Terminus-immobilization effect on peptide conformations and peptide–peptide interactions

Peptide-modified delivery systems are enabling the improvement of the targeting specificity,biocompatibility,stability,etc.However,the precise design of a peptide-decorated surface for a designated function has remained to be challenging due to a lack of mechanistic understanding of the interactions between surface-bound peptide ligands and their receptors.Enlightened by the recent report on pairwise interactions between peptides in the solution state and surface-immobilized state,we used computational simulations to explore the contributing mechanisms underlining the observed binding affinity characteristics.Molecular dynamics simulations were performed to sample and compare conformations of homo-octapeptides free in solution(mobile peptides)and bound to the surface(N-terminal fixed peptides).We found that peptides converged to more extended and rigid conformations when immobilized to the surface and confirmed that the extended structures could increase the space available to counter-interacting peptides during the peptide–peptide interactions.In addition,studies on interactions between stationary and mobile peptides revealed that main-chain/side-chain and side-chain/side-chain hydrogen bonds play an important role.The presented efforts in this work may provide supportive references for peptide design and modification on the nanoparticle surface as well as guidance for analyzing peptide–receptor interactions through an emphasis on hydrogen bonds during peptide design and an understanding of the influence on the binding affinity by the sequence-dependant conformational changes after peptide immobilization.

Zwitterionic peptides:Tunable next-generation stealth nanoparticle modifications

Adsorption of proteins to nanoparticles(NPs),a complex process that results in a protein corona,is controlled by NP surface properties that define NP interactions in vivo.Efforts to control adsorbed protein quantity through surface modification have led to improvements in circulation time or biodistribution.Still,current approaches have yet to be identified to control adsorbed protein identities within the corona.Here,we report the development and characterization of diverse zwitterionic peptides(ZIPs)for NP anti-fouling surface functionalization with specific and controllable affinity for protein adsorption profiles defined by ZIP sequence.Through serum exposure of ZIP-conjugated NPs and proteomics analysis of the resulting corona,we determined that protein adsorption profiles depend not on the exact composition of the ZIPs but on the sequence and order of charges along the sequence(charge motif).These findings pave the way for developing tunable ZIPs to orchestrate specific ZIP-NP protein adsorption profiles as a function of ZIP charge motif to better control cell and tissue specificity and pharmacokinetics and provide new tools for investigating relationships between protein corona and biological function.Furthermore,overall ZIP diversity enabled by the diversity of amino acids may ameliorate adaptive immune responses.

finDr:A web server for in silico D-peptide ligand identification

In the rapidly expanding field of peptide therapeutics,the short in vivo half-life of peptides represents a considerable limitation for drug action.D-peptides,consisting entirely of the dextrorotatory enantiomers of naturally occurring levorotatory amino acids(AAs),do not suffer from these shortcomings as they are intrinsically resistant to proteolytic degradation,resulting in a favourable pharmacokinetic profile.To experimentally identify D-peptide binders to interesting therapeutic targets,so-called mirror-image phage display is typically performed,whereby the target is synthesized in D-form and L-peptide binders are screened as in conventional phage display.This technique is extremely powerful,but it requires the synthesis of the target in D-form,which is challenging for large proteins.Here we present finDr,a novel web server for the computational identification and optimization of D-peptide ligands to any protein structure(https://findr.biologie.uni-freiburg.de/).finDr performs molecular docking to virtually screen a library of helical 12-mer peptides extracted from the RCSB Protein Data Bank(PDB)for their ability to bind to the target.In a separate,heuristic approach to search the chemical space of 12-mer peptides,finDr executes a customizable evolutionary algorithm(EA)for the de novo identification or optimization of D-peptide ligands.As a proof of principle,we demonstrate the validity of our approach to predict optimal binders to the pharmacologically relevant target phenol soluble modulin alpha 3(PSMα3),a toxin of methicillin-resistant Staphylococcus aureus(MRSA).We validate the predictions using in vitro binding assays,supporting the success of this approach.Compared to conventional methods,finDr provides a low cost and easy-to-use alternative for the identification of D-peptide ligands against protein targets of choice without size limitation.We believe finDr will facilitate D-peptide discovery with implications in biotechnology and biomedicine.

Peptide stapling with the retention of double native side-chains

All-hydrocarbon stapling strategy has been widely applied for enhancing the proteolytic stability of peptides. However, two major technical hurdles to some extent limit the development of stapled peptides for therapeutic usage: rational selection of the stapling sites and the corresponding deletion of the native side chains. Previously we described the development of the olefin-terminated amino acids with the retention of native side chains and successfully applied them in the synthesis of hydrocarbon stapled peptides with single side-chain retention. Here, we explored the feasibility and effectiveness of hydrocarbon stapling strategy characterized as double side-chains retention. Modeled after a lengthy human immunodeficiency virus-1(HIV-1) fusion inhibitor SC34 EK, Leu^(i), Ser^(i+4)and Lys^(i), Leu^(i+4)stapled peptides with the retention of double side-chains were effectively obtained. Our complementary study provided a convenient alternative to address where to install the staple in sequence for conventional all-hydrocarbon peptide stapling. Furthermore, this method not only conferred conformational reinforcement for SC34 EK with high α-helicity and protease resistance, but also preserved the structural characteristic(key peripheral residues, charge and solubility) of the linear peptide to the maximum, which are crucial for anti-HIV-1 activity.