7 research outputs found
Recommended from our members
Computational and Experimental Analysis of the Interactions Between C3 and Compstatin Family Peptides
We present the physicochemical basis of binding for several active peptides from the compstatin family against the immune system protein C3. The peptide sequences are tailored to promote enhancement of the structural and physicochemical properties that contribute to binding, including consideration of the dynamic character of the protein/ligand system. The peptide sequences are designed using: (i) computational sequence selection and approximate binding affinity calculations, (ii) molecular dynamics simulations, and (iii) rational optimization [1–3]. A subset of the new peptides has been tested in ELISA inhibition assays using human serum, and produced comparable IC50 values to those of known peptides. The most promising new designs acquire an advantage in that they combine a more optimal balance between hydrophobicity, which is important for binding, and polarity, which is important for solubility, compared to the most potent known peptides. Thus, the new peptides are good candidates to become therapeutics, upon further optimization. Given the species specificity of known compstatin family peptides for primate but not for non-primate mammals, some of the new designs aim at binding to both human and rat C3. The dual specificity design was conducted using molecular dynamics simulations based on our recent atomic detail model for compstatin-human/rat binding [3]; however, the efficacy of the new peptides for rat C3 binding and inhibition remains to be seen in experimental assays using rat serum
Recommended from our members
Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures
We have used a novel human retinal pigmented epithelial (RPE) cell-based model that mimics drusen biogenesis and the pathobiology of age-related macular degeneration to evaluate the efficacy of newly designed peptide inhibitors of the complement system. The peptides belong to the compstatin family and, compared to existing compstatin analogs, have been optimized to promote binding to their target, complement protein C3, and to enhance solubility by improving their polarity/hydrophobicity ratios. Based on analysis of molecular dynamics simulation data of peptide–C3 complexes, novel binding features were designed by introducing intermolecular salt bridge-forming arginines at the N-terminus and at position −1 of N-terminal dipeptide extensions. Our study demonstrates that the RPE cell assay has discriminatory capability for measuring the efficacy and potency of inhibitory peptides in a macular disease environment
Recommended from our members
Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures.
We have used a novel human retinal pigmented epithelial (RPE) cell-based model that mimics drusen biogenesis and the pathobiology of age-related macular degeneration to evaluate the efficacy of newly designed peptide inhibitors of the complement system. The peptides belong to the compstatin family and, compared to existing compstatin analogs, have been optimized to promote binding to their target, complement protein C3, and to enhance solubility by improving their polarity/hydrophobicity ratios. Based on analysis of molecular dynamics simulation data of peptide-C3 complexes, novel binding features were designed by introducing intermolecular salt bridge-forming arginines at the N-terminus and at position -1 of N-terminal dipeptide extensions. Our study demonstrates that the RPE cell assay has discriminatory capability for measuring the efficacy and potency of inhibitory peptides in a macular disease environment
De Novo Peptide Design with C3a Receptor Agonist and Antagonist Activities: Theoretical Predictions and Experimental Validation
Targeting the complement component 3a receptor (C3aR)
with selective
agonists or antagonists is believed to be a viable therapeutic option
for several diseases such as stroke, heart attack, reperfusion injuries,
and rheumatoid arthritis. We designed a number of agonists, partial
agonists, and antagonists of C3aR using our two-stage de novo protein
design framework. Of the peptides tested using a degranulation assay
in C3aR-transfected rat basophilic leukemia cells, two were prominent
agonists (EC<sub>50</sub> values of 25.3 and 66.2 nM) and two others
were partial agonists (IC<sub>50</sub> values of 15.4 and 26.1 nM).
Further testing of these lead compounds in a calcium flux assay in
U937 cells yielded similar results although with reduced potencies
compared to transfected cells. The partial agonists also displayed
full antagonist activity when tested in a C3aR inhibition assay. In
addition, the electrostatic potential profile was shown to potentially
discriminate between full agonists and partial agonists
Recommended from our members
De novo peptide design with C3a receptor agonist and antagonist activities: Theoretical predictions and experimental validation
Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks generally have shapes that have evolved to fit precisely into binding pockets on their targets. Such peptides can have excellent pharmaceutical properties, combining the stability and tissue penetration of small-molecule drugs with the specificity of much larger protein therapeutics. The ability to design constrained peptides with precisely specified tertiary structures would enable the design of shape-complementary inhibitors of arbitrary targets. Here we describe the development of computational methods for accurate de novo design of conformationally restricted peptides, and the use of these methods to design 18-47 residue, disulfide-crosslinked peptides, a subset of which are heterochiral and/or N-C backbone-cyclized. Both genetically encodable and non-canonical peptides are exceptionally stable to thermal and chemical denaturation, and 12 experimentally determined X-ray and NMR structures are nearly identical to the computational design models. The computational design methods and stable scaffolds presented here provide the basis for development of a new generation of peptide-based drugs