A peptide mimetic of an anti-CD4 monoclonal antibody by rational design

Casset, Florence; Roux, F.; Mouchet, Patrick; Bès, Cédric; Chardès, Thierry; Granier, Claude; Mani, Jean‐Claude; Pugnière, Martine; Laune, Daniel; Pau, Bernard; Kaczorek, Michel; Lahana, Roger; Rees, Anthony R.

doi:10.1016/s0006-291x(03)01131-8

Cited by 32 publications

(22 citation statements)

References 15 publications

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“…Monoclonal antibodies and their derivatives, such as antigen binding fragments (Fab) 2 and the corresponding complementarity determining region (CDR) peptides, have been described as plausible agents for inhibiting HIV-1. These have been directed either against gp120, the envelope glycoprotein, or more commonly, the CD4 receptor (2)(3)(4)(5)(6)(7)(8). All have shown promise.…”

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confidence: 99%

A Cell-penetrating Antibody Fragment against HIV-1 Rev Has High Antiviral Activity

Zhuang

Stahl

Watts

et al. 2014

Journal of Biological Chemistry

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Background: There is a need for alternative HIV-1 inhibitors. Results: An engineered antibody fragment (Fab) against the essential HIV-1 protein Rev significantly reduces reverse transcriptase activity in human cell culture, and synthetic antigen-binding peptides from the Fab block Rev polymerization. Conclusion: The Fab inhibits viral replication by blocking Rev function. Significance: The Fab and its antigen-binding peptides represent a new class of anti-HIV-1 agents.

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confidence: 99%

A Cell-penetrating Antibody Fragment against HIV-1 Rev Has High Antiviral Activity

Zhuang

Stahl

Watts

et al. 2014

Journal of Biological Chemistry

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“…Regarding the close analogy between these systems and the one described here, it is likely that similar binding mechanisms apply. The assumption that stable complexes reflect high affinity 1:1 interactions might lead to the incorrect conclusion that such mimics are indeed very good representatives of the parent antibodies (18).…”

Section: Discussionmentioning

confidence: 99%

“…For example, IC 50 values for the inhibition of viral reproduction were 350-fold higher (ϳ7 M) for a peptide derived from the anti-CD4 mAb ST40 (ϳ20 nM), whereas the reported affinity of the peptide for CD4 was only Ͻ3-fold lower than the antibody (K D ϭ 900 pM versus 370 pM) (18). Similarly, partial inhibition of formation of an idiotypic mAb1⅐mAb2 complex (K D ϳ1 nM) occurred only at 6.6 M for the best peptide, whereas the reported difference in affinities was only ϳ10 (19).…”

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confidence: 99%

A Combinatorial Approach for the Design of Complementarity-determining Region-derived Peptidomimetics with in Vitro Anti-tumoral Activity

Timmerman

Barderas

Desmet³

et al. 2009

Journal of Biological Chemistry

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The great success of therapeutic monoclonal antibodies has fueled research toward mimicry of their binding sites and the development of new strategies for peptide-based mimetics production. Here, we describe a new combinatorial approach for the production of peptidomimetics using the complementarity-determining regions (CDRs) from gastrin17 (pyroEGP-WLEEEEEAYGWMDF-NH 2 ) antibodies as starting material for cyclic peptide synthesis in a microarray format. Gastrin17 is a trophic factor in gastrointestinal tumors, including pancreatic cancer, which makes it an interesting target for development of therapeutic antibodies. Screening of microarrays containing bicyclic peptidomimetics identified a high number of gastrin binders. A strong correlation was observed between gastrin binding and overall charge of the peptidomimetic. Most of the best gastrin binders proceeded from CDRs containing charged residues. In contrast, CDRs from high affinity antibodies containing mostly neutral residues failed to yield good binders. Our experiments revealed essential differences in the mode of antigen binding between CDR-derived peptidomimetics (K d values in micromolar range) and the parental monoclonal antibodies (K d values in nanomolar range). However, chemically derived peptidomimetics from gastrin binders were very effective in gastrin neutralization studies using cell-based assays, yielding a neutralizing activity in pancreatic tumoral cell lines comparable with that of gastrin-specific monoclonal antibodies. These data support the use of combinatorial CDR-peptide microarrays as a tool for the development of a new generation of chemically synthesized cyclic peptidomimetics with functional activity.Antibody-based therapeutics have emerged as important components of therapies for an increasing number of debilitating and life-threatening diseases (1-3). The unique properties of antibodies provide a source of inspiration for active research in antibody engineering. Over the years, a wide range of antibody fragments (Fab, scFv) 8 and variants (dia-, tria-, tetra-, mini-bodies, single-domain antibodies, intramers, etc.) have been developed (4 -8), some of which are used today in clinical therapies (9, 10). One step further in downsizing the antibody molecule is to use peptides derived from one or more of the six hypervariable loops, or "complementarity-determining regions" (CDRs; Fig. 1A) (11). Mutational analysis of antibodycombining sites suggests that only a subset of interface contact residues is essential for binding (12, 13). Several publications have appeared since the first report on CDR-derived peptides (14), with bioactivities even approaching those of the parent antibodies in a few cases. Heap et al. (15) reported a cyclic 17-mer peptide derived from the H3 CDR of an anti-gp120 mAb with only 37-fold lower affinity (K D ϭ 7.5 nM versus 0.2 nM for the mAb) and 32-fold lower HIV-1 neutralizing capacity. Some studies also use a rational design-based approach to make antibody-like binders, with remarkably high in vivo activit...

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“…A wide variety of studies indicate that bioactive peptides can be generated using sequence information of antibody variable domains (Saragovi et al, 1991;Williams et al, 1991;Monnet et al, 1999;Levi et al, 1993Levi et al, , 2000Park et al, 2000;Laune et al, 1997Laune et al, , 2002Berezov et al, 2001;Tsumoto et al, 2002;Feng et al, 1998Feng et al, , 2005Bè s et al, 2001Bè s et al, , 2003Casset et al, 2003;Perosa et al, 2004; (wileyonlinelibrary.com) DOI:10.1002/jmr.1017 Heap et al, 2005). However, little experimental data are available to demonstrate that such peptides do indeed reproduce the structure and binding mode of the corresponding antibody paratope.…”

Section: Introductionmentioning

confidence: 99%

“…the absence of a clearly defined complex structure. Relatively poor structural mimicry of paratopes by synthetic binders is also suggested by the fact that their biological activities are typically observed at concentrations 10 2 -10 3 higher than those used with the parental antibodies (Saragovi et al, 1991;Levi et al, 2000;Tsumoto et al, 2002;Casset et al, 2003;Feng et al, 2005), with only few exceptions (Park et al, 2000;Heap et al, 2005;Qiu et al, 2007). In addition to this, binding selectivities are often poorly studied, most likely as this requires that binding and neutralization experiments were performed with a number of unrelated targets.…”

Section: Introductionmentioning

confidence: 99%

Binding of CDR‐derived peptides is mechanistically different from that of high‐affinity parental antibodies

Timmerman

Shochat

Desmet

et al. 2010

J of Molecular Recognition

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We present data that reveal crucial differences between the binding mode of anti-gastrin17 (G17, pyroEGPW-LEEEEEAYGWMDF-NH 2 ) monoclonal antibodies (mAbs) and their CDR-derived synthetic binders (SBs) with G17. The mAbs recognize the N-terminal sequence of G17 ( pyroEGPWL) with nanomolar affinity and high sequence selectivity. Molecular simulations suggest that G17 recognition is based primarily on a multitude of weak antibody-ligand interactions (H-bonding, van der Waals, etc.) inside a structurally well-defined cleft-like binding pocket. Relatively small structural changes (e.g. G-2 to A for G17) have a drastic impact on affinity, which is characteristic for antibody-like binding. In contrast, SBs recognize various sequences, including G17-unrelated targets with affinities of 1:1 complexes estimated in the 0.1-1.0 mM range. In most cases however, the G17/SB complex stoichiometries are not well-defined, giving rise to multimer aggregate formation with high apparent complex stabilities. Mutational studies on both G17 and SBs reveal the importance of positively charged (K/R) and aromatic residues (W/Y/F) for G17/SB complex formation. We propose that the synthetic binders use combinations of electrostatic, hydrophobic, and/or cation-p interactions in a variety of ways due to their intrinsic flexibility. This may also be the reason for their relatively low target specificity. We speculate that our findings are of general relevance, in showing that high-affinity mAbs do not necessarily provide the optimal basis for functional mimics design.

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A peptide mimetic of an anti-CD4 monoclonal antibody by rational design

Cited by 32 publications

References 15 publications

A Cell-penetrating Antibody Fragment against HIV-1 Rev Has High Antiviral Activity

A Cell-penetrating Antibody Fragment against HIV-1 Rev Has High Antiviral Activity

A Combinatorial Approach for the Design of Complementarity-determining Region-derived Peptidomimetics with in Vitro Anti-tumoral Activity

Binding of CDR‐derived peptides is mechanistically different from that of high‐affinity parental antibodies

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