Proteoliposomal formulations of an HIV-1 gp41-based miniprotein elicit a lipid-dependent immunodominant response overlapping the 2F5 binding motif

The mammalian apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3 or A3) family of cytidine deaminases restrict viral infections by mutating viral DNA and impeding reverse transcription. To overcome this antiviral activity, most lentiviruses express a viral accessory protein called Vif, which recruits A3 proteins to Cullin-RING E3 ubiquitin ligases such as Cul5 for ubiquitylation and subsequent proteasomal degradation. While Vif proteins from primate lentiviruses like HIV-1 utilize the transcription factor CBFβ as a non-canonical cofactor to stabilize the complex, maedi-visna virus (MVV) Vif hijacks cyclophilin A (CypA) instead. Since CBFβ and CypA are both highly conserved among mammals, the requirement for two different cellular cofactors suggests that these two A3-targeting Vif proteins have different biochemical and structural properties. To investigate this topic, we used a combination of in vitro biochemical assays and in vivo A3 degradation assays to study motifs required for MVV Vif to bind zinc ion, Cul5, and the cofactor CypA. Our results demonstrate that while some common motifs between HIV-1 Vif and MVV Vif are involved in recruiting Cul5, different determinants in MVV Vif are required for cofactor binding and stabilization of the E3 ligase complex, such as the zinc-binding motif and N- and C-terminal regions of the protein. Results from this study advance our understanding of the mechanism of MVV Vif recruitment of cellular factors and the evolution of lentiviral Vif proteins.

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The mechanism by which molecules containing the HIV gp41 core-binding motif HXXNPF inhibit HIV-1 envelope glycoprotein-mediated syncytium formation

Biochemical Journal ◽

10.1042/bj20061275 ◽

2007 ◽

Vol 403 (3) ◽

pp. 565-571 ◽

Cited By ~ 15

Author(s):

Jing-He Huang ◽

Heng-Wen Yang ◽

Shuwen Liu ◽

Jing Li ◽

Shibo Jiang ◽

...

Keyword(s):

Envelope Glycoprotein ◽

Critical Role ◽

Syncytium Formation ◽

Phage Clone ◽

Fusion Process ◽

Binding Motif ◽

Active Core ◽

Different Temperatures ◽

Hiv 1

The HIV-1 gp41 (glycoprotein 41) core plays a critical role in fusion between the viral and target cell membranes. We previously identified a gp41 core-binding motif, HXXNPF, by screening the phage display peptide libraries. In the present study, we elucidated the mechanism of action of HXXNPF motif-containing molecules of different sizes, including the phage clone L7.8 (a selected positive phage clone), L7.8-g3p* (a 10–kDa fragment of the gene 3 protein) and JCH-4 (a peptide containing 13 residues of L7.8-g3p*), regarding their respective binding abilities to the six-helix bundle and inhibition on syncytium formation at different temperatures. We found that all of the HXXNPF motif-containing molecules could bind to the gp41 core, and that their binding sites may be located in the N-helix domain. L7.8-g3p* and JCH-4 effectively inhibited HIV-1 Env (envelope glycoprotein)-mediated syncytium formation at 37 °C, while the phage clone L7.8 showed no inhibition under the same conditions. However, at suboptimal temperature (31.5 °C), all of these HXXNPF motif-containing molecules were capable of inhibiting syncytium formation. These results suggest that these HXXNPF motif-containing molecules mainly bind to the gp41 core and stop the fusion process mediated by the fusion-active core, resulting in inhibition of HIV-1 fusion and entry. The HXXNPF motif-containing molecules may be used as probes for studying the role of the HIV-1 gp41 core in the late stage of the membrane-fusion process.

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New Insights on the Versatile Role of the Cholesterol Binding Motif of the HIV-1 Glycoprotein Gp41

Biophysical Journal ◽

10.1016/j.bpj.2013.11.421 ◽

2014 ◽

Vol 106 (2) ◽

pp. 62a

Author(s):

Roland Schwarzer ◽

Andreas Herrmann ◽

Ilya Levental ◽

Andrea Gramatica

Keyword(s):

Binding Motif ◽

Glycoprotein Gp41 ◽

Hiv 1 ◽

Cholesterol Binding

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Dihydroxythiophenes Are Novel Potent Inhibitors of Human Immunodeficiency Virus Integrase with a Diketo Acid-Like Pharmacophore

Journal of Virology ◽

10.1128/jvi.00306-06 ◽

2006 ◽

Vol 80 (14) ◽

pp. 6883-6894 ◽

Cited By ~ 12

Author(s):

S. Kehlenbeck ◽

U. Betz ◽

A. Birkmann ◽

B. Fast ◽

A. H. Göller ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Retroviral Vectors ◽

Cross Resistance ◽

Binding Motif ◽

Strand Transfer ◽

Resistance Mutations ◽

Immunodeficiency Virus ◽

Viral Cdna ◽

Hiv 1

ABSTRACT We have identified dihydroxythiophenes (DHT) as a novel series of human immunodeficiency virus type 1 (HIV-1) integrase inhibitors with broad antiviral activities against different HIV isolates in vitro. DHT were discovered in a biochemical integrase high-throughput screen searching for inhibitors of the strand transfer reaction of HIV-1 integrase. DHT are selective inhibitors of integrase that do not interfere with virus entry, as shown by the inhibition of a vesicular stomatitis virus G-pseudotyped retroviral system. Moreover, in quantitative real-time PCR experiments, no effect on the synthesis of viral cDNA could be detected but rather an increase in the accumulation of 2-long-terminal-repeat cycles was detected. This suggests that the integration of viral cDNA is blocked. Molecular modeling and the structure activity relationship of DHT demonstrate that our compound fits into a two-metal-binding motif that has been suggested as the essential pharmacophore for diketo acid (DKA)-like strand transfer inhibitors (Grobler et al., Proc. Natl. Acad. Sci. USA 99:6661-6666, 2002.). This notion is supported by the profiling of DHT on retroviral vectors carrying published resistance mutations for DKA-like inhibitors where DHT showed partial cross-resistance. This suggests that DHT bind to a common site in the catalytic center of integrase, albeit with an altered binding mode. Taken together, our findings indicate that DHT are novel selective strand transfer inhibitors of integrase with a pharmacophore homologous to DKA-like inhibitors.

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F18, a Novel Small-Molecule Nonnucleoside Reverse Transcriptase Inhibitor, Inhibits HIV-1 Replication Using Distinct Binding Motifs as Demonstrated by Resistance Selection and Docking Analysis

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.05537-11 ◽

2011 ◽

Vol 56 (1) ◽

pp. 341-351 ◽

Cited By ~ 16

Author(s):

Xiaofan Lu ◽

Li Liu ◽

Xu Zhang ◽

Terrence Chi Kong Lau ◽

Stephen Kwok Wing Tsui ◽

...

Keyword(s):

Reverse Transcriptase ◽

Small Molecule ◽

Mononuclear Cells ◽

Binding Motif ◽

Drug Resistant ◽

Peripheral Blood Mononuclear ◽

Docking Analysis ◽

Hiv 1 ◽

Calanolide A

ABSTRACTNonnucleoside reverse transcriptase inhibitors (NNRTIs) are one of the key components of antiretroviral therapy drug regimen against human immunodeficiency virus type 1 (HIV-1) replication. We previously described a newly synthesized small molecule, 10-chloromethyl-11-demethyl-12-oxo-calanolide A (F18), a (+)-calanolide A analog, as a novel anti-HIV-1 NNRTI (H. Xue et al., J. Med. Chem. 53:1397–1401, 2010). Here, we further investigated its antiviral range, drug resistance profile, and underlying mechanism of action. F18 consistently displayed potent activity against primary HIV-1 isolates, including various subtypes of group M, circulating recombinant form (CRF) 01_AE, and laboratory-adapted drug-resistant viruses. Moreover, F18 displayed distinct profiles against 17 NNRTI-resistant pseudoviruses, with an excellent potency especially against one of the most prevalent strains with the Y181C mutation (50% effective concentration, 1.0 nM), which was in stark contrast to the extensively used NNRTIs nevirapine and efavirenz. Moreover, we induced F18-resistant viruses byin vitroserial passages and found that the mutation L100I appeared to be the dominant contributor to F18 resistance, further suggesting a binding motif different from that of nevirapine and efavirenz. F18 was nonantagonistic when used in combination with other antiretrovirals against both wild-type and drug-resistant viruses in infected peripheral blood mononuclear cells. Interestingly, F18 displayed a highly synergistic antiviral effect with nevirapine against nevirapine-resistant virus (Y181C). Furthermore,in silicodocking analysis suggested that F18 may bind to the HIV-1 reverse transcriptase differently from other NNRTIs. This study presents F18 as a new potential drug for clinical use and also presents a new mechanism-based design for future NNRTI.

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Molecular Characterization of Feline Immunodeficiency Virus Budding

Journal of Virology ◽

10.1128/jvi.02337-07 ◽

2007 ◽

Vol 82 (5) ◽

pp. 2106-2119 ◽

Cited By ~ 33

Author(s):

Benjamin G. Luttge ◽

Miranda Shehu-Xhilaga ◽

Dimiter G. Demirov ◽

Catherine S. Adamson ◽

Ferri Soheilian ◽

...

Keyword(s):

Feline Immunodeficiency Virus ◽

Equine Infectious Anemia Virus ◽

Binding Motif ◽

Virus Release ◽

Related Sequence ◽

Endosomal Sorting ◽

Peptide Motifs ◽

C Terminus ◽

Immunodeficiency Virus ◽

Hiv 1

ABSTRACT Infection of domestic cats with feline immunodeficiency virus (FIV) is an important model system for studying human immunodeficiency virus type 1 (HIV-1) infection due to numerous similarities in pathogenesis induced by these two lentiviruses. However, many molecular aspects of FIV replication remain poorly understood. It is well established that retroviruses use short peptide motifs in Gag, known as late domains, to usurp cellular endosomal sorting machinery and promote virus release from infected cells. For example, the Pro-Thr/Ser-Ala-Pro [P(T/S)AP] motif of HIV-1 Gag interacts directly with Tsg101, a component of the endosomal sorting complex required for transport I (ESCRT-I). A Tyr-Pro-Asp-Leu (YPDL) motif in equine infectious anemia virus (EIAV), and a related sequence in HIV-1, bind the endosomal sorting factor Alix. In this study we sought to identify and characterize FIV late domain(s) and elucidate cellular machinery involved in FIV release. We determined that mutagenesis of a PSAP motif in FIV Gag, small interfering RNA-mediated knockdown of Tsg101 expression, and overexpression of a P(T/S)AP-binding fragment of Tsg101 (TSG-5′) each inhibited FIV release. We also observed direct binding of FIV Gag peptides to Tsg101. In contrast, mutagenesis of a potential Alix-binding motif in FIV Gag did not affect FIV release. Similarly, expression of the HIV-1/EIAV Gag-binding domain of Alix (Alix-V) did not disrupt FIV budding, and FIV Gag peptides showed no affinity for Alix-V. Our data demonstrate that FIV relies predominantly on a Tsg101-binding PSAP motif in the C terminus of Gag to promote virus release in HeLa cells, and this budding mechanism is highly conserved in feline cells.

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The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by a RNA-Mediated Dimerization Mechanism

10.1101/203000 ◽

2017 ◽

Cited By ~ 1

Author(s):

Nadine M. Shaban ◽

Ke Shi ◽

Kate V. Lauer ◽

Michael A. Carpenter ◽

Christopher M. Richards ◽

...

Keyword(s):

Antiviral Activity ◽

Rna Binding ◽

Cytosine Deaminase ◽

Rnase A ◽

Binding Motif ◽

Innate And Adaptive Immunity ◽

Enzyme Preparations ◽

Gene Diversification ◽

Hiv 1

SUMMARYHuman APOBEC3H and homologous single-stranded DNA cytosine deaminases are unique to mammals. These DNA editing enzymes function in innate immunity by restricting the replication of viruses and transposons. Misregulated APOBEC3H also contributes to cancer mutagenesis. Here we address the role of RNA in APOBEC3H regulation. APOBEC3H co-purifies with RNA as an inactive protein, and RNase A treatment yields enzyme preparations with stronger DNA deaminase activity. RNA binding-defective mutants are DNA hypermutators. Chromatography profiles and crystallographic data demonstrate a mechanism in which double-stranded RNA mediates enzyme dimerization. RNA binding is required for APOBEC3H cytoplasmic localization and for packaging into HIV-1 particles and antiviral activity. Related DNA deaminases including other APOBEC3 family members and the antibody gene diversification enzyme AID also bind RNA and are predicted to have a similar RNA binding motif suggesting mechanistic conservation and relevance to innate and adaptive immunity and to multiple diseases.HIGHLIGHTSRNA inhibits human APOBEC3H DNA cytosine deaminase activityRNA binding mutants are DNA hypermutatorsX-ray structure demonstrates an RNA duplex-mediated APOBEC3H dimerization mechanismRNA binding is required for packaging into HIV-1 particles and antiviral activity

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The Arginine-Rich RNA-Binding Motif of HIV-1 Rev Is Intrinsically Disordered and Folds upon RRE Binding

Biophysical Journal ◽

10.1016/j.bpj.2013.07.022 ◽

2013 ◽

Vol 105 (4) ◽

pp. 1004-1017 ◽

Cited By ~ 33

Author(s):

Fabio Casu ◽

Brendan M. Duggan ◽

Mirko Hennig

Keyword(s):

Rna Binding ◽

Binding Motif ◽

Intrinsically Disordered ◽

Hiv 1

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Mechanism of Zinc Coordination by Point-Mutated Structures of the Distal CCHC Binding Motif of the HIV-1 NCp7 Protein†

Biochemistry ◽

10.1021/bi047349+ ◽

2005 ◽

Vol 44 (19) ◽

pp. 7315-7325 ◽

Cited By ~ 12

Author(s):

Elisa Bombarda ◽

Bernard P. Roques ◽

Yves Mély ◽

Ernst Grell

Keyword(s):

Binding Motif ◽

Zinc Coordination ◽

Hiv 1

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Identification of a Key Target Sequence To Block Human Immunodeficiency Virus Type 1 Replication within thegag-pol Transframe Domain

Journal of Virology ◽

10.1128/jvi.74.10.4621-4633.2000 ◽

2000 ◽

Vol 74 (10) ◽

pp. 4621-4633 ◽

Cited By ~ 39

Author(s):

Shizuko Sei ◽

Quan-en Yang ◽

Dennis O'Neill ◽

Kazuhisa Yoshimura ◽

Kunio Nagashima ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Human Immunodeficiency Virus Type ◽

Virus Type ◽

Binding Motif ◽

Target Sequence ◽

Viral Protease ◽

Conserved Sequence ◽

Immunodeficiency Virus ◽

Hiv 1

ABSTRACT Although the full sequence of the human immunodeficiency virus type 1 (HIV-1) genome has been known for more than a decade, effective genetic antivirals have yet to be developed. Here we show that, of 22 regions examined, one highly conserved sequence (ACTCTTTGGCAACGA) near the 3′ end of the HIV-1 gag-poltransframe region, encoding viral protease residues 4 to 8 and a C-terminal Vpr-binding motif of p6Gag protein in two different reading frames, can be successfully targeted by an antisense peptide nucleic acid oligomer named PNAPR2. A disrupted translation of gag-pol mRNA induced at the PNAPR2-annealing site resulted in a decreased synthesis of Pr160Gag-Pol polyprotein, hence the viral protease, a predominant expression of Pr55Gag devoid of a fully functional p6Gag protein, and the excessive intracellular cleavage of Gag precursor proteins, hindering the processes of virion assembly. Treatment with PNAPR2abolished virion production by up to 99% in chronically HIV-1-infected H9 cells and in peripheral blood mononuclear cells infected with clinical HIV-1 isolates with the multidrug-resistant phenotype. This particular segment of the gag-pol transframe gene appears to offer a distinctive advantage over other regions in invading viral structural genes and restraining HIV-1 replication in infected cells and may potentially be exploited as a novel antiviral genetic target.

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