A dynamic target-based pharmacophoric model mapping the CD4 binding site on HIV-1 gp120 to identify new inhibitors of gp120–CD4 protein–protein interactions

The RT (reverse transcriptase) of HIV-1 interacts with HIV-1 IN (integrase) and inhibits its enzymatic activities. However, the molecular mechanisms underling these interactions are not well understood. In order to study these mechanisms, we have analysed the interactions of HIV-1 IN with HIV-1 RT and with two other related RTs: those of HIV-2 and MLV (murine-leukaemia virus). All three RTs inhibited HIV-1 IN, albeit to a different extent, suggesting a common site of binding that could be slightly modified for each one of the studied RTs. Using surface plasmon resonance technology, which monitors direct protein–protein interactions, we performed kinetic analyses of the binding of HIV-1 IN to these three RTs and observed interesting binding patterns. The interaction of HIV-1 RT with HIV-1 IN was unique and followed a two-state reaction model. According to this model, the initial IN–RT complex formation was followed by a conformational change in the complex that led to an elevation of the total affinity between these two proteins. In contrast, HIV-2 and MLV RTs interacted with IN in a simple bi-molecular manner, without any apparent secondary conformational changes. Interestingly, HIV-1 and HIV-2 RTs were the most efficient inhibitors of HIV-1 IN activity, whereas HIV-1 and MLV RTs showed the highest affinity towards HIV-1 IN. These modes of direct protein interactions, along with the apparent rate constants calculated and the correlations of the interaction kinetics with the capacity of the RTs to inhibit IN activities, are all discussed.

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Peptides that inhibit HIV-1 integrase by blocking its protein-protein interactions

FEBS Journal ◽

10.1111/j.1742-4658.2012.08680.x ◽

2012 ◽

Vol 279 (16) ◽

pp. 2795-2809 ◽

Cited By ~ 27

Author(s):

Michal Maes ◽

Abraham Loyter ◽

Assaf Friedler

Keyword(s):

Protein Interactions ◽

Protein Protein Interactions ◽

Hiv 1

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A crosslinked and ribosylated actin trimer does not interact productively with myosin

Biochemistry and Cell Biology ◽

10.1139/bcb-2018-0082 ◽

2019 ◽

Vol 97 (2) ◽

pp. 140-147 ◽

Cited By ~ 1

Author(s):

Navneet Sidhu ◽

John F. Dawson

Keyword(s):

Binding Site ◽

Protein Interactions ◽

Binding Proteins ◽

Binding Protein ◽

Dnase I ◽

Protein Protein Interactions ◽

Adp Ribosylation ◽

Myosin Binding ◽

Pointed End

A purified F-actin-derived actin trimer that interacts with end-binding proteins did not activate or bind the side-binding protein myosin under rigor conditions. Remodeling of the actin trimer by the binding of gelsolin did not rescue myosin binding, nor did the use of different means of inhibiting the polymerization of the trimer. Our results demonstrate that ADP-ribosylation on all actin subunits of an F-actin-derived trimer inhibits myosin binding and that the binding of DNase-I to the pointed end subunits of a crosslinked trimer also remodels the myosin binding site. Taken together, this work highlights the need for a careful balance between modification of actin subunits and maintaining protein–protein interactions to produce a physiologically relevant short F-actin complex.

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Prediction of Protein-Protein Interactions between HIV-1 and Human using Support Vector Machine Combined with Multivariate Mutual Information

2020 3rd International Conference on Biomedical Engineering (IBIOMED) ◽

10.1109/ibiomed50285.2020.9487598 ◽

2020 ◽

Author(s):

Mohamad Irlin Sunggawa ◽

Alhadi Bustamam ◽

Devvi Sarwinda ◽

Patuan Pangihutan Tampubolon ◽

Wibowo Mangunwardoyo

Keyword(s):

Support Vector Machine ◽

Mutual Information ◽

Protein Interactions ◽

Support Vector ◽

Protein Protein Interactions ◽

Multivariate Mutual Information ◽

Hiv 1

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Neutralization Properties of Simian Immunodeficiency Viruses Infecting Chimpanzees and Gorillas

mBio ◽

10.1128/mbio.00296-15 ◽

2015 ◽

Vol 6 (2) ◽

Cited By ~ 17

Author(s):

Hannah J. Barbian ◽

Julie M. Decker ◽

Frederic Bibollet-Ruche ◽

Rachel P. Galimidi ◽

Anthony P. West ◽

...

Keyword(s):

T Cells ◽

Binding Site ◽

Pan Troglodytes ◽

Neutralizing Antibodies ◽

Gorilla Gorilla ◽

Protective Capacity ◽

Content Type ◽

Ccr5 Receptor ◽

Cd4 Binding Site ◽

Hiv 1

ABSTRACTBroadly cross-reactive neutralizing antibodies (bNabs) represent powerful tools to combat human immunodeficiency virus type 1 (HIV-1) infection. Here, we examined whether HIV-1-specific bNabs are capable of cross-neutralizing distantly related simian immunodeficiency viruses (SIVs) infecting central (Pan troglodytestroglodytes) (SIVcpzPtt) and eastern (Pan troglodytesschweinfurthii) (SIVcpzPts) chimpanzees (n= 11) as well as western gorillas (Gorilla gorilla gorilla) (SIVgor) (n= 1). We found that bNabs directed against the CD4 binding site (n= 10), peptidoglycans at the base of variable loop 3 (V3) (n= 5), and epitopes at the interface of surface (gp120) and membrane-bound (gp41) envelope glycoproteins (n= 5) failed to neutralize SIVcpz and SIVgor strains. In addition, apex V2-directed bNabs (n= 3) as well as llama-derived (heavy chain only) antibodies (n= 6) recognizing both the CD4 binding site and gp41 epitopes were either completely inactive or neutralized only a fraction of SIVcpzPttstrains. In contrast, one antibody targeting the membrane-proximal external region (MPER) of gp41 (10E8), functional CD4 and CCR5 receptor mimetics (eCD4-Ig, eCD4-Igmim2, CD4-218.3-E51, and CD4-218.3-E51-mim2), as well as mono- and bispecific anti-human CD4 (iMab and LM52) and CCR5 (PRO140, PRO140-10E8) receptor antibodies neutralized >90% of SIVcpz and SIVgor strains with low-nanomolar (0.13 to 8.4 nM) potency. Importantly, the latter antibodies blocked virus entry not only in TZM-bl cells but also in Cf2Th cells expressing chimpanzee CD4 and CCR5 and neutralized SIVcpz in chimpanzee CD4+T cells, with 50% inhibitory concentrations (IC50s) ranging from 3.6 to 40.5 nM. These findings provide new insight into the protective capacity of anti-HIV-1 bNabs and identify candidates for further development to combat SIVcpz infection.IMPORTANCESIVcpz is widespread in wild-living chimpanzees and can cause AIDS-like immunopathology and clinical disease. HIV-1 infection of humans can be controlled by antiretroviral therapy; however, treatment of wild-living African apes with current drug regimens is not feasible. Nonetheless, it may be possible to curb the spread of SIVcpz in select ape communities using vectored immunoprophylaxis and/or therapy. Here, we show that antibodies and antibody-like inhibitors developed to combat HIV-1 infection in humans are capable of neutralizing genetically diverse SIVcpz and SIVgor strains with considerable breadth and potency, including in primary chimpanzee CD4+T cells. These reagents provide an important first step toward translating intervention strategies currently developed to treat and prevent AIDS in humans to SIV-infected apes.

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Broad neutralization by a combination of antibodies recognizing the CD4 binding site and a new conformational epitope on the HIV-1 envelope protein

Journal of Experimental Medicine ◽

10.1084/jem.20120423 ◽

2012 ◽

Vol 209 (8) ◽

pp. 1469-1479 ◽

Cited By ~ 123

Author(s):

Florian Klein ◽

Christian Gaebler ◽

Hugo Mouquet ◽

D. Noah Sather ◽

Clara Lehmann ◽

...

Keyword(s):

Binding Site ◽

Envelope Protein ◽

Neutralizing Antibodies ◽

Conformational Epitope ◽

Broadly Neutralizing Antibodies ◽

Cd4 Binding Site ◽

Capture Method ◽

Anti Hiv ◽

Hiv 1 ◽

Viral Isolates

Two to three years after infection, a fraction of HIV-1–infected individuals develop serologic activity that neutralizes most viral isolates. Broadly neutralizing antibodies that recognize the HIV-1 envelope protein have been isolated from these patients by single-cell sorting and by neutralization screens. Here, we report a new method for anti–HIV-1 antibody isolation based on capturing single B cells that recognize the HIV-1 envelope protein expressed on the surface of transfected cells. Although far less efficient than soluble protein baits, the cell-based capture method identified antibodies that bind to a new broadly neutralizing epitope in the vicinity of the V3 loop and the CD4-induced site (CD4i). The new epitope is expressed on the cell surface form of the HIV-1 spike, but not on soluble forms of the same envelope protein. Moreover, the new antibodies complement the neutralization spectrum of potent broadly neutralizing anti-CD4 binding site (CD4bs) antibodies obtained from the same individual. Thus, combinations of potent broadly neutralizing antibodies with complementary activity can account for the breadth and potency of naturally arising anti–HIV-1 serologic activity. Therefore, vaccines aimed at eliciting anti–HIV-1 serologic breadth and potency should not be limited to single epitopes.

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Neutralization of genetically diverse HIV-1 strains by IgA antibodies to the gp120–CD4-binding site from long-term survivors of HIV infection

AIDS ◽

10.1097/qad.0b013e3283376e88 ◽

2010 ◽

Vol 24 (6) ◽

pp. 875-884 ◽

Cited By ~ 21

Author(s):

Stephanie Planque ◽

Maria Salas ◽

Yukie Mitsuda ◽

Marcin Sienczyk ◽

Miguel A Escobar ◽

...

Keyword(s):

Hiv Infection ◽

Binding Site ◽

Iga Antibodies ◽

Cd4 Binding Site ◽

Long Term Survivors ◽

Hiv 1

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A distinct class of plant and animal viral proteins that disrupt mitosis by directly interrupting the mitotic entry switch Wee1-Cdc25-Cdk1

Science Advances ◽

10.1126/sciadv.aba3418 ◽

2020 ◽

Vol 6 (20) ◽

pp. eaba3418

Author(s):

Huaibing Jin ◽

Zhiqiang Du ◽

Yanjing Zhang ◽

Judit Antal ◽

Zongliang Xia ◽

...

Keyword(s):

Protein Interactions ◽

Viral Proteins ◽

Plant Viruses ◽

Amino Acid Residues ◽

Protein Protein Interactions ◽

Common Amino Acid ◽

Mitotic Entry ◽

Distinct Class ◽

Barley Yellow Dwarf ◽

Hiv 1

Many animal viral proteins, e.g., Vpr of HIV-1, disrupt host mitosis by directly interrupting the mitotic entry switch Wee1-Cdc25-Cdk1. However, it is unknown whether plant viruses may use this mechanism in their pathogenesis. Here, we report that the 17K protein, encoded by barley yellow dwarf viruses and related poleroviruses, delays G2/M transition and disrupts mitosis in both host (barley) and nonhost (fission yeast, Arabidopsis thaliana, and tobacco) cells through interrupting the function of Wee1-Cdc25-CDKA/Cdc2 via direct protein-protein interactions and alteration of CDKA/Cdc2 phosphorylation. When ectopically expressed, 17K disrupts the mitosis of cultured human cells, and HIV-1 Vpr inhibits plant cell growth. Furthermore, 17K and Vpr share similar secondary structural feature and common amino acid residues required for interacting with plant CDKA. Thus, our work reveals a distinct class of mitosis regulators that are conserved between plant and animal viruses and play active roles in viral pathogenesis.

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