Covalent Inhibition of HIV‐1 Integrase by <i>N</i>‐Succinimidyl Peptides

Chandra, Koushik; Das, Priyadip; Samarasimhareddy, Mamidi; Hurevich, Mattan; Iosub-Amir, Anat; Metanis, Norman; Reches, Meital; Friedler, Assaf

doi:10.1002/cmdc.201600190

Cited by 6 publications

(8 citation statements)

References 69 publications

(217 reference statements)

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“…We, therefore, studied the fibrillization of the peptide at different concentrations and in the presence of IN using AFM topography analysis. The conditions were analogous to those of the in vitro enzymatic IN assay in our previous studies . The AFM images indicated that the size and density of the fibrils increased as the concentration of peptide increased from 16 to 160 μM in the presence of 400‐nM IN (Figure D–B).…”

Section: Introductionsupporting

confidence: 59%

“…To gain an insight into the structures formed by this peptide, we performed Transmission electron microscope cryo‐(TEM) and atomic force microscope (AFM) analysis under the same conditions tested in the enzyme‐linked immunosorbent assay we performed previously . Both cryo‐TEM and AFM analysis indicated that the peptide formed fibrils under the examined conditions (see electronic supporting information (ESI) for experimental details including TEM and AFM, Figure A,B).…”

Section: Introductionmentioning

confidence: 98%

“…Targeting the interactions between IN and LEDGF/p75 is an important strategy for the development of anti‐HIV drugs . We have recently reported the covalent inhibition of IN by modifying LEDGF 361–370 with succinimide at its N‐terminus . This covalent inhibition is mediated by the binding of the succinimide ring of the peptide terminus to the amine group of a lysine residue in IN.…”

Section: Introductionmentioning

confidence: 99%

“…We synthesized the inhibitory peptide Su‐WNSLK Ac IDNLDV‐NH 2 according to the protocol we used previously .…”

Section: Introductionmentioning

confidence: 99%

“…Thus, the contribution of IN–peptide complex to fibril formation is negligible. Our previous results suggested that the monomers of the peptide are the species that covalently binds and inhibits IN . Covalent inhibition demands a constant source of monomers for complete inhibition, and this is possible only when the local concentration of the monomers is relatively high .…”

Section: Introductionmentioning

confidence: 99%

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Peptide fibrils as monomer storage of the covalent HIV‐1 integrase inhibitor

Chandra

Das

Metanis

et al. 2017

Journal of Peptide Science

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We have recently reported the covalent inhibition of HIV-1 integrase by an N-terminal succinimide-modified lens epithelium-derived growth factor (361-370) peptide. We also showed that this peptide is proteolytically stable. Here, we show that this inhibitor is stored as fibrils that serve as a stock for the inhibitory monomers. The fibrils increase the local concentration of the peptide at the target protein. When the monomers bind integrase, the equilibrium between the fibrils and their monomers shifts towards the formation of peptide monomers. The combination of fibril formation and subsequent proteolytic stability of the peptide may bring to new strategy for developing therapeutic agents. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

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Section: Introductionsupporting

confidence: 59%

Section: Introductionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

“…We synthesized the inhibitory peptide Su‐WNSLK Ac IDNLDV‐NH 2 according to the protocol we used previously .…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Peptide fibrils as monomer storage of the covalent HIV‐1 integrase inhibitor

Chandra

Das

Metanis

et al. 2017

Journal of Peptide Science

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A simple method for developing lysine targeted covalent protein reagents

Gabizon,

Tivon,

Reddi

et al. 2023

Nat Commun

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Peptide-based covalent probes can target shallow protein surfaces not typically addressable using small molecules, yet there is a need for versatile approaches to convert native peptide sequences into covalent binders that can target a broad range of residues. Here we report protein-based thio-methacrylate esters—electrophiles that can be installed easily on unprotected peptides and proteins via cysteine side chains, and react efficiently and selectively with cysteine and lysine side chains on the target. Methacrylate phosphopeptides derived from 14-3-3-binding proteins irreversibly label 14-3-3σ via either lysine or cysteine residues, depending on the position of the electrophile. Methacrylate peptides targeting a conserved lysine residue exhibit pan-isoform binding of 14-3-3 proteins both in lysates and in extracellular media. Finally, we apply this approach to develop protein-based covalent binders. A methacrylate-modified variant of the colicin E9 immunity protein irreversibly binds to the E9 DNAse, resulting in significantly higher thermal stability relative to the non-covalent complex. Our approach offers a simple and versatile route to convert peptides and proteins into potent covalent binders.

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Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2

Luzik

Rogacheva

Izmailov

et al. 2019

Sci Rep

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We have investigated covalent conjugation of VPPPVPPRRRX′ peptide (where X′ denotes Nε-chloroacetyl lysine) to N-terminal SH3 domain from adapter protein Grb2. Our experimental results confirmed that the peptide first binds to the SH3 domain noncovalently before establishing a covalent linkage through reaction of X′ with the target cysteine residue C32. We have also confirmed that this reaction involves a thiolate-anion form of C32 and follows the SN2 mechanism. For this system, we have developed a new MD-based protocol to model the formation of covalent conjugate. The simulation starts with the known coordinates of the noncovalent complex. When two reactive groups come into contact during the course of the simulation, the reaction is initiated. The reaction is modeled via gradual interpolation between the two sets of force field parameters that are representative of the noncovalent and covalent complexes. The simulation proceeds smoothly, with no appreciable perturbations to temperature, pressure or volume, and results in a high-quality MD model of the covalent complex. The validity of this model is confirmed using the experimental chemical shift data. The new MD-based approach offers a valuable tool to explore the mechanics of protein-peptide conjugation and build accurate models of covalent complexes.

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Covalent Inhibition of HIV‐1 Integrase by N‐Succinimidyl Peptides

Cited by 6 publications

References 69 publications

Peptide fibrils as monomer storage of the covalent HIV‐1 integrase inhibitor

Peptide fibrils as monomer storage of the covalent HIV‐1 integrase inhibitor

A simple method for developing lysine targeted covalent protein reagents

Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2

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