Type 1 Protease Inhibitor, A-790742 ». Antimicrobial Agents and Chemotherapy 52, no 4 (22 janvier 2008) : 1337–44. http://dx.doi.org/10.1128/aac.01132-07.

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ABSTRACT A-790742 is a potent human immunodeficiency virus type 1 (HIV-1) protease inhibitor, with 50% effective concentrations ranging from 2 to 7 nM against wild-type HIV-1. The activity of this compound is lowered by approximately sevenfold in the presence of 50% human serum. A-790742 maintained potent antiviral activity against lopinavir-resistant variants generated in vitro as well as against a panel of molecular clones containing proteases derived from HIV-1 patient isolates with multiple protease mutations. During in vitro selection, A-790742 selected two primary mutations (V82L and I84V) along with L23I, L33F, K45I, A71V/A, and V77I in the pNL4-3 background and two other mutations (A71V and V82G) accompanied by M46I and L63P in the HIV-1 RF background. HIV-1 pNL4-3 clones with a single V82L or I84V mutation were phenotypically resistant to A-790742 and ritonavir. Taking these results together, A-790742 displays a favorable anti-HIV-1 profile against both the wild type and a large number of mutants resistant to other protease inhibitors. The selection of the uncommon V82L and V82G mutations in protease by A-790742 suggests the potential for an advantageous resistance profile with this protease inhibitor.
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25

Meek, Thomas D. « Inhibitors of HIV-1 Protease ». Journal of Enzyme Inhibition 6, no 1 (janvier 1992) : 65–98. http://dx.doi.org/10.3109/14756369209041357.

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Papa, Anna, Evagelia Papadimitriou, Androniki Papoutsi et Antonis Antoniadis. « M36I, protease gene, HIV-1 ». AIDS 17, no 12 (août 2003) : 1858–59. http://dx.doi.org/10.1097/00002030-200308150-00019.

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Baures, Paul W. « Heterocyclic HIV-1 Protease Inhibitors ». Organic Letters 1, no 2 (juillet 1999) : 249–52. http://dx.doi.org/10.1021/ol990586y.

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Louis, John M., Rieko Ishima, Issa Nesheiwat, Lewis K. Pannell, Shannon M. Lynch, Dennis A. Torchia et Angela M. Gronenborn. « Revisiting Monomeric HIV-1 Protease ». Journal of Biological Chemistry 278, no 8 (4 décembre 2002) : 6085–92. http://dx.doi.org/10.1074/jbc.m209726200.

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Ikezoe, Takayuki, Yasuko Hisatake, Tamotsu Takeuchi, Yuji Ohtsuki, Yang Yang, Jonathan W. Said, Hirokuni Taguchi et H. Phillip Koeffler. « HIV-1 Protease Inhibitor, Ritonavir ». Cancer Research 64, no 20 (15 octobre 2004) : 7426–31. http://dx.doi.org/10.1158/0008-5472.can-03-2677.

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Bonini, Carlo, Lucia Chiummiento, Margherita De Bonis, Nadia Di Blasio, Maria Funicello, Paolo Lupattelli, Rocco Pandolfo, Francesco Tramutola et Federico Berti. « Synthesis of New Thienyl Ring Containing HIV-1 Protease Inhibitors : Promising Preliminary Pharmacological Evaluation against Recombinant HIV-1 Proteases§ ». Journal of Medicinal Chemistry 53, no 4 (25 février 2010) : 1451–57. http://dx.doi.org/10.1021/jm900846f.

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31

Prabu-Jeyabalan, Moses, Ellen A. Nalivaika, Nancy M. King et Celia A. Schiffer. « Structural Basis for Coevolution of a Human Immunodeficiency Virus Type 1 Nucleocapsid-p1 Cleavage Site with a V82A Drug-Resistant Mutation in Viral Protease ». Journal of Virology 78, no 22 (15 novembre 2004) : 12446–54. http://dx.doi.org/10.1128/jvi.78.22.12446-12454.2004.

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ABSTRACT Maturation of human immunodeficiency virus (HIV) depends on the processing of Gag and Pol polyproteins by the viral protease, making this enzyme a prime target for anti-HIV therapy. Among the protease substrates, the nucleocapsid-p1 (NC-p1) sequence is the least homologous, and its cleavage is the rate-determining step in viral maturation. In the other substrates of HIV-1 protease, P1 is usually either a hydrophobic or an aromatic residue, and P2 is usually a branched residue. NC-p1, however, contains Asn at P1 and Ala at P2. In response to the V82A drug-resistant protease mutation, the P2 alanine of NC-p1 mutates to valine (AP2V). To provide a structural rationale for HIV-1 protease binding to the NC-p1 cleavage site, we solved the crystal structures of inactive (D25N) WT and V82A HIV-1 proteases in complex with their respective WT and AP2V mutant NC-p1 substrates. Overall, the WT NC-p1 peptide binds HIV-1 protease less optimally than the AP2V mutant, as indicated by the presence of fewer hydrogen bonds and fewer van der Waals contacts. AlaP2 does not fill the P2 pocket completely; PheP1′ makes van der Waals interactions with Val82 that are lost with the V82A protease mutation. This loss is compensated by the AP2V mutation, which reorients the peptide to a conformation more similar to that observed in other substrate-protease complexes. Thus, the mutant substrate not only binds the mutant protease more optimally but also reveals the interdependency between the P1′ and P2 substrate sites. This structural interdependency results from coevolution of the substrate with the viral protease.
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Kádas, János, Péter Boross, Irene T. Weber, Péter Bagossi, Krisztina Matúz et József Tözsér. « C-terminal residues of mature human T-lymphotropic virus type 1 protease are critical for dimerization and catalytic activity ». Biochemical Journal 416, no 3 (26 novembre 2008) : 357–64. http://dx.doi.org/10.1042/bj20071132.

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HTLV-1 [HTLV (human T-cell lymphotrophic virus) type 1] is associated with a number of human diseases. HTLV-1 protease is essential for virus replication, and similarly to HIV-1 protease, it is a potential target for chemotherapy. The primary sequence of HTLV-1 protease is substantially longer compared with that of HIV-1 protease, and the role of the ten C-terminal residues is controversial. We have expressed C-terminally-truncated forms of HTLV-1 protease with and without N-terminal His tags. Removal of five of the C-terminal residues caused a 4–40-fold decrease in specificity constants, whereas the removal of an additional five C-terminal residues rendered the protease completely inactive. The addition of the N-terminal His tag dramatically decreased the activity of HTLV-1 protease forms. Pull-down experiments carried out with His-tagged forms, gel-filtration experiments and dimerization assays provided the first unequivocal experimental results for the role of the C-terminal residues in dimerization of the enzyme. There is a hydrophobic tunnel on the surface of HTLV-1 protease close to the C-terminal ends that is absent in the HIV-1 protease. This hydrophobic tunnel can accommodate the extra C-terminal residues of HTLV-1 protease, which was predicted to stabilize the dimer of the full-length enzyme and provides an alternative target site for protease inhibition.
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33

Pan, Bo Wen, Jun Wei Xiao, Su Mei Li, Xin Yang, Xia Zhou, Qing Wen Sun, Mei Chen et al. « Inhibitors of HIV-1 and Cathepsin L Proteases Identified from the Insect Gall of Hypericum kouytchense ». Pharmaceuticals 15, no 12 (30 novembre 2022) : 1499. http://dx.doi.org/10.3390/ph15121499.

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Hypericum kouytchense Lévl is a semi-evergreen plant of the Hypericaceae family. Its roots and seeds have been used in a number of traditional remedies for antipyretic, detoxification, anti-inflammatory, antimicrobial and antiviral functions. However, to date, no bioactivity compounds have been characterized from the insect gall of H. kouytchens. In this study, we evaluated the antiviral activities of different extracts from the insect gall of H. kouytchen against cathepsin L, HIV-1 and renin proteases and identified the active ingredients using UPLC–HRMS. Four different polar extracts (HW, H30, H60 and H85) of the H. kouytchense insect gall exhibited antiviral activities with IC50 values of 10.0, 4.0, 3.2 and 17.0 µg/mL against HIV-1 protease; 210.0, 34.0, 24.0 and 30.0 µg/mL against cathepsin L protease; and 180.0, 65.0, 44.0 and 39.0 µg/mL against human renin, respectively. Ten compounds were identified and quantified in the H. kouytchense insect gall extracts. Epicatechin, eriodictyol and naringenin chalcone were major ingredients in the extracts with contents ranging from 3.9 to 479.2 µg/mg. For HIV-1 protease, seven compounds showed more than 65% inhibition at a concentration of 1000.0 µg/mL, especially for hypericin and naringenin chalcone with IC50 values of 1.8 and 33.0 µg/mL, respectively. However, only hypericin was active against cathepsin L protease with an IC50 value of 17,100.0 µg/mL, and its contents were from 0.99 to 11.65 µg/mg. Furthermore, we attempted to pinpoint the interactions between the active compounds and the proteases using molecular docking analysis. Our current results imply that the extracts and active ingredients could be further formulated and/or developed for potential prevention and treatment of HIV or SARS-CoV-2 infections.
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34

Wlodawer, A., M. Miller, M. Jaskolski, B. Sathyanarayana, E. Baldwin, I. Weber, L. Selk, L. Clawson, J. Schneider et S. Kent. « Conserved folding in retroviral proteases : crystal structure of a synthetic HIV-1 protease ». Science 245, no 4918 (2 août 1989) : 616–21. http://dx.doi.org/10.1126/science.2548279.

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35

Bossi, Philippe, Mireille Mouroux, Anne Yvon, François Bricaire, Henri Agut, Jean-Marie Huraux, Christine Katlama et Vincent Calvez. « Polymorphism of the Human Immunodeficiency Virus Type 1 (HIV-1) Protease Gene and Response of HIV-1-Infected Patients to a Protease Inhibitor ». Journal of Clinical Microbiology 37, no 9 (1999) : 2910–12. http://dx.doi.org/10.1128/jcm.37.9.2910-2912.1999.

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In order to analyze the impact of protease gene polymorphism on response to regimens containing a protease inhibitor, the entire protease coding domain from 58 human immunodeficiency virus type 1 (HIV-1)-infected patients who were protease inhibitor naive was sequenced before therapy was started. Plasma HIV-1 RNA levels were measured at baseline and at month 3 and month 6 after treatment. All patients were treated with a combination of two reverse transcriptase inhibitors and a protease inhibitor (saquinavir EOF [n = 28], ritonavir [n = 16], or indinavir [n = 14]). Before treatment, 30 different positions whose codons differed from the subtype B consensus sequence were observed. Major mutations associated with protease inhibitor resistance were not observed. No statistical correlation between the number of amino acid differences and the treatment efficacy at month 3 (−2.4 log) or month 6 (−2.7 log) was observed. At baseline, genotypic analysis of the HIV-1 protease gene of patients who have never received a protease inhibitor does not allow prediction of the efficacy of regimens containing a protease inhibitor.
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36

Hu, Qing-Xiu, Guo-Qing Zhang, Rui-Ying Zhang, Dan-Dan Hu, He-Xiang Wang et Tzi Bun Ng. « A Novel Aspartic Protease with HIV-1 Reverse Transcriptase Inhibitory Activity from Fresh Fruiting Bodies of the Wild MushroomXylaria hypoxylon ». Journal of Biomedicine and Biotechnology 2012 (2012) : 1–8. http://dx.doi.org/10.1155/2012/728975.

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A novel aspartic protease with HIV-1 RT inhibitory activity was isolated and characterized from fruiting bodies of the wild mushroomXylaria hypoxylon. The purification protocol comprised distilled water homogenization and extraction step, three ion exchange chromatographic steps (on DEAE-cellulose, Q-Sepharose, and CM-cellulose in succession), and final purification was by FPLC on Superdex 75. The protease was adsorbed on all the three ion exchangers. It was a monomeric protein with a molecular mass of 43 kDa as estimated by SDS-PAGE and FPLC. Its N-terminal amino acid sequence was HYTELLSQVV, which exhibited no sequence homology to other proteases reported. The activity of the protease was adversely affected by Pepstatin A, indicating that it is an aspartic protease. The protease activity was maximal or nearly so in the pH range 6–8 and in the temperature range 35–60°C. The purified enzyme exhibited HIV-1 RT inhibitory activity with an IC50value of 8.3 μM, but was devoid of antifungal, ribonuclease, and hemagglutinating activities.
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37

Mammano, Fabrizio, Caroline Petit et François Clavel. « Resistance-Associated Loss of Viral Fitness in Human Immunodeficiency Virus Type 1 : Phenotypic Analysis of Protease andgag Coevolution in Protease Inhibitor-Treated Patients ». Journal of Virology 72, no 9 (1 septembre 1998) : 7632–37. http://dx.doi.org/10.1128/jvi.72.9.7632-7637.1998.

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ABSTRACT We have studied the phenotypic impact of adaptative Gag cleavage site mutations in patient-derived human immunodeficiency virus type 1 (HIV-1) variants having developed resistance to the protease inhibitor ritonavir or saquinavir. We found that Gag mutations occurred in a minority of resistant viruses, regardless of the duration of the treatment and of the protease mutation profile. Gag mutations exerted only a partial corrective effect on resistance-associated loss of viral fitness. Reconstructed viruses with resistant proteases displayed multiple Gag cleavage defects, and in spite of Gag adaptation, several of these defects remained, explaining the limited corrective effect of cleavage site mutations on fitness. Our data provide clear evidence of the interplay between resistance and fitness in HIV-1 evolution in patients treated with protease inhibitors.
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38

Cordelier, Pierre, et David S. Strayer. « Mechanisms of α1-antitrypsin inhibition of cellular serine proteases and HIV-1 protease that are essential for HIV-1 morphogenesis ». Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease 1638, no 3 (juillet 2003) : 197–207. http://dx.doi.org/10.1016/s0925-4439(03)00084-x.

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39

Rhee, Soo-Yon, Jonathan Taylor, W. Jeffrey Fessel, David Kaufman, William Towner, Paolo Troia, Peter Ruane et al. « HIV-1 Protease Mutations and Protease Inhibitor Cross-Resistance ». Antimicrobial Agents and Chemotherapy 54, no 10 (26 juillet 2010) : 4253–61. http://dx.doi.org/10.1128/aac.00574-10.

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ABSTRACT The effects of many protease inhibitor (PI)-selected mutations on the susceptibility to individual PIs are unknown. We analyzed in vitro susceptibility test results on 2,725 HIV-1 protease isolates. More than 2,400 isolates had been tested for susceptibility to fosamprenavir, indinavir, nelfinavir, and saquinavir; 2,130 isolates had been tested for susceptibility to lopinavir; 1,644 isolates had been tested for susceptibility to atazanavir; 1,265 isolates had been tested for susceptibility to tipranavir; and 642 isolates had been tested for susceptibility to darunavir. We applied least-angle regression (LARS) to the 200 most common mutations in the data set and identified a set of 46 mutations associated with decreased PI susceptibility of which 40 were not polymorphic in the eight most common HIV-1 group M subtypes. We then used least-squares regression to ascertain the relative contribution of each of these 46 mutations. The median number of mutations associated with decreased susceptibility to each PI was 28 (range, 19 to 32), and the median number of mutations associated with increased susceptibility to each PI was 2.5 (range, 1 to 8). Of the mutations with the greatest effect on PI susceptibility, I84AV was associated with decreased susceptibility to eight PIs; V32I, G48V, I54ALMSTV, V82F, and L90M were associated with decreased susceptibility to six to seven PIs; I47A, G48M, I50V, L76V, V82ST, and N88S were associated with decreased susceptibility to four to five PIs; and D30N, I50L, and V82AL were associated with decreased susceptibility to fewer than four PIs. This study underscores the greater impact of nonpolymorphic mutations compared with polymorphic mutations on decreased PI susceptibility and provides a comprehensive quantitative assessment of the effects of individual mutations on susceptibility to the eight clinically available PIs.
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Hernandez-Sanchez, Pedro G., Sandra E. Guerra-Palomares, J. Rafael Arguello, Daniel E. Noyola et Christian A. Garcia-Sepulveda. « Mexican HIV-1 Protease Sequence Diversity ». AIDS Research and Human Retroviruses 36, no 2 (1 février 2020) : 161–66. http://dx.doi.org/10.1089/aid.2019.0201.

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Beck, Z., G. Morris et J. Elder. « Defining HIV-1 Protease Substrate Selectivity ». Current Drug Target -Infectious Disorders 2, no 1 (1 mars 2002) : 37–50. http://dx.doi.org/10.2174/1568005024605837.

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Ishima, Rieko, Rodolfo Ghirlando, József Tözsér, Angela M. Gronenborn, Dennis A. Torchia et John M. Louis. « Folded Monomer of HIV-1 Protease ». Journal of Biological Chemistry 276, no 52 (11 octobre 2001) : 49110–16. http://dx.doi.org/10.1074/jbc.m108136200.

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Catamancio, Simona La Seta, et Stefano Rusconi. « HIV-1 protease inhibitors in development ». Expert Opinion on Investigational Drugs 11, no 3 (mars 2002) : 387–95. http://dx.doi.org/10.1517/13543784.11.3.387.

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Margolin, Nara, Albert Dee, Mei Lai et Chris J. Vlahos. « Purification of Recombinant HIV-1 Protease ». Preparative Biochemistry 21, no 2-3 (juin 1991) : 163–73. http://dx.doi.org/10.1080/10826069108018011.

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45

Heal, J. W., S. A. Wells, E. Jimenez-Roldan, R. F. Freedman et R. A. Römer. « Rigidity analysis of HIV-1 protease ». Journal of Physics : Conference Series 286 (1 mars 2011) : 012006. http://dx.doi.org/10.1088/1742-6596/286/1/012006.

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46

Vacca, J. P., P. M. D. Fitzgerald, M. K. Holloway, R. W. Hungate, K. E. Starbuck, L. J. Chen, P. L. Darke, P. S. Anderson et J. R. Huff. « Conformationally constrained HIV-1 protease inhibitors ». Bioorganic & ; Medicinal Chemistry Letters 4, no 3 (février 1994) : 499–504. http://dx.doi.org/10.1016/0960-894x(94)80025-1.

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Vacca, Joseph P., et Jon H. Condra. « Clinically effective HIV-1 protease inhibitors ». Drug Discovery Today 2, no 7 (juillet 1997) : 261–72. http://dx.doi.org/10.1016/s1359-6446(97)01053-2.

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Blanco, Raquel, Luis Carrasco et Iván Ventoso. « Cell Killing by HIV-1 Protease ». Journal of Biological Chemistry 278, no 2 (4 octobre 2002) : 1086–93. http://dx.doi.org/10.1074/jbc.m205636200.

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Rozzelle, James E., Deborah S. Dauber, Stephen Todd, Robert Kelley et Charles S. Craik. « Macromolecular Inhibitors of HIV-1 Protease ». Journal of Biological Chemistry 275, no 10 (10 mars 2000) : 7080–86. http://dx.doi.org/10.1074/jbc.275.10.7080.

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Yao, Shao, Reena Zutshi et Jean Chmielewski. « Endothiopeptide inhibitors of HIV-1 protease ». Bioorganic & ; Medicinal Chemistry Letters 8, no 6 (mars 1998) : 699–704. http://dx.doi.org/10.1016/s0960-894x(98)00100-0.

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