Screening nonspecific interactions of peptides without background interference

A cysteine-specific solubilizing tag strategy enables efficient chemical protein synthesis of difficult targets

We developed a new cysteine-specific solubilizing tag strategy via a cysteine-conjugated succinimide. This solubilizing tag remains stable under common native chemical ligation conditions and can be efficiently removed with palladium-based catalysts. Utilizing this approach, we synthesized two proteins containing notably difficult peptide segments: interleukin-2 (IL-2) and insulin. This IL-2 chemical synthesis represents the simplest and most efficient approach to date, which is enabled by the cysteine-specific solubilizing tag to synthesize and ligate long peptide segments. Additionally, we synthesized a T8P insulin variant, previously identified in an infant with neonatal diabetes. We show that T8P insulin exhibits reduced bioactivity (a 30-fold decrease compared to standard insulin), potentially contributing to the onset of diabetes in these patients. In summary, our work provides an efficient tool to synthesize challenging proteins and opens new avenues for exploring research directions in understanding their biological functions.

Antifouling strategies for electrochemical sensing in complex biological media

Surface fouling poses a significant challenge that restricts the analytical performance of electrochemical sensors in both in vitro and in vivo applications. Biofouling resistance is paramount to guarantee the reliable operation of electrochemical sensors in complex biofluids (e.g., blood, serum, and urine). Seeking efficient strategies for surface fouling and establishing highly sensitive sensing platforms for applications in complex media have received increasing attention in the past. In this review, we provide a comprehensive overview of recent research efforts focused on antifouling electrochemical sensors. Initially, we present a detailed illustration of the concept about biofouling along with an exploration of four key antifouling mechanisms. Subsequently, we delve into the commonly employed antifouling strategies in the fabrication of electrochemical sensors. These encompass physical surface topography (micro/nanostructure coatings and filtration membranes) and chemical surface modifications (PEG and its derivatives, zwitterionic polymers, peptides, proteins, and various other antifouling materials). The progress in antifouling electrochemical sensors is proposed concerning the antifouling mechanisms as well as sensing capability assessments (e.g., sensitivity, stability, and practical application ability). Finally, we summarize the evolving trends in the field and highlight some key remaining limitations.

Identification of the First Sulfobetaine Hydrogel-Binding Peptides via Phage Display Assay

Using the M13 phage display, a series of 7- and 12-mer peptides which interact with new sulfobetaine hydrogels are identified. Two peptides each from the 7- and 12-mer peptide libraries bind to the new sulfobetaine hydrogels with high affinity compared to the wild-type phage lacking a dedicated hydrogel binding peptide. This is the first report of peptides binding to zwitterionic sulfobetaine hydrogels and the study therefore opens up the pathway toward new phage or peptide/hydrogel hybrids with high application potential.

Minimizing the off-target frequency of the CRISPR/Cas9 system via zwitterionic polymer conjugation and peptide fusion

The clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated protein 9 (Cas9) system is a powerful genome-editing tool that is widely used in many different applications. However, the high-frequency mutations induced by RNA-guided Cas9 at sites other than the intended on-target sites are a major concern that impedes therapeutic and clinical applications. A deeper analysis shows that most off-target events result from the non-specific mismatch between single guide RNA (sgRNA) and target DNA. Therefore, minimizing the non-specific RNA-DNA interaction can be an effective solution to this issue. Here we provide two novel methods at the protein and mRNA levels to minimize this mismatch issue by chemically conjugating Cas9 with zwitterionic pCB polymers or genetically fusing Cas9 with zwitterionic (EK)_n peptides. The zwitterlated or EKylated CRISPR/Cas9 ribonucleoproteins (RNPs) show reduced off-target DNA editing while maintaining a similar level of on-target gene editing activity. Results show that the off-target efficiency of zwitterlated CRISPR/Cas9 is reduced on average by 70% and can be as high as 90% when compared with naive CRISPR/Cas9 editing. These approaches provide a simple and effective way to streamline the development of genome editing with the potential to accelerate a wide array of biological and therapeutic applications based on CRISPR/Cas9 technology.

AlphaFold2 and its applications in the fields of biology and medicine

AlphaFold2 (AF2) is an artificial intelligence (AI) system developed by DeepMind that can predict three-dimensional (3D) structures of proteins from amino acid sequences with atomic-level accuracy. Protein structure prediction is one of the most challenging problems in computational biology and chemistry, and has puzzled scientists for 50 years. The advent of AF2 presents an unprecedented progress in protein structure prediction and has attracted much attention. Subsequent release of structures of more than 200 million proteins predicted by AF2 further aroused great enthusiasm in the science community, especially in the fields of biology and medicine. AF2 is thought to have a significant impact on structural biology and research areas that need protein structure information, such as drug discovery, protein design, prediction of protein function, et al. Though the time is not long since AF2 was developed, there are already quite a few application studies of AF2 in the fields of biology and medicine, with many of them having preliminarily proved the potential of AF2. To better understand AF2 and promote its applications, we will in this article summarize the principle and system architecture of AF2 as well as the recipe of its success, and particularly focus on reviewing its applications in the fields of biology and medicine. Limitations of current AF2 prediction will also be discussed.

Impacts of a Zwitterionic Peptide on its Fusion Protein

Therapeutic proteins frequently need to be modified with high-molecular-weight molecules to improve their pharmacokinetic properties. The genetic linkage of therapeutic proteins to a high-molecular-weight zwitterionic peptide, termed EKP, offers a promising approach. As with any protein modification, EKP could impact the structural behavior and receptor binding properties of the linked therapeutic protein, thereby altering its bioactivity. To evaluate the effects of EKP on therapeutic proteins, we study the receptor binding properties of high-molecular-weight EKP linked to the growth colony-stimulating factor (GCSF) using the genetically based yeast display platform. We find that yeast-displayed EKP-GCSF and GCSF exhibits similar binding to its receptor GCSF-R, suggesting that EKP does not hinder receptor binding. Furthermore, yeast-displayed EKP-GCSF demonstrates protection against thermal denaturation compared to GCSF. Similarly, to study the structural effects of EKP on GCSF, we employ in silico modeling using alphaFold2 in conjunction with molecular dynamics (MD) simulations. Likewise, in silico modeling reveals that EKP does not alter the structural behavior of GCSF. Finally, we demonstrate the functional benefits of EKP, by which the EKP-GCSF fusion protein produced in Escherichia coli exhibits improved pharmacokinetics and prolonged bioactivity in vivo.

Rational design of smart nano-platforms based on antifouling-nanomaterials toward multifunctional bioanalysis

The ability to design nanoprobe devices with the capability of quantitative/qualitative operation in complex media will probably underpin the main upcoming progress in healthcare research and development. However, the biomolecules abundances in real samples can considerably alter the interface performance, where unwanted adsorption/adhesion can block signal response and significantly decrease the specificity of the assay. Herein, this review firstly offers a brief outline of several significances of fabricating high-sensitivity and low-background interfaces to adjust various targets' behaviors induced via bioactive molecules on the surface. Besides, some important strategies to resist non-specific protein adsorption and cell adhesion, followed by imperative categories of antifouling reagents utilized in the construction of high-performance solid sensory interfaces, are discussed. The next section specifically highlights the various nanocomposite probes based on antifouling-nanomaterials for electrode modification containing carbon nanomaterials, noble metal nanoparticles, magnetic nanoparticles, polymer, and silicon-based materials in terms of nanoparticles, rods, or porous materials through optical or chemical strategies. We specially outline those nanoprobes that are capable of identification in complex media or those using new constructions/methods. Finally, the necessity and requirements for future advances in this emerging field are also presented, followed by opportunities and challenges.

Sequence Effect of Peptide-Based Materials on Delivering Interferon-α (IFN-α): A Molecular Dynamic Perspective

Peptide-based biomaterials exhibit great potentials in developing drug delivery platforms due to their biocompatibility and biodegradability beyond poly(ethylene glycol). How different amino acids in peptides used for delivery play their roles is still unclear at the microscopic level. This work compared the assembly behaviors of a series of peptides around interferon-α (IFN-α). Through all-atom molecular simulations, the sequence effect of peptides on delivering interferon-α was quantitively characterized. The hydrophobic elastin-like peptide (VPGAG)_n preferred to self-aggregate into dense clusters, rather than encapsulate IFN-α. The hydrophilic zwitterionic peptides with repeating unit "KE" tended to phase-separate from IFN-α in the mixture. In contrast, peptides with a hybrid sequence, i.e., (VPKEG)_n, exhibited the highest contact preference, and the formed protective shell endowed IFN-α with better thermal stability and stealth property and achieved a subtle balance between protecting IFN-α and subsequent releasing. Further energy decomposition analysis revealed that the positively charged Lys contributed most to the binding affinity while the negatively charged Glu contributed most to the hydrophilic property of peptide-based materials. In summary, this article reveals why peptides composed of repeating hydrophobic and charged residues could be a potential choice for delivering therapeutic proteins in the form of solution.

Antifouling Strategies for Electrochemical Biosensing: Mechanisms and Performance toward Point of Care Based Diagnostic Applications

Although there exist numerous established laboratory-based technologies for sample diagnostics and analyte detection, many medical and forensic science applications require point of care based platforms for rapid on-the-spot sample analysis. Electrochemical biosensors provide a promising avenue for such applications due to the portability and functional simplicity of the technology. However, the ability to develop such platforms with the high sensitivity and selectivity required for analysis of low analyte concentrations in complex biological samples remains a paramount issue in the field of biosensing. Nonspecific adsorption, or fouling, at the electrode interface via the innumerable biomolecules present in these sample types (i.e., serum, urine, blood/plasma, and saliva) can drastically obstruct electrochemical performance, increasing background "noise" and diminishing both the electrochemical signal magnitude and specificity of the biosensor. Consequently, this review aims to discuss strategies and concepts used throughout the literature to prevent electrode surface fouling in biosensors and to communicate the nature of the antifouling mechanisms by which they operate. Evaluation of each antifouling strategy is focused primarily on the fabrication method, experimental technique, sample composition, and electrochemical performance of each technology highlighting the overall feasibility of the platform for point of care based diagnostic/detection applications.

Molecular simulation of zwitterionic polypeptides on protecting glucagon-like peptide-1 (GLP-1)

Owing to their anti-fouling properties, zwitterionic polypeptides demonstrate great advantage on protecting protein drugs. When conjugated to glucagon-like peptide-1 (GLP-1), a drug for type-II diabetes, zwitterionic polypeptides confer better pharmacokinetics than uncharged counterparts. However, its microscopic mechanism is still unclear due to the complicated conformational space. To address this challenge, this work explored the interaction modes of GLP-1 with the unconnected repeat units, instead of the full-length polypeptides. The three repeat units are two zwitterionic pentapeptides VPKEG and VPREG, and one uncharged control VPGAG. Our molecular simulations revealed that the helical conformation of GLP-1 was stabilized by adding 40 polypeptides. Both VPGAG and VPREG formed dense packing shells around GLP-1, but the driving forces were hydrophobic and electrostatic interactions, respectively. In contrast, the packing shell composed of VPKEG was most loose, while could still stabilize GLP-1. The moderate electrostatic interactions endowed VPKEG an anti-fouling property, thereby avoiding non-specific interaction with other amino acids. The strong electrostatic interactions exerted by arginine promoted atomic contacts between VPREG and other residues, making it as "hydrophobic" as VPGAG. In summary, the combination of hydrophobic and moderate electrostatic interactions in VPKEG brings about a subtle balance between stabilizing GLP-1 and avoiding non-specific interaction.

Size-Transformable Hyaluronan Stacked Self-Assembling Peptide Nanoparticles for Improved Transcellular Tumor Penetration and Photo-Chemo Combination Therapy

Size-transformable nanomedicine has the potential to overcome systemic and local barriers, leading to efficient accumulation and penetration throughout the tumor tissue. However, the design of this type of nanomedicine was seldom based on active targeting and intracellular size transformation. Here, we report an intracellular size-transformable nanosystem, in which small and positively charged nanoparticles (<30 nm) prepared from the self-assembly of an amphiphilic hexadecapeptide derivative was coated by folic acid- and dopamine-decorated hyaluronan (HA) to form large and negatively charged nanoparticles (∼130 nm). This nanosystem has been proven to improve the blood circulation half-life of the drug and prevent premature intravascular drug leakage from the nanocarrier. Once accumulated in the tumor, the nanoparticles were prone to HA- and folic acid-mediated cellular uptake, followed by intracellular size transformation and discharge of transformed small nanoparticles. The size-transformable nanosystem facilitated the transcytosis-mediated tumor penetration and improved the internalization of nanoparticles by cells and the intracellular release of 7-ethyl-10 hydroxycamptothecin. With an indocyanine green derivative as the intrinsic component of the amphiphilic polymer, the nanosystem has exhibited additional theranostic functions: photoacoustic imaging, NIR-laser-induced drug release, and synergistic chemotherapy and phototherapy, leading to a 50% complete cure rate in a subcutaneous B16 melanoma model. This nanosystem with multimodalities and efficient tumor penetration has shown potentials in improving anticancer efficacy.

Identification of peptide coatings that enhance diffusive transport of nanoparticles through the tumor microenvironment

In solid tumors, increasing drug penetration promotes their regression and improves the therapeutic index of compounds. However, the heterogeneous extracellular matrix (ECM) acts as a steric and interaction barrier that hinders effective transport of therapeutics, including nanomedicines. Specifically, the interactions between the ECM and surface physicochemical properties of nanomedicines (e.g. charge, hydrophobicity) affect their diffusion and penetration. To address the challenges using existing surface chemistries, we used peptide-presenting phage libraries as a high-throughput approach to screen and identify peptides as coatings with desired physicochemical properties that improve diffusive transport through the tumor microenvironment. Through iterative screening against the ECM and identification by next-generation DNA sequencing and analysis, we selected individual clones and quantify their transport by diffusion assays. Here, we identified a net-neutral charge, hydrophilic peptide P4 that facilitates significantly higher diffusive transport of phage than negative control through in vitro tumor ECM. Through alanine mutagenesis, we confirmed that the hydrophilicity, charge, and spatial ordering impact diffusive transport. The P4 phage clone exhibited almost 200-fold improved uptake in ex vivo pancreatic tumor xenografts compared to the negative control. Nanoparticles coated with P4 exhibited ∼40-fold improvement in diffusivity in pancreatic tumor tissues, and P4-coated particles demonstrated less hindered diffusivity through the ECM compared to functionalized control particles. By leveraging the power of molecular diversity using phage display, we can greatly expand the chemical space of surface chemistries that can improve the transport of nanomedicines through the complex tumor microenvironment to ultimately improve their efficacy.

Resistance of Zwitterionic Peptide Monolayers to Biofouling

Self-assembled monolayers (SAMs) are widely used in science and engineering, and recent progress has demonstrated the utility of zwitterionic peptides with alternating lysine (K) and glutamic acid (E) residues for antifouling purposes. Aiming at developing a peptide-based fouling-resistant SAM suitable for presentation of surface-attached pheromones for barnacle larvae, we have investigated five different peptide SAMs, where four are based on the EK motif, and the fifth was designed based on general principles for fouling resistance. The SAMs were formed by self-assembly onto gold substrates via cysteine residues on the peptides, and formation of SAMs was verified via ellipsometry, wettability, infrared reflection-absorption spectroscopy and cyclic voltammetry. Settlement of cypris larvae of the barnacle Balanus (=Amphibalanus) amphitrite, the target of pheromone studies, was tested. SAMs were also subjected to fouling assays using protein solutions, blood serum, and the bacterium Mycobacterium marinum. The results confirm the favorable antifouling properties of EK-containing peptides in most of the assays, although this did not apply to the barnacle larvae settlement test, where settlement was low on only one of the peptide SAMs. The one peptide that had antifouling properties for barnacles did not contain a pheromone motif, and would not be susceptible to degredation by common serine proteases. We conclude that the otherwise broadly effective antifouling properties of EK-containing peptide SAMs is not directly applicable to barnacles, and that great care must be exercised in the design of peptide-based SAMs for presentation of barnacle-specific ligands.

Antifouling (Bio)materials for Electrochemical (Bio)sensing

(Bio)fouling processes arising from nonspecific adsorption of biological materials (mainly proteins but also cells and oligonucleotides), reaction products of neurotransmitters oxidation, and precipitation/polymerization of phenolic compounds, have detrimental effects on reliable electrochemical (bio)sensing of relevant analytes and markers either directly or after prolonged incubation in rich-proteins samples or at extreme pH values. Therefore, the design of antifouling (bio)sensing interfaces capable to minimize these undesired processes is a substantial outstanding challenge in electrochemical biosensing. For this purpose, efficient antifouling strategies involving the use of carbon materials, metallic nanoparticles, catalytic redox couples, nanoporous electrodes, electrochemical activation, and (bio)materials have been proposed so far. In this article, biomaterial-based strategies involving polymers, hydrogels, peptides, and thiolated self-assembled monolayers are reviewed and critically discussed. The reported strategies have been shown to be successful to overcome (bio)fouling in a diverse range of relevant practical applications. We highlight recent examples for the reliable sensing of particularly fouling analytes and direct/continuous operation in complex biofluids or harsh environments. Opportunities, unmet challenges, and future prospects in this field are also pointed out.

Long circulating genetically encoded intrinsically disordered zwitterionic polypeptides for drug delivery

The clinical utility of many peptide and protein drugs is limited by their short in-vivo half-life. To address this limitation, we report a new class of polypeptide-based materials that have a long plasma circulation time. The design of these polypeptides is motivated by the hypothesis that incorporating a zwitterionic sequence, within an intrinsically disordered polypeptide motif, would impart "stealth" behavior to the polypeptide and increase its plasma residence time, a behavior akin to that of synthetic stealth polymers. We designed these zwitterionic polypeptides (ZIPPs) with a repetitive (VPX₁X₂G)_n motif, where X₁ and X₂ are cationic and anionic amino acids, respectively, and n is the number of repeats. To test this hypothesis, we synthesized a set of ZIPPs with different pairs of cationic and anionic residues with varied chain length. We show that a combination of lysine and glutamic acid in the ZIPP confer superior pharmacokinetics, for both intravenous and subcutaneous administration, compared to uncharged control polypeptides. Finally, to demonstrate their clinical utility, we fused the best performing ZIPP sequence to glucagon-like peptide-1 (GLP1), a peptide drug used for treatment of type-2 diabetes and show that the ZIPP-GLP1 fusion outperforms an uncharged polypeptide of the same molecular weight in a mouse model of type-2 diabetes.

Mixed Self-Assembled Aptamer and Newly Designed Zwitterionic Peptide as Antifouling Biosensing Interface for Electrochemical Detection of alpha-Fetoprotein

A sensitive and low-fouling aptasensor for alpha-fetoprotein (AFP) was developed based on mixed self-assembled aptamers and newly designed zwitterionic peptides, where densely immobilized peptides formed an antifouling layer to resist nonspecific protein adsorption, and sparsely attached aptamers acted as the recognizing layer to achieve target binding. The obtained biosensing interface responded to the target AFP with a strikingly selective and sensitive manner, exhibited excellent protein-resistant performance even in complex human serum solution, and showed promising feasibility for the quantitative analysis of AFP in real human serum samples.

Strategies to reduce aspecific adsorption of peptides and proteins in liquid chromatography-mass spectrometry based bioanalyses: an overview

In the drug-discovery setting, the development of new peptide and protein-based biopharmaceuticals attracts increased attention from the pharmaceutical industry and consequently demands the development of high-throughput LC-MS methods. Regulatory guidelines require bioanalytical methods to be validated not only in terms of linearity, sensitivity, accuracy, precision, selectivity and stability, but also in terms of carryover. Carryover results from the aspecific adsorption of analyte(s) to parts of the analytical system and thus introduces bias in both identification and quantification assays. Moreover, nonspecific binding occurs at the surface of materials used during sample preparation, such as pipette tips, sample tubes and LC-vials. Hence, linearity, sensitivity and repeatability of the analyses are negatively affected. Due to the great diversity in physicochemical properties of biomolecules, there is no general approach available to minimize adsorption phenomena. Therefore, we aim to present different strategies which can be generically applied to reduce nonspecific binding of peptides and proteins. In the first part of this review, a systematic approach is proposed to guide the reader through the different solvents which can be used to dissolve the analyte of interest. Indeed, proper solubilization is one of the most important factors for a successful analysis. In addition, alternative approaches are described to improve analyte recovery from the sample vial. The second part focuses on strategies to efficiently reduce adsorption at components of the autosampler, column and mass spectrometer. Thereby carryover is reduced while maintaining a sufficiently wide dynamic range of the assay.

Standardizing and simplifying analysis of peptide library data

Peptide libraries allow researchers to quickly find hundreds of peptide sequences with a desired property. Currently, the large amount of data generated from peptide libraries is analyzed by hand, where researchers search for repeating patterns in the peptide sequences. Such patterns are called motifs. In this work, we describe a set of algorithms which allow quick, efficient, and standard analysis of peptide libraries. Four main techniques are described: (1) choice of the number of motifs present in a peptide library; (2) separation of the peptides into groups of similar sequences; (3) fitting of a model to the peptides to extract motifs; (4) analysis of the library using quantitative structure-property relationships if no clear motifs are present. The application of five previously published data sets shows these techniques can automatically repeat the work of experts quickly and allow much more flexibility in analysis. A new way of visually presenting peptide libraries is also described, which allows visual inspection of the grouping and spread of sequences. The algorithms have been implemented in an open-source plug-in called "peplib" and an online web application.