Short Peptide Ligands Research Articles

LiF-MS+, a revised technique for mapping peptide-protein interactions.

Short linear motifs are sequences of amino acids present in unstructured polypeptide regions that function as ligands for specific sites on folded protein domains. These interactions, which often occur with low to modest affinity, modulate dynamic biological processes such as signal transduction and membrane trafficking. We recently described Ligand Footprinting-Mass Spectrometry (LiF-MS), a technique that rapidly and precisely maps sites at which short peptide ligands bind their biologically relevant recognition sites on folded protein domains. This approach marks the binding location of a peptide ligand on a structured protein using a cleavable crosslinker appended to the ligand that leaves behind a stable chemical modification following cleavage. This modification serves as a mass tag detectable by mass spectrometry, pinpointing sites of peptide ligand binding. Here we present LiF-MS+, an improved version of the footprinting technique that replaces the butanol mass tag with 1-butylpyrrolidine, which is positively charged at neutral pH and thus aids in ionization of the crosslinked peptide for analysis by mass spectrometry. We show ligand-mediated butylpyrrolidine footprinting effectively maps the well characterized binding interaction of the p38α mitogen-activated protein kinase (MAPK) with a MKK6 D-motif short linear motif peptide ligand, uncovering additional binding site information not observed in our original experiment. LiF-MS+ is thus a straightforward improvement of our previously published methodology for mapping the binding of short linear motifs to folded protein domains.

Microfluidic Immunosensor Platform for Sensitive Detection of Human Epidermal Growth Factor Receptor-2 Based on Enhanced Cathode Electrochemiluminescence of Bimetallic Nanoclusters.

In this work, a microfluidic immunosensor chip was developed by incorporating microfluidic technology with electrochemiluminescence (ECL) for sensitive detection of human epidermal growth factor receptor-2 (HER2). The immunosensor chip can achieve robust reproducibility in mass production by integrating multiple detection units in a series. Notably, nanoscale materials can be better adapted to microfluidic systems, greatly enhancing the accuracy of the immunosensor chip. Ag@Au NCs closed by glutathione (GSH) were introduced in the ECL microfluidic immunosensor system with excellent and stable ECL performance. The synthesized CeO2-Au was applied as a coreaction promoter in the ECL signal amplification system, which made the result of HER2 detection more reliable. In addition, the designed microfluidic immunosensor chip integrated the biosensing system into a microchip, realizing rapid and accurate detection of HER2 by its high throughput and low usage. The developed short peptide ligand NARKFKG (NRK) achieved an effective connection between the antibody and nanocarrier for improving the detection efficiency of the sensor. The immunosensor chip had better storage stability and sensitivity than traditional detection methods, with a wide detection range from 10 fg·mL-1 to 100 ng·mL-1 and a low detection limit (LOD) of 3.29 fg·mL-1. In general, a microfluidic immunosensor platform was successfully constructed, providing a new idea for breast cancer (BC) clinical detection.

Signal-Enhanced Immunosensor-Based MOF-Derived ZrO2 Nanomaterials as Electrochemiluminescence Emitter for D-Dimer Detection.

Metal oxide nanomaterials have garnered significant attention in the field of electrochemiluminescence (ECL) sensing due to their efficient, stable, and nontoxic properties. However, the current research on metal oxide nanomaterials has primarily focused on their cathodic luminescence properties, with limited reports on their anodic ECL properties. In this study, we utilized MOF-derived ZrO2 nanomaterials as luminophores to generate stable anodic ECL signals in the presence of the coreactant tripropylamine (TPrA). Additionally, a signal-enhancing immunosensor was developed to analyze D-dimer by incorporating the coreaction accelerator Cu-doped TiO2 (TiO2-Cu). The ZrO2 synthesized by calcining UiO-67 demonstrated nontoxicity and biocompatibility, exhibiting efficient and stable ECL emission in a TPrA solution. The inclusion of TiO2-Cu as a coreaction accelerator in the immunosensor resulted in the formation of a ternary system of ZrO2/TiO2-Cu/TPrA. The Cu doping effectively narrowed the bandgap of TiO2 and enhanced its conductivity. As a substrate, TiO2-Cu reacted with more TPrA, generating sufficient free radicals to effectively enhance the ECL signal of ZrO2. In this article, a short peptide ligand, NFC (NARKFYKGC), was designed to immobilize antibodies and maintain the activity of antigen-binding sites during the construction of the immunosensor. The developed immunosensor was used for the accurate detection of D-dimers, with a wide linear range of 0.05-600 ng/mL and a low detection limit of 21 pg/mL..

Zirconium dioxide as electrochemiluminescence emitter for D-dimer determination based on dual-quenching sensing strategy

The ECL emission of simple and stable zirconium dioxide nanomaterials has always been a blank slate in the ECL sensors field. In this work, zirconium dioxide (ZrO2)-titanium dioxide (TiO2)-gold nanoparticle (AuNPs) composite (ZT-Au), a novel self-enhanced ECL emitter, was introduced the system of dual-quenching ECL immunosensor. The anodic luminescence of ZrO2 in the system of tripropylamine (TPrA) as a co-reagent was first reported and explored. Meanwhile, TiO2 was designed into the ECL scheme as a co-reaction accelerator to form the ZrO2/TPrA/TiO2 ternary system, which can efficiently amplify the ECL signal of the emitter. In addition, cuprous oxide-triaminophenol (Cu2O-APF) as the quencher was devoted to the dual-quenching sensing strategy. The dual-quenching mechanism that effectively boosted the immunosensor sensitivity was adequately investigated and conjectured in this paper. The sensing model based on the luminophor ZT-Au and the quencher Cu2O-APF was utilized for the detection of D-dimer, a reliable marker for the diagnosis and evaluation of thrombotic diseases. The short peptide ligands NARKFYKGC (NFC) with efficient biological affinity were used to site-directionally capture antibodies for adequately protecting the activity of antigen binding sites during the construction of the immunosensor. The implemented immunosensor was equipped with a broad linear range of 0.01–500 ng/mL and a low detection limit of 3.6 pg/mL. The original methodology opens up the field of vision for the detection of additional biomarkers.

High-Efficiency CdSe Quantum Dots/Fe3O4@MoS2/S2O82- Electrochemiluminescence System Based on a Microfluidic Analysis Platform for the Sensitive Detection of Neuron-Specific Enolase.

In this work, based on electrochemiluminescence (ECL) technology and self-assembled portable disease detection chips, a bioactivity-maintained sensing platform was developed for the quantitative detection of neuron-specific enolase. First, we prepared Fe3O4@MoS2 nanocomposites as an efficient catalyst to accelerate the reduction of persulfate (S2O82-). Specifically, abundant sulfate radicals (SO4•-) were generated because of cyclic conversion between Fe2+ and Fe3+. Meanwhile, MoS2 nanoflowers with a high specific surface area could not only load more Fe3O4 but also solve its agglomeration problem, which greatly improved the catalytic efficiency. Moreover, a biosensor chip was constructed by standard lithography processes for disease detection, which had good sensitivity and portability. According to the above strategies, the developed portable sensing platform played the part of promoting the practical application of bioanalysis in early tumor screening and clinical diagnosis. In addition, we developed a short peptide ligand (NARKFYKG, NAR) to avoid the occupation of antigen binding sites by specifically connecting to Fc fragments in antibodies. Thus, the binding efficiency of antibodies and the activity of biosensors were improved due to the introduction of NAR.

De novo discovery of peptide-based affinity ligands for the fab fragment of human immunoglobulin G

Antibody fragments and their engineered variants show true potential as next-generation therapeutics as they combine excellent targeting with superior biodistribution and blood clearance. Unlike full antibodies, however, antibody fragments do not yet have a standard platform purification process for large-scale production. Short peptide ligands are viable alternatives to protein ligands in affinity chromatography. In this work, an integrated computational and experimental scheme is described to de novo design 9-mer peptides that bind to Fab fragments. The first cohort of designed sequences was tested experimentally using human polyclonal Fab, and the top performing sequence was selected as a prototype for a subsequent round of ligand refinement in silico. The resulting peptides were conjugated to chromatographic resins and evaluated via equilibrium and dynamic binding studies using human Fab-κ and Fab-λ. The equilibrium studies returned values of binding capacities up to 32 mg of Fab per mL of resin with mild affinity (KD ∼ 10−5 M) that are conducive to high product capture and recovery. Dynamic studies returned values of product yield up to ∼90%. Preliminary purification studies provided purities of 83–93% and yields of 11–89%. These results lay the groundwork for future development of these ligands towards biomanufacturing translation.

Imaging of Tumor-Associated Vascular Prostate-Specific Membrane Antigen in Woodchuck Model of Hepatocellular Carcinoma.

BACKGROUND AND AIMS:Radiolabeled short peptide ligands targeting prostate-specific membrane antigen (PSMA) were developed initially for imaging and treatment of prostate cancers. While many nonprostate solid tumors including hepatocellular carcinoma (HCC) express little PSMA, their neovasculature expresses a high level of PSMA, which is avid for Gallium-68-labeled PSMA-targeting radio-ligand (68Ga-PSMA-11) for positron emission tomography (PET). However, the lack of a spontaneous animal model of tumor-associated vascular PSMA overexpression has hindered the development and assessment of PSMA-targeting radioligands for imaging and therapy of the nonprostatic cancers. We identified detectable indigenous PSMA expression on tumor neovascular endothelia in a naturally occurring woodchuck model of HCC.METHODS:Molecular docking was performed with 3 bait PSMA ligands and compared between human and woodchuck PSMA. Initially, PET images were acquired dynamically after intravenously injecting 37 MBq (1.0 mCi) of 68Ga-PSMA-11 into woodchuck models of HCC. Subsequently, 10-minute static PET scans were conducted for other animals 1-hour after injection due to HCC and liver background uptake stabilization at 30–45 minutes after injection. Liver tissue samples were harvested after imaging, fresh-frozen for quantitative reverse transcription polymerase chain reaction and western blot for validation, or fixed for histology for correlation.RESULTS:Our preclinical studies confirmed the initial clinical findings of 68Ga-PSMA-11 uptake in HCC. The agents (ligands and antibodies) developed against human PSMA were found to be reactive against the woodchuck PSMA.CONCLUSION:This animal model offers a unique opportunity for investigating the biogenesis of tumor-associated vascular PSMA, its functional role(s), and potentials for future treatment strategies targeting tumor vascular PSMA using already developed PSMA-targeting agents.

Peptide Affinity Chromatography Applied to Therapeutic Antibodies Purification.

The interest in therapeutic monoclonal antibodies (mAbs) has significantly grown in the pharmaceutical industry, exceeding 100 FDA mAbs approved. Although the upstream processing of their industrial production has been significantly improved in the last years, the downstream processing still depends on immobilized protein A affinity chromatography. The high cost, low capacity and short half-life of immobilized protein A chromatography matrices, encouraged the design of alternative short-peptide ligands for mAb purification. Most of these peptides have been obtained by screening combinatorial peptide libraries. These low-cost ligands can be easily produced by solid-phase peptide synthesis and can be immobilized on chromatographic supports, thus obtaining matrices with high capacity and selectivity. Furthermore, matrices with immobilized peptide ligands have longer half-life than those with protein A due to the higher stability of the peptides. In this review the design and synthesis of peptide ligands, their immobilization on chromatographic supports and the evaluation of the affinity supports for their application in mAb purification is described.

Peptide-Based Electrochemiluminescence Biosensors Using Silver Nanoclusters as Signal Probes and Pd-Cu2O Hybrid Nanoconcaves as Coreactant Promoters for Immunoassays.

Metal nanoclusters (NCs) possess high light stability and biocompatibility because of their unique quantum size effect, which has gradually become a new type of electrochemiluminescence (ECL) nanomaterial for immunoassays. However, the luminescence efficiency of metal NCs is too low to meet the needs of trace analysis, which limits its application. Herein, Ag NCs served as signal probes and Pd-Cu2O hybrid nanoconcaves served as coreaction promoters, developing a highly efficient peptide-based biosensor for neuron-specific enolase (NSE) detection. Utilizing the reversible cycle of Cu+/Cu2+ and the reduction characteristics of Pd NPs, Pd-Cu2O greatly accelerates the reduction of S2O82-. Meanwhile, Pd-Cu2O has good hydrogen evolution activity, which promotes the generation of oxygen by improving the redox efficiency of the overall reaction, thus increasing the yield of active intermediates (OH•) to promote the reduction of S2O82-. Specially, this is an effective attempt to use the hydrogen evolution reaction (HER) to accelerate the ECL emission of the S2O82- system. In addition, a short peptide ligand (NARKFYKGC, NFC) was developed to implement the targeted immobilization of antibodies, which can specifically bind to the Fc fragment of antibodies, thereby avoiding the occupation of the antigen binding site (Fab fragment). The introduction of NFC not only improves the binding efficiency of antibodies but also protects its bioactivity, thus significantly improving the sensitivity of the biosensor. Based on these strategies, the proposed biosensor provides a new perspective for the applications of metal NCs in ECL systems.

Focused peptide library screening as a route to a superior affinity ligand for antibody purification

Affinity chromatography is the linchpin of antibody downstream processing and typically relies on bacterial immunoglobulin (Ig)-binding proteins, epitomized by staphylococcal protein A-based ligands. However, such affinity ligands are fairly costly and suffer from chemical instability, leading to ligand denaturation and leaching from chromatographic support. Innovations in this area are aimed at developing robust and highly selective antibody ligands capable of withstanding harsh column sanitization conditions. We report the development and first-stage characterization of a selective short linear peptide ligand of the IgG Fc region capable of capturing all four IgG subclasses. The ligand was discovered through in vitro directed evolution. A focused phage-display library based on a previously identified peptide lead was subjected to a single-round screen against a pool of human IgG. The hits were identified with next-generation sequencing and ranked according to the enrichment ratio relative to their frequency in the pre-screened library. The top enriched peptide GSYWYNVWF displaying highest affinity for IgG was coupled to bromohydrin-activated agarose beads via a branched linker. The resulting affinity matrix was characterized with a dynamic binding capacity of approx. 43 mg/mL, on par with commercially employed protein A-based resin.

Protein A-based ligands for affinity chromatography of antibodies

Protein A chromatography is a key technology in the industrial production of antibodies, and a variety of commercial protein A adsorbents are available in shelf. High stability and binding capacity of a protein A adsorbent are two key issues for successful practice of protein A chromatography. Earlier versions of protein A adsorbents ever exhibited serious fragility to typical cleaning-in-place protocols (e.g. washing with sodium hydroxide solution), and suffered from low binding capacity, harsh elution, ligand leakage and other problems involved in industrial applications. During the last three decades, various techniques and approaches have been applied in the improvement of chemical stability and enhancement of binding capacity of protein A-based ligands and adsorbents for antibody purifications. This mini-review focuses on the technical explorations in protein A-based affinity adsorbents, especially protein A-based ligands, including the efforts to increase the chemical stability by site-directed mutations and to improve the binding capacity by ligand polymerization and site-directed immobilization. Moreover, the efforts to develop short peptide ligands based on the structure of protein A, including the biomimetic design strategies and the synthesis of peptide-mixed mode hybrid ligands are discussed. These peptide and peptide-based hybrid ligands exhibit high affinity and selectivity to antibodies, but noteworthy differences in the binding mechanism of antibody from protein A. As a result, bound antibody to the ligands could be effectively eluted under mild conditions. Perspectives for the development of the protein A-based peptide ligands have been extensively discussed, suggesting that the ligands represent a direction for technological development of antibody purification.

Design of Affinity Chromatography Peptide Ligands Through Combinatorial Peptide Library Screening.

In this chapter, a protocol to design affinity chromatography matrices with short peptide ligands immobilized for protein purification is described. The first step consists of the synthesis of a combinatorial peptide library on the hydroxymethylbenzoyl (HMBA)-ChemMatrix resin by the divide-couple-recombine (DCR) method using the Fmoc chemistry. Next, the library is screened with the protein of interest labeled with a fluorescent dye or biotin. Subsequently, peptides contained on positive beads are identified by tandem matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS/MS), and those sequences showing greater consensus are synthesized in larger quantities and immobilized on chromatographic supports. Finally, target protein adsorption on peptide affinity matrices is evaluated through equilibrium adsorption isotherms and breakthrough curves.

Coassembly Generates Peptide Hydrogel with Wound Dressing Material Properties.

Multicomponent self-assembly of peptides is a powerful strategy to fabricate novel functional materials with synergetic properties that can be used for several nanobiotechnological applications. In the present study, we used a coassembly strategy to generate an injectable ultrashort bioactive peptide hydrogel formed by mixing a dipeptide hydrogelator with a macrophage attracting short chemotactic peptide ligand. Coassembly does not impede hydrogelation as shown by cryo-transmission electron microscopy (cryo-TEM), scanning electron microscopy, and rheology. Biocompatibility was shown by cytotoxicity assays and confocal microscopy. The hydrogels release the entrapped skin antibiotic ciprofloxacin, among others, in a slow and continuous manner. Such bioinspired advanced functional materials can find applications as wound dressing materials to treat chronic wound conditions like diabetic foot ulcer.

Protocol for bevacizumab purification using Ac-PHQGQHIGVSK-agarose

Bevacizumab is a monoclonal antibody, produced in CHO cells, used for the treatment of many human cancers. It is an anti-vascular endothelial growth factor (antsi-VEGF) that blocks the growth of tumor blood vessels. Nowadays its purification is achieved by affinity chromatography (AC) using protein A which is a very expensive ligand. On the other hand, the peptide Ac-PHQGQHIGVSK contained in the VEGF fragment binds bevacizumab with high affinity. This short peptide ligand has higher stability and lower cost than protein A and it can be prepared very easily by solid phase peptide synthesis. The present protocol describes the synthesis of Ac-PHQGQHIGVSK-agarose and its use for affinity chromatography purification of bevacizumab from a clarified CHO cell culture.•Ac-PHQGQHIGVSK-agarose capacity and selectivity are equivalent to those of protein A matrices.•The peptide ligand shows a greater stability and lower cost. The lack of Trp, Met or Cys in the peptide ligand prevents its oxidation and extends the useful life of the chromatographic matrix.•Mild conditions used during chromatography preserved the integrity of bevacizumab.

Direct solid-phase peptide synthesis on chitosan microparticles for targeting tumor cells

An EGFR-targeting peptide with Ala-Glu-Tyr-Leu-Arg sequence was assembled directly onto the surface of spray-dried chitosan microparticles using solid-phase peptide synthesis with Fmoc chemistry. Both targeted and scrambled peptides were cleaved from chitosan with enzymatic digestion, isolated using reversed-phase HPLC, then identified with LC/MS/MS and amino acid analysis. Particles with conjugated peptides and fluorescent-labeled were characterized for binding with A549 (cancer) and WI-26 VA4 (normal) lung cells using flow cytometry and confocal microscopy. The purity of peptide synthesis was in the range of 74–77%. The cell binding studies revealed that particles modified with the peptide bind to lung cancer cells 8.3 times higher than the normal lung cells. The binding potential of surface-modified targeted particles to the tumor cells was compared with scrambled and unmodified ones and was found to be significantly different. The binding was 7.3–7.5-fold higher than the scrambled and unmodified particles, respectively. Modification of chitosan particles with direct assembly of Ala-Glu-Tyr-Leu-Arg peptide on their surface enhanced their targeting potential to lung cancer cells and could be used as a potential carrier for delivery and therapy. This approach can further be utilized for assembly of other short peptide ligands on micro- or nanoparticulate systems for tumor targeting.

A new tetrapeptide biomimetic chromatographic resin for antibody separation with high adsorption capacity and selectivity

Biomimetic affinity chromatography with short peptide ligands is a developing technology, which has great potential for antibody separation and purification. In this study, a tetrapeptide library with critical residues of natural ligands to hIgG was constructed and a novel tetrapeptide ligand (Ac-FYHE) with high LibDock scores was selected by molecular docking. Then, Ac-FYHE ligand was linked to agarose bead to prepare a new chromatography resin. The properties of antibody adsorption were measured and evaluated by static/dynamic adsorption. It was found that the resin with ligand Ac-FYHE has high binding capacity and selectivity for hIgG. The results showed the Qm-hIgG of Ac-FYHE-4FF resin was 87.9 mg/g resin while the Qm-BSA of this resin was only 16.5 mg/g resin at pH 7.0. Moreover, at pH 7.0, Q10% of Ac-FYHE-4FF resin was 24.1 mg/mL for hIgG but just 2.1 mg/mL for BSA, which presented high selectivity of the screened resin at pH 7.0. Subsequently, the adsorption and separation properties of the Ac-FYHE-4FF resin were further investigated. As a result, with the addition of 0.5 M NaCl, Qm decreased by less than 20% but Qm decreased by 70% with the addition of 50% (v/v) ethylene glycol, which indicated that hydrophobic interaction would be the driving force for the binding between resin and hIgG. Besides, pH 7.5 and pH 4.5 could be the optimal loading and elution condition for hIgG, respectively. Finally, the Ac-FYHE-4FF resin was applied to separate mAb or/and hIgG from BSA containing feedstock, CHO cell culture supernatant and human serum, and the purity and recovery were both more than 90% with only one-step separation. The results indicate that the Ac-FYHE-4FF resin developed in this work would be promising for antibody separation and purification.

A minimalist peptide ligand for IgG by minimizing the binding domain of protein A

Large scale application of antibody related drug has been promoting the development of short ligand with low cost and high stability for affinity chromatographic purification of immunoglobulin G (IgG). This study presents a strategy to design a short peptide ligand by minimizing the IgG binding portion from a commercial ligand of Protein A. A short hexapeptide (FYEILH) was thus screened out by the real screening technique of STD-NMR. It presented a comparable binding activity to Protein A, with the dissociation constant (Kd) of 1.8 × 10−6 mol/L, the static binding capacity of 49.7 mg/mL, and the purity of 94% for hIgG from chromatographic purification of serum feedstock in a single step. Epitope mapping analysis by STD-NMR indicated that the carboxy groups of the charged residue E (glutamic acid) in FYEILH was the most adjacent part in binding with hIgG molecule and thus the electronic interactions among them was the dominating binding mechanism. Such mechanism was a little different from Protein A and consequently leaded to its much milder chromatographic conditions of loading at pH 6.0 and eluting at 0.5 mol/L NaCl. The study provided a strategy of reducing larger binding domains of huge Protein A molecule to smaller functional peptide ligand, and offered a potential alternative ligand with low synthesis cost for IgG purification.

Peptide ligand-based ELISA reagents for antibody detection

Detection of specific antibodies has numerous research, therapeutic and diagnostic applications. Short peptide ligands that bind specifically to antibodies with continuous epitopes can be derived from epitope mapping experiments. Short peptide ligands (mimotopes) specific to antibodies with discontinuous epitopes can be identified by screening complex peptide libraries. In an effort to enhance practical utility of such peptide ligands, we describe here a simple approach to turn such target antibody-specific peptide ligands into specific ELISA detection reagents. We show that a simple addition of biotinylated peptide ligands to commonly available horseradish peroxidase (HRP)-labeled streptavidin (or HRP-anti-biotin antibody), or digoxigenin-labeled peptides to HRP-anti-digoxigenin antibody detection reagents transformed these generic detection reagents into sensitive target antibody-specific reagents. ELISA assays performed using these reagents exhibited excellent analytical properties indicating their practical utility for antibody detection. One generic detection reagent can be readily transformed into many different specific ELISA reagents by a simple mix and match design using an appropriate target-specific peptide ligand. Simplicity of preparation of these ELISA reagents for detecting antibodies should facilitate their practical applications.

Computer-aided design of short peptide ligands targeting tumor necrosis factor-alpha for adsorbent applications.

Tumor necrosis factor alpha (TNF-α) is a pro-inflammatory cytokine active in the bodily immune response and serious inflammatory diseases. Traditional ligands targeting TNF-α focus on antibodies and receptors, which always associate with low efficacy and specificity. In the present study, two peptide ligands (T1: Ac-RKEM-NH2 and T2: Ac-RHCLS-NH2) were designed by computer simulation technology considering the weak interactions between TNF-α and its receptor TNFR1. Calculations of binding free energy (BFE) were made by the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) method between T1 or T2 and TNF-α (-22.68 and -14.23 kcal mol-1, respectively). To assess the affinity levels, short peptide ligands were fixed on polyvinyl alcohol (PVA) microspheres; adsorption tests showed a stronger affinity of both PVA-T1 and PVA-T2 to TNF-α in PBS buffer than PVA microspheres (79.20 ± 1.32 and 74.27 ± 1.10 vs. 39.03 ± 1.25 pg mg-1, respectively). Moreover, PVA-T1 (74.8%, 17.60 ± 2.98 pg mg-1) and PVA-T2 (63.2%, 15.30 ± 4.81 pg mg-1) exhibit significantly enhanced TNF-α adsorption from the plasma of rats with sepsis to blank PVA and commercial XAD-7 resin. In conclusion, our results show that T1 designed by computer-aided molecular design (CAMD) exhibits a stronger affinity to TNF-α and it can significantly enhance PVA microsphere adsorption efficiency of TNF-α in plasma.

Genetic coding algorithm for sense and antisense peptide interactions

Sense and antisense peptides, i.e. peptides specified by complementary DNA and RNA sequences, interact with increased probability. Biro, Blalock, Mekler, Root-Bernstein and Siemion investigated the recognition rules of peptide—peptide interaction based on the complementary coding of DNA and RNA sequences in 3′→5′ and 5′→3′ directions. After more than three decades of theoretical and experimental investigations, the efficiency of this approach to predict peptide—peptide binding has been experimentally verified for more than 50 ligand—receptor systems, and represents a promising field of research. The natural genetic coding algorithm for sense and antisense peptide interactions combines following elements: of amino acid physico-chemical properties, stereochemical interaction, and bidirectional transcription. The interplay of these factors influences the specificity of sense—antisense peptide interactions, and affects the selection and evolution of peptide ligand—receptor systems. Complementary mRNA codon—tRNA anticodon complexes, and recently discovered Carter-Wolfenden tRNA acceptor-stem code, provide the basis for the rational modeling of peptide interactions based on their hydrophobic and lipophilic amino acid physico-chemical properties. It is shown that the interactions of complementary amino acid pairs according to the hydrophobic and lipophilic properties strongly depend on the central (second) purine base of the mRNA codon and its pyrimidine complement of the tRNA anticodon. This enables the development of new algorithms for the analysis of structure, function and evolution of protein and nucleotide sequences that take into account the residue's tendency to leave water and enter a nonpolar condensed phase considering its mass, size and accessible surface area. The practical applications of the sense—antisense peptide modeling are illustrated using different interaction assay types based on: microscale thermophoresis (MST), tryptophan fluorescence spectroscopy (TFS), nuclear magnetic resonance spectroscopy (NMR), and magnetic particles enzyme immunoassay (MPEIA). Various binding events and circumstances were considered, e.g., in situations with—short antisense peptide ligand (MST), L- and D-enantiomer acceptors (TFS), in low affinity conditions (NMR), and with more than one antisense peptide targeting hormone (MPEIA).