PPubMed7 Aug 2015Cited 38×

<i> In Silico </i> Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands <i> In Silico </i> Generation of Peptides

Anna Russo, Pasqualina Liana Scognamiglio, Rolando Pablo Hong Enriquez, Carlo Santambrogio, Rita Grandori, Daniela Marasco, Antonio Giordano, Giacinto Scoles, Sara Fortuna, Yang Zhang

Abstract

'Rolando Pablo Hong Enriquez' 'Carlo Santambrogio' 'Rita Grandori' 'Daniela Marasco' 'Antonio Giordano' 'Giacinto Scoles' 'Sara Fortuna' 'Yang Zhang'] Short peptides can be designed in silico and synthesized through automated techniques, making them advantageous and versatile protein binders. A number of docking-based algorithms allow for a computational screening of peptides as binders. Here we developed ex-novo peptides targeting the maltose site of the Maltose Binding Protein, the prototypical system for the study of protein ligand recognition. We used a Monte Carlo based protocol, to computationally evolve a set of octapeptides starting from a polialanine sequence. We screened in silico the candidate peptides and characterized their binding abilities by surface plasmon resonance, fluorescence and electrospray ionization mass spectrometry assays. These experiments showed the designed binders to recognize their target with micromolar affinity. We finally discuss the obtained results in the light of further improvement in the ex-novo optimization of peptide based binders.

A figure from <i> In Silico </i> Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands <i> In Silico </i> Generation of Peptides — fig. from the paper

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In silico designed octapeptides bind the maltose‑binding protein with micromolar affinity, with peptide MBP‑9 showing KD ≈70 μM.

What’s new

i.Developed an ex‑novo peptide design workflow combining replica‑exchange Monte Carlo with AutoDock Vina docking
ii.Evolved and screened octapeptides targeting the maltose‑binding site of MBP, identifying high‑affinity candidates
iii.Experimentally validated the computational predictions using SPR, fluorescence quenching, and ESI‑MS
iv.Introduced a correction scheme for docking energies using non‑binding site references

How they did it

Starting from a poly‑alanine octapeptide, the authors iteratively evolved sequences using a Monte Carlo replica‑exchange protocol coupled with AutoDock Vina scoring to predict binding to the MBP maltose pocket. The top candidates were chemically synthesized and their interactions with MBP were measured by surface plasmon resonance, tryptophan fluorescence quenching, and electrospray‑ionization mass spectrometry. Binding energies from docking were corrected by subtracting energies obtained on a non‑binding site.

What they found

MBP‑9 displayed a dissociation constant KD = 72 ± 3 μM by SPR (1:1 Langmuir model)
Fluorescence quenching gave KD = 65 ± 10 μM for MBP‑9, consistent with SPR
ESI‑MS showed MBP‑9 formed 1:1 complexes (≈33% of protein) and 1:2 complexes (≈5%)
Initial docking energies for the first eight peptides corresponded to 3.28–5.11 kcal mol⁻¹ (micromolar range)
Corrected docking binding energies correlated well with experimental ΔG values despite the small dataset

Caveats

✕Docking scores missed sequence‑dependent entropic contributions, requiring empirical correction
✕The dataset is very small, limiting statistical confidence in the correlation between computed and experimental affinities
✕Potential non‑specific binding to other MBP domains could not be fully excluded
✕Only the maltose‑binding protein was examined, so broader applicability of the workflow remains untested

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