Peptide Scaffolds: Flexible Molecular Structures With Diverse Therapeutic Potentials

Conformationally adaptive therapeutic peptides for diseases caused by intrinsically disordered proteins (IDPs). New paradigm for drug discovery: Target the target, not the arrow

The traditional model of protein structure determined by the amino acid sequence is today seriously challenged by the fact that approximately half of the human proteome is made up of proteins that do not have a stable 3D structure, either partially or in totality. These proteins, called intrinsically disordered proteins (IDPs), are involved in numerous physiological functions and are associated with severe pathologies, e.g. Alzheimer, Parkinson, Creutzfeldt-Jakob, amyotrophic lateral sclerosis (ALS), and type 2 diabetes. Targeting these proteins is challenging for two reasons: i) we need to preserve their physiological functions, and ii) drug design by molecular docking is not possible due to the lack of reliable starting conditions. Faced with this challenge, the solutions proposed by artificial intelligence (AI) such as AlphaFold are clearly unsuitable. Instead, we suggest an innovative approach consisting of mimicking, in short synthetic peptides, the conformational flexibility of IDPs. These peptides, which we call adaptive peptides, are derived from the domains of IDPs that become structured after interacting with a ligand. Adaptive peptides are designed with the aim of selectively antagonizing the harmful effects of IDPs, without targeting them directly but through selected ligands, without affecting their physiological properties. This "target the target, not the arrow" strategy is promised to open a new route to drug discovery for currently undruggable proteins.

Tailored Presentation of Carbohydrates on a Coiled Coil-Based Scaffold for Asialoglycoprotein Receptor Targeting

The coiled-coil folding motif represents an ideal scaffold for the defined presentation of ligands due to the possibility of positioning them at specific distances along the axis. We created a coiled-coil glycopeptide library to characterize the distances between the carbohydrate-binding sites of the asialoglycoprotein receptors (ASGPR) on hepatocytes. The components of the glycopeptide library vary for the number of displayed ligands (galactose), their position on the peptide sequence, and the space between peptide backbone and carbohydrate. We determined the binding of the glycopeptides to the hepatocytes, and we established the optimal distance and orientation of the galactose moieties for interaction with the ASGPR using flow cytometry. We confirmed that the binding occurs through endocytosis mediated by ASGPR via inhibition studies with cytochalasin D; fluorescence microscopy studies display the uptake of the carrier peptides inside the cell. Thus, this study demonstrates that the coiled-coil motif can be used as reliable scaffold for the rational presentation of ligands.

Conjugation Approach To Produce a Staphylococcus aureus Synbody with Activity in Serum

Synbodies show promise as a new class of synthetic antibiotics. Here, we explore improvements in their activity and production through conjugation chemistry. Maleimide conjugation is a widely used conjugation strategy due to its high yield, selectivity, and low cost. We used this strategy to conjugate two antibacterial peptides to produce a bivalent antibacterial peptide, called a synbody that has bactericidal activity against methicillin resistant Staphylococcus aureus (MRSA). The synbody was prepared by conjugation of a partially d-amino acid substituted synthetic antibacterial peptide to a bis-maleimide scaffold. The synbody slowly degrades in serum, but also undergoes exchange reactions with other serum proteins, such as albumin. Therefore, we hydrolyzed the thiosuccinimide ring using a mild hydrolysis protocol to produce a new synbody with similar bactericidal activity. The synbody was now resistant to exchange reactions and maintained bactericidal activity in serum for 2 h. This work demonstrates that low-cost maleimide coupling can be used to produce antibacterial peptide conjugates with activity in serum.

Solvent effects on the conformational preferences of model peptoids. MP2 study

The influence of aqueous environment on the main-chain conformation (ω0 , ϕ, and ψ dihedral angles) of two model peptoids: N-acetyl-N-methylglycine N'-methylamide (Ac-N(Me)-Gly-NHMe) (1) and N-acetyl-N-methylglycine N',N'-dimethylamide (Ac-N(Me)-Gly-NMe₂) (2) was investigated by MP2/6-311++G(d,p) method. The Ramachandran maps of both studied molecules with cis and trans configuration of the N-terminal amide bond in the gas phase and in water environment were obtained and all energy minima localized. The polarizable continuum model was applied to estimate the solvation effect on conformation. Energy minima of the Ac-N(Me)-Gly-NHMe and Ac-N(Me)-Gly-NMe₂ have been analyzed in terms of the possible hydrogen bonds and C = O dipole attraction. To validate the theoretical results obtained, conformations of the similar structures gathered in the Cambridge Crystallographic Data Centre were analyzed. Obtained results indicate that aqueous environment in model peptoids 1 and 2 favors the conformation F (ϕ and ψ = -70º, 180º), and additionally significantly increases the percentage of structures with cis configuration of N-terminal amide bond in studied compounds.

Characterization of N-Boc/Fmoc/Z-N'-formyl-gem-diaminoalkyl derivatives using electrospray ionization multi-stage mass spectrometry

N-Boc/Fmoc/Z-N'-formyl-gem-diaminoalkyl derivatives, intermediates particularly useful in the synthesis of partially modified retro-inverso peptides, have been characterized by both positive and negative ion electrospray ionization (ESI) ion-trap multi-stage mass spectrometry (MS(n)). The MS(2) collision induced dissociation (CID) spectra of the sodium adduct of the formamides derived from the corresponding N-Fmoc/Z-amino acids, dipeptide and tripeptide acids show the [M + Na-NH2CHO](+) ion, arising from the loss of formamide, as the base peak. Differently, the MS(2) CID spectra of [M + Na](+) ion of all the N-Boc derivatives yield the abundant [M + Na-C4H8](+) and [M + Na-Boc + H](+) ions because of the loss of isobutylene and CO2 from the Boc protecting function. Useful information on the type of amino acids and their sequence in the N-protected dipeptidyl and tripeptidyl-N'-formamides is provided by MS(2) and subsequent MS(n) experiments on the respective precursor ions. The negative ion ESI mass spectra of these oligomers show, in addition to [M-H](-), [M + HCOO](-) and [M + Cl](-) ions, the presence of in-source CID fragment ions deriving from the involvement of the N-protecting group. Furthermore, MS(n) spectra of [M + Cl](-) ion of N-protected dipeptide and tripeptide derivatives show characteristic fragmentations that are useful for determining the nature of the C-terminal gem-diamino residue. The present paper represents an initial attempt to study the ESI-MS behavior of these important intermediates and lays the groundwork for structural-based studies on more complex partially modified retro-inverso peptides.

PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides

In the context of the renewed interest of peptides as therapeutics, it is important to have an on-line resource for 3D structure prediction of peptides with well-defined structures in aqueous solution. We present an updated version of PEP-FOLD allowing the treatment of both linear and disulphide bonded cyclic peptides with 9-36 amino acids. The server makes possible to define disulphide bonds and any residue-residue proximity under the guidance of the biologists. Using a benchmark of 34 cyclic peptides with one, two and three disulphide bonds, the best PEP-FOLD models deviate by an average RMS of 2.75 Å from the full NMR structures. Using a benchmark of 37 linear peptides, PEP-FOLD locates lowest-energy conformations deviating by 3 Å RMS from the NMR rigid cores. The evolution of PEP-FOLD comes as a new on-line service to supersede the previous server. The server is available at: http://bioserv.rpbs.univ-paris-diderot.fr/PEP-FOLD.