Secondary Structure and Conformational Stability of the Antigen Residues Making Contact with Antibodies

Analysis of how antigen mutations disrupt antibody binding interactions toward enabling rapid and reliable antibody repurposing

Antibody repurposing is the process of changing a known antibody so that it binds to a mutated antigen. One of the findings to emerge from the Coronavirus Disease 2019 (COVID-19) pandemic was that it was possible to repurpose neutralizing antibodies for Severe Acute Respiratory Syndrome, a related disease, to work for COVID-19. Thus, antibody repurposing is a possible pathway to prepare for and respond to future pandemics, as well as personalizing cancer therapies. For antibodies to be successfully repurposed, it is necessary to know both how antigen mutations disrupt their binding and how they should be mutated to recover binding, with this work describing an analysis to address the first of these topics. Every possible antigen point mutation in the interface of 246 antibody-protein complexes were analyzed using the Rosetta molecular mechanics force field. The results highlight a number of features of how antigen mutations affect antibody binding, including the effects of mutating critical hotspot residues versus other positions, how many mutations are necessary to be likely to disrupt binding, the prevalence of indirect effects of mutations on binding, and the relative importance of changing attractive versus repulsive energies. These data are expected to be useful in guiding future antibody repurposing experiments.

Using Short Molecular Dynamics Simulations to Determine the Important Features of Interactions in Antibody-Protein Complexes

The last few years have seen the rapid proliferation of machine learning methods to design binding proteins. Although these methods have shown large increases in experimental success rates compared to prior approaches, the majority of their predictions fail when they are experimentally tested. It is evident that computational methods still struggle to distinguish the features of real protein binding interfaces from false predictions. Short molecular dynamics simulations of 20 antibody-protein complexes were conducted to identify features of interactions that should occur in binding interfaces. Intermolecular salt bridges, hydrogen bonds, and hydrophobic interactions were evaluated for their persistences, energies, and stabilities during the simulations. It was found that only the hydrogen bonds where both residues are stabilized in the bound complex are expected to persist and meaningfully contribute to binding between the proteins. In contrast, stabilization was not a requirement for salt bridges and hydrophobic interactions to persist. Still, interactions where both residues are stabilized in the bound complex persist significantly longer and have significantly stronger energies than other interactions. Two hundred and twenty real antibody-protein complexes and 8194 decoy complexes were used to train and test a random forest classifier using the features of expected persistent interactions identified in this study and the macromolecular features of interaction energy (IE), buried surface area (BSA), IE/BSA, and shape complementarity. It was compared to a classifier trained only on the expected persistent interaction features and another trained only on the macromolecular features. Inclusion of the expected persistent interaction features reduced the false positive rate of the classifier by two- to five-fold across a range of true positive classification rates.

Peptide-based nanomaterials and their diverse applications

The supramolecular self-assembly of peptides offers a promising avenue for both materials science and biological applications. Peptides have garnered significant attention in molecular self-assembly, forming diverse nanostructures with α-helix, β-sheet, and random coil conformations. These self-assembly processes are primarily driven by the amphiphilic nature of peptides and stabilized by non-covalent interactions, leading to complex nanoarchitectures responsive to environmental stimuli. While extensively studied in biomedical applications, including drug delivery and tissue engineering, their potential applications in the fields of piezoresponsive materials, conducting materials, catalysis and energy harvesting remain underexplored. This review comprehensively elucidates the diverse material characteristics and applications of self-assembled peptides. We discuss the multi-stimuli-responsiveness of peptide self-assemblies and their roles as energy harvesters, catalysts, liquid crystalline materials, glass materials and contributors to electrical conductivity. Additionally, we address the challenges and present future perspectives associated with peptide nanomaterials. This review aims to provide insights into the versatile applications of peptide self-assemblies while concisely summarizing their well-established biomedical roles that have previously been extensively reviewed by various research groups, including our group.

M2e-Derived Peptidyl and Peptide Amphiphile Micelles as Novel Influenza Vaccines

Background: A significant problem with current influenza vaccines is their reliance on predictions of the most prevalent strains for the upcoming season, with inaccurate forecasts greatly reducing the overall efficacy of the immunization campaign. A universal influenza vaccine, which leverages epitopes conserved across many, if not all, strains of influenza, could reduce the need for extremely accurate forecasting. The highly conserved ectodomain of the influenza M2 protein contains a B cell epitope in the M22-16 region, making it a promising candidate as a universal influenza vaccine. Unfortunately, free peptide antigens alone are limited as vaccines due to their poor stability and weak immunogenicity in vivo. To improve the potential of peptide vaccines, immunostimulatory micellar nanoparticles can be generated from them by lipid conjugation (i.e., peptide amphiphiles-PAs). Methods: M22-16 peptides and Palm2K-M22-16-(KE)4 PAs were synthesized and characterized. BALB/c mice were subcutaneously vaccinated with these formulations, and ELISAs were conducted on serum collected from the vaccinated mice to evaluate induced antibody responses. Results: Unlike other peptide antigens previously studied, the unmodified M22-16 peptide micellized without any peptidyl or lipid modifications. M22-16 peptidyl micelles (PMs) were spherical with largely undefined secondary structure somewhat different from the cylindrical, β-sheet-containing Palm2K-M22-16-(KE)4 peptide amphiphile micelles (PAMs). Differences in physical properties were found to correlate with slightly different immune responses with PAMs eliciting higher antibody titers after the initial immunization, whereas both micelle types elicited strong IgG titers after a prime-boost regimen. Conclusions: These results suggest the viability of PAMs as single-dose vaccines, while both PMs and PAMs show potential using a multi-dose immunization approach.

Phage Immunoprecipitation and Sequencing-a Versatile Technique for Mapping the Antibody Reactome

Characterizing the antibody reactome for circulating antibodies provide insight into pathogen exposure, allergies, and autoimmune diseases. This is important for biomarker discovery, clinical diagnosis, and prognosis of disease progression, as well as population-level insights into the immune system. The emerging technology phage display immunoprecipitation and sequencing (PhIP-seq) is a high-throughput method for identifying antigens/epitopes of the antibody reactome. In PhIP-seq, libraries with sequences of defined lengths and overlapping segments are bioinformatically designed using naturally occurring proteins and cloned into phage genomes to be displayed on the surface. These libraries are used in immunoprecipitation experiments of circulating antibodies. This can be done with parallel samples from multiple sources, and the DNA inserts from the bound phages are barcoded and subjected to next-generation sequencing for hit determination. PhIP-seq is a powerful technique for characterizing the antibody reactome that has undergone rapid advances in recent years. In this review, we comprehensively describe the history of PhIP-seq and discuss recent advances in library design and applications.

Development of Inhibitory Compounds for Metallo-beta-lactamase through Computational Design and Crystallographic Analysis

Metallo-β-lactamases (MBL) deactivate β-lactam antibiotics through a catalytic reaction caused by two zinc ions at the active center. Since MBLs deteriorate a wide range of antibiotics, they are dangerous factors for bacterial multidrug resistance. In this work, organic synthesis, computational design, and crystal structure analysis were performed to obtain potent MBL inhibitors based on a previously identified hit compound. The hit compound comprised 3,4-dihydro-2(1H)-quinolinone linked with a phenyl-ether-methyl group via a thiazole ring. In the first step, the thiazole ring was replaced with a tertiary amine to avoid the planar structure. In the second step, we virtually modified the compound by keeping the quinolinone backbone. Every modified compound was bound to a kind of MBL, imipenemase-1 (IMP-1), and the binding pose was optimized by a molecular mechanics calculation. The binding scores were evaluated for the respective optimized binding poses. Given the predicted binding poses and calculated binding scores, candidate compounds were determined for organic syntheses. The inhibitory activities of the synthesized compounds were measured by an in vitro assay for two kinds of MBLs, IMP-1 and New Delhi metallo-β-lactamase (NDM-1). A quinolinone connected with an amine bound with methyl-phenyl-ether-propyl and cyclohexyl-ethyl showed a 50% inhibitory concentration of 4.8 μM. An X-ray crystal analysis clarified the binding structure of a synthesized compound to IMP-1. The δ-lactam ring of quinolinone was hydrolyzed, and the generated carboxyl group was coordinated with zinc ions. The findings on the chemical structure and binding pose are expected to be a base for developing MBL inhibitors.

New materials-based on gelatin coordinated with zirconium or aluminum for ecological retanning

Ecological retanning agent is an effective way to solve the pollution source of leather manufacturing industry. In this study, the gelatin from chrome-containing leather shavings in the leather industry was used to realize sustainable leather post-tanning. The gelatin hydrolysate (GH) coordinated with Zr4+ or Al3+ to prepare eco-friendly retanning agents GH-Zr and GH-Al. The successful coordination between GH and metal ions was characterized by FTIR and XPS. The retanning agents were characterized by FTIR curve-fitting and circular dichroism spectroscopy. The results showed that the conformation of the secondary structure of the polypeptide became ordered and stable after coordinating with the metal ions. The particle size and weight average molecular weight of the retanning agents were ~1700 nm and ~2100, respectively, measured by nanoparticle size analyzer and gel permeation chromatography (GPC). The retanning agents were applied to retanning of chrome tanned leather and glutaraldehyde tanned leather. The abundant free amino from retanning agents can consume the free formaldehyde. Meanwhile, retanning agents can effectively improve the multiple binding sites, resulting in favorable thickening rate (>110 %) and excellent dye and fatliquor absorption rate with ~99.91 % and ~93.18 %. Thus, this strategy can provide a viable choice for solid leather waste and sustainable development of the leather industry.

Sticklac-Derived Natural Compounds Inhibiting RNase H Activity of HIV-1 Reverse Transcriptase

The emergence of drug-resistant viruses is a serious concern in current chemotherapy for human immunodeficiency virus type-1 (HIV-1) infectious diseases. Hence, antiviral drugs aiming at targets that are different from those of approved drugs are still required, and the RNase H activity of HIV-1 reverse transcriptase is a suitable target. In this study, a search of a series of natural compounds was performed to identify the RNase H inhibitors. Three compounds were found to block the RNase H enzymatic activity. A laccaic acid skeleton was observed in all three natural compounds. A hydroxy phenyl group is connected to an anthraquinone backbone in the skeleton. An acetamido-ethyl, amino-carboxy-ethyl, and amino-ethyl are bound to the phenyl in laccaic acids A, C, and E, respectively. Laccaic acid C showed a 50% inhibitory concentration at 8.1 μM. Laccaic acid C also showed inhibitory activity in a cell-based viral proliferation assay. Binding structures of these three laccaic acids were determined by X-ray crystallographic analysis using a recombinant protein composed of the HIV-1 RNase H domain. Two divalent metal ions were located at the catalytic center in which one carbonyl and two hydroxy groups on the anthraquinone backbone chelated two metal ions. Molecular dynamics simulations were performed to examine the stabilities of the binding structures. Laccaic acid C showed the strongest binding to the catalytic site. These findings will be helpful for the design of potent inhibitors with modification of laccaic acids to enhance the binding affinity.

Application Progress of the Single Domain Antibody in Medicine

The camelid-derived single chain antibody (sdAb), also termed VHH or nanobody, is a unique, functional heavy (H)-chain antibody (HCAb). In contrast to conventional antibodies, sdAb is a unique antibody fragment consisting of a heavy-chain variable domain. It lacks light chains and a first constant domain (CH1). With a small molecular weight of only 12~15 kDa, sdAb has a similar antigen-binding affinity to conventional Abs but a higher solubility, which exerts unique advantages for the recognition and binding of functional, versatile, target-specific antigen fragments. In recent decades, with their unique structural and functional features, nanobodies have been considered promising agents and alternatives to traditional monoclonal antibodies. As a new generation of nano-biological tools, natural and synthetic nanobodies have been used in many fields of biomedicine, including biomolecular materials, biological research, medical diagnosis and immune therapies. This article briefly overviews the biomolecular structure, biochemical properties, immune acquisition and phage library construction of nanobodies and comprehensively reviews their applications in medical research. It is expected that this review will provide a reference for the further exploration and unveiling of nanobody properties and function, as well as a bright future for the development of drugs and therapeutic methods based on nanobodies.

Analysis of conformational stability of interacting residues in protein binding interfaces

After approximately 60 years of work, the protein folding problem has recently seen rapid advancement thanks to the inventions of AlphaFold and RoseTTAFold, which are machine-learning algorithms capable of reliably predicting protein structures from their sequences. A key component in their success was the inclusion of pairwise interaction information between residues. As research focus shifts towards developing algorithms to design and engineer binding proteins, it is likely that knowledge of interaction features at protein interfaces can improve predictions. Here, 574 protein complexes were analyzed to identify the stability features of their pairwise interactions, revealing that interactions between pre-stabilized residues are a selected feature in protein binding interfaces. In a retrospective analysis of 475 de novo designed binding proteins with an experimental success rate of 19%, inclusion of pairwise interaction pre-stabilization parameters increased the frequency of identifying experimentally successful binders to 40%.

In Silico Identification of Inhibitory Compounds for SARS-Cov-2 Papain-Like Protease

Virtual screening with high-performance computers is a powerful and cost-effective technique in drug discovery. A chemical database is searched to find candidate compounds firmly bound to a target protein, judging from the binding poses and/or binding scores. The severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) infectious disease has spread worldwide for the last three years, causing severe slumps in economic and social activities. SARS-Cov-2 has two viral proteases: 3-chymotrypsin-like (3CL) and papain-like (PL) protease. While approved drugs have already been released for the 3CL protease, no approved agent is available for PL protease. In this work, we carried out in silico screening for the PL protease inhibitors, combining docking simulation and molecular mechanics calculation. Docking simulations were applied to 8,820 molecules in a chemical database of approved and investigational compounds. Based on the binding poses generated by the docking simulations, molecular mechanics calculations were performed to optimize the binding structures and to obtain the binding scores. Based on the binding scores, 57 compounds were selected for in vitro assay of the inhibitory activity. Five inhibitory compounds were identified from the in vitro measurement. The predicted binding structures of the identified five compounds were examined, and the significant interaction between the individual compound and the protease catalytic site was clarified. This work demonstrates that computational virtual screening by combining docking simulation with molecular mechanics calculation is effective for searching candidate compounds in drug discovery.

Computational and Crystallographic Analysis of Binding Structures of Inhibitory Compounds for HIV-1 RNase H Activity

Chemotherapy of human immunodeficiency virus type-1 (HIV-1) has significantly developed over the last three decades. The emergence of drug-resistant variants is, however, still a severe problem. The RNase H activity of HIV-1 reverse transcriptase is an attractive target for a new class of antiviral drugs because there is no approved inhibitor. The nitro-furan-carbonyl and nitro-thiophene-carbonyl groups are potent scaffolds for the HIV-1 RNase H inhibitor. In this work, the binding structures of six inhibitory compounds were obtained by X-ray crystal analysis in a complex with a recombinant protein of HIV-1 RNase H domain. Every inhibitory compound was found to be bound to the catalytic site with the furan- or thiophene-ring coordinated to two divalent metal ions at the binding pocket. All the atoms in nitro, furan, carbonyl, and two metals were aligned in the nitro-furan derivatives. The straight line connecting nitro and carboxyl groups was parallel to the plane made by two metal ions and a furan O atom. The binding modes of the nitro-thiophene derivatives were slightly different from those of the nitro-furan ones. The nitro and carbonyl groups deviated from the plane made by two metals and a thiophene S atom. Molecular dynamics simulations suggested that the furan O or thiophene S atom and carbonyl O atom were firmly coordinated to the metal ions. The simulations made the planar nitro-furan moiety well aligned to the line connecting the two metal ions. In contrast, the nitro-thiophene derivatives were displaced from the initial positions after the simulations. The computational findings will be a sound basis for developing potent inhibitors for HIV-1 RNase H activity.

The identification of the key residues E829 and R845 involved in transient receptor potential melastatin 2 channel gating

Transient receptor potential melastatin 2 (TRPM2), a non-selective cation channel, is involved in many physiological and pathological processes, including temperature sensing, synaptic plasticity regulation, and neurodegenerative diseases. However, the gating mechanism of TRPM2 channel is complex, which hinders its functional research. With the discovery of the Ca2+ binding site in the S2–S3 domain of TRPM2 channel, more and more attention has been drawn to the role of the transmembrane segments in channel gating. In this study, we focused on the D820-F867 segment around the S2 domain, and identified the key residues on it. Functional assays of the deletion mutants displayed that the deletions of D820-W835 and L836-P851 destroyed channel function totally, indicating the importance of these two segments. Sequence alignments on them found three polar and charged residues with high conservation (D820, E829, and R845). D820A, E829A, and R845A which removed the charge and the side chain of the residues were tested by 500 μM adenosine diphosphate-ribose (ADPR) or 50 mM Ca2+. E829A and R845A affected the characteristic of channel currents, while D820A behaved similarly to WT, indicating the participations of E829 and R845 in channel gating. The charge reversing mutants, E829K and R845D were then constructed and the electrophysiological tests showed that E829A and E829K made the channel lose function. Interestingly, R845A and R845D exhibited an inactivation process when using 500 μM ADPR, but activated normally by 50 mM Ca2+. Our data suggested that the negative charge at E829 took a vital part in channel activation, and R845 increased the stability of the Ca2+ combination in S2-S3 domain, thus guaranteeing the opening of TRPM2 channel. In summary, our identification of the key residues E829 and R845 in the transmembrane segments of TRPM2. By exploring the gating process of TRPM2 channel, our work helps us better understand the mechanism of TRPM2 as a potential biomarker in neurodegenerative diseases, and provides a new approach for the prediction, diagnosis, and prognosis of neurodegenerative diseases.