De novo design of potential peptide analogs against the main protease of Omicron variant using in silico studies.

SARS-CoV-2 and its variants are crossing the immunity barrier induced through vaccination. Recent Omicron sub-variants are highly transmissible and have a low mortality rate. Despite the low severity of Omicron variants, these new variants are known to cause acute post-infectious syndromes. Nowadays, novel strategies to develop new potential inhibitors for SARS-CoV-2 and other Omicron variants have gained prominence. For viral replication and survival the main protease of SARS-CoV-2 plays a vital role. Peptide-like inhibitors that mimic the substrate peptide have already proved to be effective in inhibiting the Mpro of SARS-CoV-2 variants. Our systematic canonical amino acid point mutation analysis on the native peptide has revealed various ways to improve the native peptide of the main protease. Multi mutation analysis has led us to identify and design potent peptide-analog inhibitors that act against the Mpro of the Omicron sub-variants. Our in-depth analysis of all-atom molecular dynamics studies has paved the way to characterize the atomistic behavior of Mpro in Omicron variants. Our goal is to develop potent peptide-analogs that could be therapeutically effective against Omicron and its sub-variants.

Light-Fueled Primitive Replication and Selection in Biomimetic Chemical Systems.

The concept of chemically evolvable replicators is central to abiogenesis. Chemical evolvability requires three essential components: energy-harvesting mechanisms for nonequilibrium dissipation, kinetically asymmetric replication and decomposition pathways, and structure-dependent selective templating in the autocatalytic cycles. We observed a UVA light-fueled chemical system displaying sequence-dependent replication and replicator decomposition. The system was constructed with primitive peptidic foldamer components. The photocatalytic formation-recombination cycle of thiyl radicals was coupled with the molecular recognition steps in the replication cycles. Thiyl radical-mediated chain reaction was responsible for the replicator death mechanism. The competing and kinetically asymmetric replication and decomposition processes led to light intensity-dependent selection far from equilibrium. Here, we show that this system can dynamically adapt to energy influx and seeding. The results highlight that mimicking chemical evolution is feasible with primitive building blocks and simple chemical reactions.

Rationally designed foldameric adjuvants enhance antibiotic efficacy via promoting membrane hyperpolarization.

The negative membrane potential of bacterial cells influences crucial cellular processes. Inspired by the molecular scaffold of the antimicrobial peptide PGLa, we have developed antimicrobial foldamers with a computer-guided design strategy. The novel PGLa analogues induce sustained membrane hyperpolarization. When co-administered as an adjuvant, the resulting compounds - PGLb1 and PGLb2 - have substantially reduced the level of antibiotic resistance of multi-drug resistant Escherichia coli, Klebsiella pneumoniae and Shigella flexneri clinical isolates. The observed antibiotic potentiation was mediated by hyperpolarization of the bacterial membrane caused by the alteration of cellular ion transport. Specifically, PGLb1 and PGLb2 are selective ionophores that enhance the Goldman-Hodgkin-Katz potential across the bacterial membrane. These findings indicate that manipulating bacterial membrane electrophysiology could be a valuable tool to overcome antimicrobial resistance.

An electrophilic warhead library for mapping the reactivity and accessibility of tractable cysteines in protein kinases.

Targeted covalent inhibitors represent a viable strategy to block protein kinases involved in different disease pathologies. Although a number of computational protocols have been published for identifying druggable cysteines, experimental approaches are limited for mapping the reactivity and accessibility of these residues. Here, we present a ligand based approach using a toolbox of fragment-sized molecules with identical scaffold but equipped with diverse covalent warheads. Our library represents a unique opportunity for the efficient integration of warhead-optimization and target-validation into the covalent drug development process. Screening this probe kit against multiple kinases could experimentally characterize the accessibility and reactivity of the targeted cysteines and helped to identify suitable warheads for designed covalent inhibitors. The usefulness of this approach has been confirmed retrospectively on Janus kinase 3 (JAK3). Furthermore, representing a prospective validation, we identified Maternal embryonic leucine zipper kinase (MELK), as a tractable covalent target. Covalently labelling and biochemical inhibition of MELK would suggest an alternative covalent strategy for MELK inhibitor programs.

DPP-4 Cleaves α/ß-Peptide Bonds: Substrate Specificity and Half-Lives.

The incorporation of ß-amino acids into a peptide sequence has gained particular attention as ß- and α/ß-peptides have shown remarkable proteolytic stability, even after a single homologation at the scissile bond. Several peptidases have been shown to cleave such bonds with high specificity but at a much slower rate compared to α-peptide bonds. In this study, a series of analogs of dipeptidyl peptidase-4 (DPP-4) substrate inhibitors were synthesized in order to investigate whether ß-amino acid homologation at the scissile bond could be a valid approach to improving peptide stability towards DPP-4 degradation. DPP-4 cleaved the α/ß-peptide bond after the N-terminal penultimate Pro with a broad specificity and retained full activity regardless of the ß3 -amino acid side chain and peptide length. Significantly improved half-lives were observed for ß3 Ile-containing peptides. Replacing the penultimate Pro with a conformationally constrained Pro mimetic led to proteolytic resistance. DPP-4 cleavage of α/ß-peptide bonds with a broad promiscuity represents a new insight into the stability of peptide analogs containing ß-amino acids as such analogs were thought to be stable towards enzymatic degradation.

Routing Nanomolar Protein Cargoes to Lipid Raft-Mediated/Caveolar Endocytosis through a Ganglioside GM1-Specific Recognition Tag.

There is a pressing need to develop ways to deliver therapeutic macromolecules to their intracellular targets. Certain viral and bacterial proteins are readily internalized in functional form through lipid raft-mediated/caveolar endocytosis, but mimicking this process with protein cargoes at therapeutically relevant concentrations is a great challenge. Targeting ganglioside GM1 in the caveolar pits triggers endocytosis. A pentapeptide sequence WYKYW is presented, which specifically captures the glycan moiety of GM1 (K D = 24 nm). The WYKYW-tag facilitates the GM1-dependent endocytosis of proteins in which the cargo-loaded caveosomes do not fuse with lysosomes. A structurally intact immunoglobulin G complex (580 kDa) is successfully delivered into live HeLa cells at extracellular concentrations ranging from 20 to 160 nm, and escape of the cargo proteins to the cytosol is observed. The short peptidic WYKYW-tag is an advantageous endocytosis routing sequence for lipid raft-mediated/caveolar cell delivery of therapeutic macromolecules, especially for cancer cells that overexpress GM1.

Multilevel structure-activity profiling reveals multiple green tea compound families that each modulate ubiquitin-activating enzyme and ubiquitination by a distinct mechanism.

We developed and implemented a reconstituted system to screen for modulators of the ubiquitination of proliferating cell nuclear antigen, a process that activates pathways of DNA damage tolerance and drug resistance. We identified the primary putatively health-beneficial green tea polyphenol epigallocatechin gallate (EGCG) and certain related small molecules as potent inhibitors of ubiquitination. EGCG directly and reversibly targets the ubiquitin-activating enzyme Uba1, blocking formation of the Uba1~ubiquitin thioester conjugate and thus ubiquitination and in the cell. Structure-activity relationship profiles across multiple biochemical and cellular assays for a battery of EGCG analogues revealed distinct chemical and mechanism-of-action clusters of molecules, with catechin gallates, alkyl gallates, and myricetin potently inhibiting ubiquitination. This study defines a number of related though distinct first-in-class inhibitors of ubiquitination, each series with its own unique activity pattern and mechanistic signature.

Foldameric probes for membrane interactions by induced ß-sheet folding.

Design strategies were devised for α/ß-peptide foldameric analogues of the antiangiogenic anginex with the goal of mimicking the diverse structural features from the unordered conformation to a folded ß-sheet in response to membrane interactions. Structure-activity relationships were investigated in the light of different ß-sheet folding levels.

Predicting order and disorder for ß-peptide foldamers in water.

Following a quantitative validation approach, we tested the AMBER ff03 and GAFF force fields with the TIP3P explicit water model in molecular dynamic simulations of ß-peptide foldamers. The test sequences were selected to represent a wide range of folding behavior in water: compact helix, strand mimetic geometry, and the state of disorder. The combination AMBER ff03-TIP3P successfully predicted the experimentally observed conformational properties and reproduced the NOE distances and backbone (3)J coupling data at a good level. GAFF was unable to produce folded structures correctly due to its biased torsion potentials. We can recommend AMBER ff03-TIP3P for simulations involving ß-peptide sequences in aqueous media including ordered and disordered structures.

Peptides containing ß-amino acid patterns: challenges and successes in medicinal chemistry.

The construction of bioactive peptides using ß-amino acid-containing sequence patterns is a very promising strategy to obtain analogues that exhibit properties of high interest for medicinal chemistry applications. ß-Amino acids have been shown to modulate the conformation, dynamics, and proteolytic susceptibility of native peptides. They can be either combined with α-amino acids by following specific patterns, which results in backbone architectures with well-defined orientations of the side chain functional groups, or assembled in de novo-designed bioactive ß- or α,ß-peptidic sequences. Such peptides display various biological functions, including antimicrobial activity, inhibition of protein-protein interactions, agonism/antagonism of GPCR ligands, and anti-angiogenic activity.

Foldameric α/ß-peptide analogs of the ß-sheet-forming antiangiogenic anginex: structure and bioactivity.

The principles of ß-sheet folding and design for α-peptidic sequences are well established, while those for sheet mimetics containing homologated amino acid building blocks are still under investigation. To reveal the structure-function relations of ß-amino-acid-containing foldamers, we followed a top-down approach to study a series of α/ß-peptidic analogs of anginex, a ß-sheet-forming antiangiogenic peptide. Eight anginex analogs were developed by systematic α → ß(3) substitutions and analyzed by using NMR and CD spectroscopy. The foldamers retained the ß-sheet tendency, though with a decreased folding propensity. ß-Sheet formation could be induced by a micellar environment, similarly to that of the parent peptide. The destructuring effect was higher when the α → ß(3) exchange was located in the ß-sheet core. Analysis of the ß-sheet stability versus substitution pattern and the local conformational bias of the bulky ß(3)V and ß(3)I residues revealed that a mismatch between the H-bonding preferences of the α- and ß-residues played a minor role in the structure-breaking effect. Temperature-dependent CD and NMR measurements showed that the hydrophobic stabilization was scaled-down for the α/ß-peptides. Analysis of the biological activity of the foldamer peptides showed that four anginex derivatives dose-dependently inhibited the proliferation of a mouse endothelial cell line. The α → ß(3) substitution strategy applied in this work can be a useful approach to the construction of bioactive ß-sheet mimetics with a reduced aggregation tendency and improved pharmacokinetic properties.

Self-association-driven transition of the ß-peptidic H12 helix to the H18 helix.

Various patterns of foldameric oligomers formed by trans-ABHC ((1S,2S,3S,5S)-2-amino-6,6-dimethylbicyclo[3.3.1]heptane-3-carboxylic acid) and ß(3)-hSer residues were studied. NMR, ECD and molecular modelling demonstrated that octameric and nonameric sequences with multiple i-i+3 ABHC pair repulsions attain the ß-H18 helix in CD(3)OH. As a close relative of the α-helix, this helix type is stabilized by i-i+4 backbone H-bond interactions. The formation of the ß-H18 helix was found to be solvent- and concentration-dependent. Upon dilution, the ß-H18 → ß-H12 helix transition was revealed by concentration-dependent ECD, DOSY-NMR and TEM measurements.

Peptidic foldamers: ramping up diversity.

Non-natural folded polymers (foldamers) display considerable versatility, and the design of such molecules is of great current interest. In this respect, peptidic foldamers are perhaps the best-characterized systems, as they populate a number of residue-controlled secondary structures, which have found various biological applications and have also led to the creation of nanostructured materials. This critical review covers recent developments related to diverse building blocks and modern foldamer design principles, such as the stereochemical patterning methods. The recent achievements concerning tertiary/quaternary structures and the self-assembling foldameric nanostructures are also addressed (176 references).

Building ß-peptide H10/12 foldamer helices with six-membered cyclic side-chains: fine-tuning of folding and self-assembly.

The ability of the ß-peptidic H10/12 helix to tolerate side-chains containing six-membered alicyclic rings was studied. cis-2-Aminocyclohex-3-ene carboxylic acid (cis-ACHEC) residues afforded H10/12 helix formation with alternating backbone configuration. Conformational polymorphism was observed for the alternating cis-ACHC hexamer, where chemical exchange takes place between the major left-handed H10/12 helix and a minor folded conformation. The hydrophobically driven self-assembly was achieved for the cis-ACHC-containing helix which was observed as vesicles ~100 nm in diameter.

Galectin-1-asialofetuin interaction is inhibited by peptides containing the tyr-xxx-tyr motif acting on the glycoprotein.

Galectin-1 (Gal-1), a ubiquitous beta-galactoside-binding protein expressed by various normal and pathological tissues, has been implicated in cancer and autoimmune/inflammatory diseases in consequence of its regulatory role in adhesion, cell viability, proliferation, and angiogenesis. The functions of Gal-1 depend on its affinity for beta-galactoside-containing glycoconjugates; accordingly, the inhibition of sugar binding blocks its functions, hence promising potential therapeutic tools. The Tyr-Xxx-Tyr peptide motifs have been reported to be glycomimetic sequences, mainly on the basis of their inhibitory effect on the Gal-1-asialofetuin (ASF) interaction. However, the results regarding the efficacy of the Tyr-Xxx-Tyr motif as a glycomimetic inhibitor are still controversial. The present STD and trNOE NMR experiments reveal that the Tyr-Xxx-Tyr peptides studied do not bind to Gal-1, whereas their binding to ASF is clearly detected. (15)N,(1)H HSQC titrations with (15)N-labeled Gal-1 confirm the absence of any peptide-Gal-1 interaction. These data indicate that the Tyr-Xxx-Tyr peptides tested in this work are not glycomimetics as they interact with ASF via an unrevealed molecular linkage.

Design of peptidic foldamer helices: a stereochemical patterning approach.

Assembly language: The programmed sequences of stereochemical building blocks lead to novel biomimetic helices. The rational design approach offers new possibilities for creating periodic secondary structures.

Copper(II) and zinc(II) ion binding properties of a MAP type branched ligand with histidines as surface functionalities.

A novel branched peptide type ligand consisting of three lysines as branching units and four histidines as functional groups has been designed and prepared by solid phase peptide synthesis. The N-terminal histidines offer eight primary protonation/metal ion binding sites: four amino and four imidazole groups, capable of binding up to two metal ions. We examined the protonation equilibria, and the complex formation processes with copper(II) and zinc(II) ions in c(M):c(L) = 1:1 and 2:1 initial concentration ratio in aqueous solutions. The composition, speciation and the solution structure of the complexes have been determined by combined pH-potentiometric titrations, visible absorption, circular dichroism and NMR spectroscopy. In the case of both metal ions, mono- and dimetallic complexes formed with bis-histamine type coordination as the main species. While above pH 8 the precipitation of a neutral complex was observed for both metal ions, in the copper(II) containing systems it dissolved in alkaline solutions (pH > 11.0). The resulting complex in an equimolar system displays deprotonated amide-nitrogen coordination, with fused five-membered chelate rings around the metal ion in [CuLH(-3)](-). At the same time, only one copper(II) is able to coordinate in the same manner in the [Cu(2)LH(-5)](-) species. The second metal ion is probably surrounded by two amide nitrogens and two others either from amino or imidazole donor groups.

Ligand-induced flocculation of neurotoxic fibrillar Abeta(1-42) by noncovalent crosslinking.

Aggregation of the amyloid-beta (Abeta) peptides has a pivotal role in Alzheimer's disease (AD). Small molecules and short peptides/peptidomimetics can exert their full protective effects against Abeta within a short time-frame, but the exact mechanism of action is unclear. Time-dependent NMR spectroscopic binding and replacement experiments were carried out for peptide LPFFD and thioflavine T (ThT) on neurotoxic fibrillar Abeta(1-42), which revealed transient binding behavior for both compounds, and complex time-dependent features in the replacement experiments. The results of particle size measurements through the use of diffuse light-scattering and transmission electron microscopy support the conclusions that the studied ligands induced interfibrillar association on a short timescale, which explains the NMR spectroscopic binding and replacement results. zeta-Potential measurements revealed a slightly increased electrostatic stability of the Abeta fibrils upon ligand binding; this suggests that the interfibrillar assembly is driven by specific noncovalent cross-linking interactions. A specific surface and mobility decrease due to the ligand-induced flocculation of the Abeta fibrils can explain the neuroprotective effects.