Principles of Inter-Amino-Acid Recognition Revealed by Binding Energies between Homogeneous Oligopeptides

Computational electrostatic engineering of nanobodies for enhanced SARS-CoV-2 receptor binding domain recognition

This study presents a novel computational approach for engineering nanobodies (Nbs) for improved interaction with receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Using Protein Structure Reliability reports, RBD (7VYR_R) was selected and refined for subsequent Nb-RBD interactions. By leveraging electrostatic complementarity (EC) analysis, we engineered and characterized five Electrostatically Complementary Nbs (ECSb1-ECSb5) based on the CeVICA library's SR6c3 Nb. Through targeted modifications in the complementarity-determining regions (CDR) and framework regions (FR), we optimized electrostatic interactions to improve binding affinity and specificity. The engineered Nbs (ECSb3, ECSb4, and ECSb5) demonstrated high binding specificity for AS3, CA1, and CA2 epitopes. Interestingly, ECSb1 and ECSb2 selectively engaged with AS3 and CA1 instead of AS1 and AS2, respectively, due to a preference for residues that conferred superior binding complementarities. Furthermore, ECSbs significantly outperformed SR6c3 Nb in MM/GBSA results, notably, ECSb4 and ECSb3 exhibited superior binding free energies of -182.58 kcal.mol-1 and -119.07 kcal.mol-1, respectively, compared to SR6c3 (-105.50 kcal.mol-1). ECSbs exhibited significantly higher thermostability (100.4-148.3 kcal·mol⁻1) compared to SR6c3 (62.6 kcal·mol⁻1). Similarly, enhanced electrostatic complementarity was also observed for ECSb4-RBD and ECSb3-RBD (0.305 and 0.390, respectively) relative to SR6c3-RBD (0.233). Surface analyses confirmed optimized electrostatic patches and reduced aggregation propensity in the engineered Nb. This integrated EC and structural engineering approach successfully developed engineered Nbs with enhanced binding specificity, increased thermostability, and reduced aggregation, laying the groundwork for novel therapeutic applications targeting the SARS-CoV-2 spike protein.

Specific Rosetta-based protein-peptide prediction protocol allows the design of novel cholinesterase inhibitor peptides

The search for novel cholinesterase inhibitors is essential for advancing treatments for neurodegenerative disorders such as Alzheimer's disease (AD). In this study, we employed the Rosetta pepspec module, originally developed for designing peptides targeting protein-protein interactions, to design de novo peptides targeting the peripheral aromatic site (PAS) of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE). A total of nine peptides were designed for human AChE (hAChE), T. californica AChE (TcAChE), and human BChE (hBChE). These peptides were synthesized using Fmoc-SPPS and tested in vitro using Ellman's reaction to evaluate their inhibitory potency. Peptide 11tA, designed for TcAChE, exhibited potent inhibition of hAChE (IC50 = 1.21 ± 0.25 µM) and demonstrated strong antioxidant activity against DPPH radicals and lipid peroxidation, making it a promising multitherapeutic candidate for AD. Peptide 11hB, designed for hBChE, showed the highest inhibitory activity against hBChE, with a Ki of 12.69 ± 1.27 µM, making it the most potent natural amino acid peptide reported against hBChE. The computational protocol effectively distinguished the specific characteristics of each enzyme target. Toxicity assessments, including hemolysis tests and A. salina lethality assays, revealed no toxic effects at low concentrations, further supporting the potential of these peptides for peptide-based drug development in AD. This study underscores the growing potential of peptides as alternatives to small-molecule drugs. It demonstrates that computational protocols for protein-protein interactions can be successfully adapted to design high-affinity peptide inhibitors.

Metabolic profiles and potential antioxidant mechanisms of hawk tea

Hawk tea has received increasing attention for its unique flavor and potential health benefits, with antioxidant function being one of its significant bioactivities. However, the metabolic profiles, potential antioxidant components, and action mechanisms of different types of hawk tea are still unclear. In this study, the chemical components of five hawk teas were determined using untargeted metabolomics. Then, the potential antioxidant metabolites and their possible action mechanisms were revealed by integrating network pharmacology and molecular docking. The results showed that the metabolic profiles of various hawk teas differed significantly, but the content of flavonoids was the highest in each group. Network pharmacology analyses suggested that 11 potential antioxidant metabolites-four of which were the same metabolites with high levels in the five types, and seven were differential metabolites-could be involved in several metabolic pathways in vivo. These pathways included the MAPK and PI3K/AKT signaling pathways, which may be closely related to antioxidant activity. Finally, molecular docking revealed potential antioxidant metabolites bound to 25 core antioxidant targets through hydrogen bonding and hydrophobic interactions. Among them, artemisinin, astragalin, isoquercetrin, isoquercitrin, kaempferol-3-glucuronide, and UDP-L-rhamnose exhibited low binding energies to core antioxidant targets such as AKT1, RELA, and MTOR, forming stable conformation. These insights lay the basis for further elucidating the antioxidant mechanism of hawk tea.

Position-Regulated Electrostatic Interactions for Single Amino Acid Revealed by Aspartic Acid-Scanning Mutagenesis

We have examined in this contribution the electrostatic interactions between single arginine and aspartic acid by analyzing the peptide-peptide binding characteristics involving arginine-aspartic acid, arginine-glycine, arginine-tryptophan and tryptophan-glycine interactions. The results of aspartic acid mutagenesis revealed that the interactions between arginine and aspartic acid have significant dependence on the position and composition of amino acids. While the primary interaction can be attributed to arginine-tryptophan contacts originated from the indole moieties with the main chains of 14-mers containing N-H and C=O moieties, pronounced enhancement could be identified in association with the electrostatic side-chain-side-chain interactions between arginine and aspartic acid. An optimal separation of 2~4 amino acids between two adjacent aspartic acid and tryptophan binding sites can be identified to achieve maximal enhancement of binding interactions. Such observed separation dependence may be utilized to unravel cooperative effects in heterogeneous interactions between single pair of amino acids.

Peptide-based coacervates in therapeutic applications

Coacervates are droplets formed by liquid‒liquid phase separation. An increasing number of studies have reported that coacervates play an important role in living cells, such as in the generation of membraneless organelles, and peptides contribute to condensate droplet formation. Peptides with versatile functional groups and special secondary structures, including α-helices, β-sheets and intrinsically disordered regions, provide novel insights into coacervation, such as biomimetic protocells, neurodegenerative diseases, modulations of signal transmission, and drug delivery systems. In this review, we introduce different types of peptide-based coacervates and the principles of their interactions. Additionally, we summarize the thermodynamic and kinetic mechanisms of peptide-based coacervates and the associated factors, including salt, pH, and temperature, affecting the phase separation process. We illustrate recent studies on modulating the functions of peptide-based coacervates applied in biological diseases. Finally, we propose their promising broad applications and describe the challenges of peptide-based coacervates in the future.

Peptide Binder with High-Affinity for the SARS-CoV-2 Spike Receptor-Binding Domain

Rapid antigen detection tests are urgently needed for the early diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The discovery of a binder with high affinity and selectivity for the biomarkers presented by SARS-CoV-2 is crucial to the development of the rapid antigen detection method. We utilized the surface biopanning to identify a peptide binder R1 from a phage-displayed peptide library consisting of 109 independent phage recombinants. The R1 peptide exhibited high-affinity for specific binding with the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with a dissociation constant KD of (7.5 ± 1.9) × 10-10 M, which maintained high binding affinity with the RBD derived from Gamma, Lambda, Delta, and Omicron variants. The composition and sequence dependence of binding characteristics in R1-RBD interactions was revealed by the binding affinity fluctuations between RBD and the scrambled sequences or single-site mutants of R1. The R1-functionalized gold nanoparticles possessed concentration-dependent response to RBD and selectivity over bovine serum albumin and human serum albumin. The peptide binder R1 shows the potential to be used for constructing a rapid detection method for the early-stage diagnostics for SARS-CoV-2.

Principles of Amino Acid and Nucleotide Revealed by Binding Affinities between Homogeneous Oligopeptides and Single-stranded DNA Molecule s

We have determined the binding strengths between nucleotides of adenine, thymine, guanine and cytosine in homogeneous single stranded DNAs and homo-octapeptides consisting of 20 common amino acids. We use a bead-based fluorescence assay for these measurements in which octapeptides are immobilized on the bead surface and ssDNAs are in solutions. The results provide a molecular basis for analyzing selectivity, specificity and polymorphisms of amino-acid-nucleotide interactions. Comparative analyses of the distribution of the binding energies reveal unique binding strengths patterns assignable to each pair of DNA nucleotide and amino acid originating from the chemical structures. Pronounced favorable (such as Arg-G , etc.) and unfavorable (such as Ile-T , etc.) binding interactions can be identified in selected groups of amino acid and nucleotide pairs that could provide basis to elucidate energetics of amino-acid-nucleotide interactions. Such interaction selectivity, specificity and polymorphism manifest the contributions from DNA backbone, DNA bases, as well as main chain and side chain of the amino acids.

A novel CD123-targeted therapeutic peptide loaded by micellar delivery system combats refractory acute myeloid leukemia

Acute myeloid leukemia (AML) is a common malignant heterogeneous hematopoietic disease with very low average 5-year survival rate due to the refractory feature and high rate of relapse. CD123 is highly expressed on multiple types of AML cells, especially leukemia stem cells, and closely associated with the poor prognosis of AML. Aiming to meet the urgent demand to targeted therapeutics for the refractory AML patients, herein we synthesize a CD123 antagonistic peptide (PO-6) loaded in nanomicelles (^mPO-6), and investigated its therapeutic effect and pharmacokinetics on a lab-established refractory AML mice model (AE & CKIT^D816V). It is shown that the PO-6 can effectively bind to the CD123⁺ AML cells and the micellar formulation ^mPO-6 increases the dissolution stability and the specific binding capacity. When injected intravenously, ^mPO-6 significantly prolongs the survival of the refractory AML mice by interfering CD123/IL-3 axis, evidenced by the down regulation of phosphorylation of STAT5 and PI3K/AKT and the inhibition of activated NF-κB in the nucleus, as well as by the analysis results of next generation RNA-sequencing (RNA-seq) with the bone marrow of the AML mice. The antagonistic effect leads to the significantly reduction of AML cells infiltration in the bone marrow of the AML mice. In conclusion, ^mPO-6 could provide a potent antagonistic therapeutic approach for targeted treatment of AML.

Synthetic Neutralizing Peptides Inhibit the Host Cell Binding of Spike Protein and Block Infection of SARS-CoV-2

Antiviral treatments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been extensively pursued to conquer the pandemic. To inhibit the viral entry to the host cell, we designed and obtained three peptide sequences via quartz crystal microbalance measurement screening, which showed high affinity at nanomole to the S1 subunit of the spike protein and wild-type SARS-CoV-2 pseudovirus. Circular dichroism spectroscopy measurements revealed significant conformation changes of the S1 protein upon encounter with the three peptides. The peptides were able to effectively block the infection of a pseudovirus to 50% by inhibiting the host cell lines binding with the S1 protein, evidenced by the results from Western blotting and pseudovirus luciferase assay. Moreover, the combination of the three peptides could increase the inhibitory rate to 75%. In conclusion, the three chemically synthetic neutralizing peptides and their combinations hold promising potential as effective therapeutics in the prevention and treatment of COVID-19.

Members of the Legionella pneumophila Sde family target tyrosine residues for phosphoribosyl-linked ubiquitination

Legionella pneumophila establishes a replication vacuole by translocating hundreds of protein effectors through a type IV secretion system (T4SS). Among these translocated effectors are members of the Sde family, which catalyze phosphoribosyl-linked ubiquitination (pR-Ub) of host targets. Previous work has posited that Sde proteins solely target serine (Ser) residues within acceptor protein substrates. We show here that SdeC-mediated pR-Ub modification results from a stepwise reaction that also modifies tyrosine (Tyr) residues. Unexpectedly, the presence of an HA tag on Ub resulted in poly-pR-ubiquitination, consistent with the HA tag acting as an acceptor target. Interrogation of phosphoribosyl-linked HA-Ub revealed that Tyr4 was the preferred targeted residue, based on LC-MS/MS analysis of the crosslinked product. Further analysis using synthetic HA variants revealed promiscuous modification of Tyr, as crosslinking was prevented only by constructing a triple mutant in which all three Tyr within the HA sequence were substituted with Phe. Although previous work has indicated that Ser is the sole acceptor residue, we found no evidence of Ser preference over Tyr using Tyr → Ser replacement mutants. This work demonstrates that pR-ubiquitination by the Sde family is not limited to Ser-modification as previously proposed, and broadens the potential sites targeted by this family.

During infection, Legionella pneumophila translocates hundreds of effectors into host cells. Among these, the Sde family effector SdeC catalyzes atypical ubiquitination of host targets at tyrosine, not only serine, residues.

Opposite Regulatory Effects of Immobilized Cations on the Folding Vs. Assembly of Melittin

Ions are crucial in modulating the protein structure. For the free ions in bulk solution, ammonium is kosmotropic (structure forming) and guanidinium is chaotropic (structure breaking) to the protein structure within the Hofmeister series. However, the effect of immobilized ions on a protein surface is less explored. Herein, we explored the influence of two immobilized cations (ammonium in the side chain of lysine and guanidinium in the side chain of arginine) on the folding and assembly of melittin. Melittin adopts an α-helix structure and is driven by hydrophobic interactions to associate into a helical bundle. To test the influence of immobilized cations on the peptide structure, we designed the homozygous mutants exclusively containing ammonium (melittin-K) or guanidinium (melittin-R) and compared the differences of melittin-K vs. melittin-R in their folding, assembly, and molecular functions. The side chains of lysine and arginine differ in their influences on the folding and assembly of melittin. Specifically, the side chain of R increases the α-helical propensity of melittin relative to that of K, following an inverse Hofmeister series. In contrast, the side chain of K favors the assembly of melittin relative to the side chain of R in line with a direct Hofmeister series. The opposite regulatory effects of immobilized cations on the folding and assembly of melittin highlight the complexity of the noncovalent interactions that govern protein intermolecular architecture.

Composition-dependent multivalency of peptide-peptide interactions revealed by tryptophan-scanning mutagenesis

We have examined in this contribution the composition dependence of binding characteristics in peptide-peptide interactions between an oligopeptide octa-glycine and a series of tryptophan-containing octapeptides. The binding energy associated with tryptophan-glycine interactions manifests pronounced stepwise binding characteristics as the number of tryptophan increases from 0 to 8 in the octapeptides consisting only of glycine and can be attributed to mono-, di-, and tri-valent peptide-peptide interactions. At the same time, only weak fluctuations in binding energy were observed as the number of tryptophan increases from 2 to 7. Such distinctive nonlinearity of composition-dependent tryptophan-glycine binding energy characteristics due to continuously varying tryptophan compositions in the octapeptides could be considered as a reflection of combinatorial contributions due to the hydrogen bonds originated from the indole moieties of tryptophan with the main chains of octapeptide of glycine containing N-H and C=O moieties and the van der Waals interactions (including π-π and π-CH interactions) between peptides.

Force-Field Simulations of a Hydrated Lanreotide-Based Derivative: Hydration, Dynamics, and Numerical Evidence of Self-Assembly in Dimers

Recently, self-organization of the cyclic octapeptide lanreotide and lanreotide-based derivatives in a nanotube to from a dimer structure has been experimentally evidenced. While the nature of the interactions between both monomers has been strongly investigated no molecular details of the hydration of the monomer and the formation of the dimer have been provided. Using molecular dynamics simulations, this work focuses on the structure, hydration, and dynamics of water and an analog of lanreotide. To do so, several models of monomers based on different schemes of partial charges and electrostatic interaction calculations are considered. By comparison with the experiments, we show that the model based on the combination of the AMBER force-field, CHELPG charge calculation, Ewald sum is the most relevant. Additionally, by mapping the interfacial hydration of the lanreotide monomer we evidence a heterogeneous surface in terms of hydrophilicity involving heterogeneous hydration. Furthermore, we show a slowdown in the translational dynamics of water molecules located close to the lanreotide surface. We also provide the molecular details of the self-assembly in the dimer in terms of structure, hydration, and energy.

Efficient isolation and quantification of circulating tumor cells in non-small cell lung cancer patients using peptide-functionalized magnetic nanoparticles

Background

Circulating tumor cells (CTCs) carry a wealth of information on primary and metastatic tumors critical for enhancing the understanding of the occurrence, progression and metastasis of non-small cell lung cancer (NSCLC). However, the low sensitivity of traditional tumor detection methods limits the application of CTCs in the treatment and disease surveillance of NSCLC. Therefore, CTCs isolation and detection with high sensitivity is highly desired especially for NSCLC patients, which is significant because of high occurrence and mortality. While it is very challenging because of the lower expression of CTC positive biomarkers such as epithelial cell adhesion molecules and cytokeratins (EpCAM and CKs), herein we report a method based on peptide-functionalized magnetic nanoparticles with high CTC capture efficiency, which demonstrates superiority in NSCLC clinical applications.

Methods

For analysis and comparison of the peptide-functionalized magnetic nanoparticles (TumorFisher, Nanopep Corp.) and the antibody-modified magnetic beads (CellSearch, Janssen Diagnostics, LLC), two NSCLC cell lines, A549 and NCI-H1975 were chosen to measure the binding affinity and capture efficiency. In order to compare the effect of the clinical application of these two detection systems, 7 early stage patients with NSCLC were enrolled in this study. To further explore the clinical utility of CTC counting in different stages, 81 NSCLC patients in stage I–IV were enrolled for CTC enumeration and statistical analysis.

Results

The binding affinities of the recognition peptide to A549 and NCI-H1975 are 76.7%±11.0% and 70.1%±4.8%, respectively, which is similar with the positive control group (anti-EpCAM antibodies). CTCs were captured in 5/7 (71.4%) of early stage NSCLC patients with NSCLC in TumorFisher system, which is higher than CellSearch, and the false negative of TumorFisher is much lower than CellSearch. In a larger clinical cohort, the CTC numbers of NSCLC patients varied in different stages and the overall detection rate of TumorFisher was 59/81 (72.8%), with the similar proportion in stage I (21/29, 72.4%), II (17/22, 77.3%) and III (16/21, 76.2%).

Conclusions

Highly efficient CTC isolation technique based on peptide-magnetic nanoparticles was firstly applied in NSCLC patients. Compared with the antibody-based the technique, the higher CTC detection rates (71.4%) in NSCLC patient blood samples were demonstrated for the patients in different stages, I–IV, especially in early stages. This indicates the feasibility of the clinical utility of this new technique in early stage screening, prognosis and therapy evaluation of NSCLC.

Discriminating changes in protein structure using tyrosine conjugation

Chemical modification of proteins has been crucial in engineering protein-based therapies, targeted biopharmaceutics, molecular probes, and biomaterials. Here, we explore the use of a conjugation-based approach to sense alternative conformational states in proteins. Tyrosine has both hydrophobic and hydrophilic qualities, thus allowing it to be positioned at protein surfaces, or binding interfaces, or to be buried within a protein. Tyrosine can be conjugated with 4-phenyl-3H-1,2,4-triazole-3,5(4H)-dione (PTAD). We hypothesized that individual protein conformations could be distinguished by labeling tyrosine residues in the protein with PTAD. We conjugated tyrosine residues in a well-folded protein, bovine serum albumin (BSA), and quantified labeled tyrosine with liquid chromatography with tandem mass spectrometry. We applied this approach to alternative conformations of BSA produced in the presence of urea. The amount of PTAD labeling was found to relate to the depth of each tyrosine relative to the protein surface. This study demonstrates a new use of tyrosine conjugation using PTAD as an analytic tool able to distinguish the conformational states of a protein.

Position-coded multivalent peptide-peptide interactions revealed by tryptophan-scanning mutagenesis

We demonstrate in this contribution the evidence that significant cooperative binding effect can be identified for the amino acid sites that are determinant to the binding characteristics in peptide-peptide interactions. The analysis of tryptophan-scanning mutagenesis of the 14-mer peptide consisting only of glycine provides a mapping of position-dependent contributions to the binding energy. The pronounced tryptophan-associated peptide-peptide interactions are originated from the indole moieties with the main chains of 14-mer glycines containing N-H and CO moieties. Specifically, with the presence of two tryptophans as determinant amino acids, cooperative binding can be observed, which are dependent on relative positions of the two tryptophans with a "volcano"-like characteristics. An optimal separation of 6-10 amino acids between two adjacent binding sites can be identified to achieve maximal binding interactions.

Peptide-enabled receptor-binding-quantum dots for enhanced detection and migration inhibition of cancer cells

We report the efforts to construct active targeting quantum dots using receptor-binding peptide for enhanced detection and migration inhibition of cancer cells. Peptide E5 has specific binding with chemokine receptor 4 (CXCR4), which is a transmembrane G-coupled receptor involved in the metastasis of various types of cancers. E5 was introduced to the surface of CdSe/ZnS quantum dots via biotin-streptavidin interactions. The constructed CXCR4-targeting quantum dots (E5@QDs) was observed to display improved detection sensitivity and significantly enhanced binding affinity for CXCR4 over-expressed cancer cells, and the ability to inhibit cancer cells migration induced by CXCL12.

Biomolecular Phase Separation: From Molecular Driving Forces to Macroscopic Properties

Biological phase separation is known to be important for cellular organization, which has recently been extended to a new class of biomolecules that form liquid-like droplets coexisting with the surrounding cellular or extracellular environment. These droplets are termed membraneless organelles, as they lack a dividing lipid membrane, and are formed through liquid-liquid phase separation (LLPS). Elucidating the molecular determinants of phase separation is a critical challenge for the field, as we are still at the early stages of understanding how cells may promote and regulate functions that are driven by LLPS. In this review, we discuss the role that disorder, perturbations to molecular interactions resulting from sequence, posttranslational modifications, and various regulatory stimuli play on protein LLPS, with a particular focus on insights that may be obtained from simulation and theory. We finally discuss how these molecular driving forces alter multicomponent phase separation and selectivity.

Bead based facile assay for sensitive quantification of native state green fluorescent protein

A facile method for the quantification of native state protein is strongly required to accurately determine the amount of expressed protein of interest. Here we report a simple bead-based assay, which can sensitively quantify the amount of native state green fluorescent protein using Ni-NTA (nickel-nitrilotriacetic acid)-modified microbead particles. The bead-based method is simple and straightforward to perform and it showed a highly sensitive capability to detect the expressed fluorescent protein because of the enriched fluorescent protein on the beads.

Spatial Separation of Microbeads into Detection Levels by a Bioorthogonal Porous Hydrogel for Size-Selective Analysis and Increased Multiplexity

Multiplex detection techniques are emerging within the fields of life science research and medical diagnostics where it is mandatory to analyze a great number of molecules. The detection techniques need to be highly efficient but often involve complicated and expensive fabrication procedures. Here, we present the immobilization and geometric separation of fluorescence-labeled microbeads for a multiplex detection in k levels. A compound of differently sized target molecules (DNA, proteins) is channeled into the respective detection levels by making use of a hydrogel as a size selective filter. The immobilized microbeads (10-20 μm) are considerably larger than the pores of the hydrogel network and therefore stay fixed at the well bottom and in higher elevations, respectively. Small biomolecules can diffuse through the pores of the network, whereas medium-sized biomolecules pass slower and large molecules will be excluded. Besides filtering, this method discriminates the used microbeads into k levels and thereby introduces a geometric multiplexity. Additionally, the exclusion of large entities enables the simultaneous detection of two target molecules, which exhibit the same affinity interaction. The hydrogel is formed through the combination of two macromonomers. One component is a homobifunctional polyethylene glycol linker, carrying a strained alkyne (PEG-BCN) and the second component is the azide-functionalized dendritic polyglycerol (dPG-N₃). They react via the bioorthogonal strain-promoted azide alkyne cycloaddition (SPAAC). The hydrogel creates a solution-like environment for the diffusion of the investigated biomolecules all the while providing a stable, bioinert, and surface bound network.