N-terminal α-amino group modification of antibodies using a site-selective click chemistry method

Antibody-based near-infrared fluorogenic probes for wash-free imaging of cell-surface proteins

BACKGROUND

Cell-surface proteins, which are closely associated with various physiological and pathological processes, have drawn much attention in drug discovery and disease diagnosis. Thus, wash-free imaging of the target cell-surface protein under its native environment is critical and helpful for early detection and prognostic evaluation of diseases.

RESULTS

To minimize the interference from autofluorescence and fit the penetration depth towards tissue samples, we developed a fluorogenic antibody-based probe, Ab-Cy5.5, which will liberate > 5-fold turn-on near-infrared (NIR) emission in the presence of its target antigen within 10 min.

SIGNIFICANCE

By taking advantage of the fluorescence-quenched dimeric H-aggregation of Cy5.5, Ab-Cy5.5 with Cy5.5 attached at the N-terminus showed negligible background signal, allowing direct imaging of the target cell-surface protein in both living cells and tissue samples without washing.

Precision engineering of antibodies: A review of modification and design in the Fab region

The binding of functional groups to antibodies is crucial for disease treatment, diagnosis, and basic scientific research. Traditionally, antibody modifications have focused on the Fc region to maintain antigen-antibody binding activity. However, such modifications may impact critical antibody functions, including immune cell surface receptor activation, cytokine release, and other immune responses. In recent years, modifications targeting the antigen-binding fragment (Fab) region have garnered increasing attention. Precise modifications of the Fab region not only maximize the retention of antigen-antibody binding capacity but also enhance numerous physicochemical properties of antibodies. This paper reviews the chemical, biological, biochemical, and computer-assisted methods for modifying the Fab region of antibodies, discussing their advantages, limitations, recent advances, and future trends.

Accelerating antibody discovery and design with artificial intelligence: Recent advances and prospects

Therapeutic antibodies are the largest class of biotherapeutics and have been successful in treating human diseases. However, the design and discovery of antibody drugs remains challenging and time-consuming. Recently, artificial intelligence technology has had an incredible impact on antibody design and discovery, resulting in significant advances in antibody discovery, optimization, and developability. This review summarizes major machine learning (ML) methods and their applications for computational predictors of antibody structure and antigen interface/interaction, as well as the evaluation of antibody developability. Additionally, this review addresses the current status of ML-based therapeutic antibodies under preclinical and clinical phases. While many challenges remain, ML may offer a new therapeutic option for the future direction of fully computational antibody design.

Detection of SARS-CoV-2 in saliva by a low-cost LSPR-based sensor

The SARS-CoV-2 pandemic started more than 3 years ago, but the containment of the spread is still a challenge. Screening is imperative for informed decision making by government authorities to contain the spread of the virus locally. The access to screening tests is disproportional, due to the lack of access to reagents, equipment, finances or because of supply chain disruptions. Low and middle-income countries have especially suffered with the lack of these resources. Here, we propose a low cost and easily constructed biosensor device based on localized surface plasmon resonance, or LSPR, for the screening of SARS-CoV-2. The biosensor device, dubbed "sensor" for simplicity, was constructed in two modalities: (1) viral detection in saliva and (2) antibody against COVID in saliva. Saliva collected from 18 patients were tested in triplicates. Both sensors successfully classified all COVID positive patients (among hospitalized and non-hospitalized). From the COVID negative patients 7/8 patients were correctly classified. For both sensors, sensitivity was determined as 100% (95% CI 79.5-100) and specificity as 87.5% (95% CI 80.5-100). The reagents and equipment used for the construction and deployment of this sensor are ubiquitous and low-cost. This sensor technology can then add to the potential solution for challenges related to screening tests in underserved communities.

Recent Progress in Antibody Epitope Prediction

Recent progress in epitope prediction has shown promising results in the development of vaccines and therapeutics against various diseases. However, the overall accuracy and success rate need to be improved greatly to gain practical application significance, especially conformational epitope prediction. In this review, we examined the general features of antibody-antigen recognition, highlighting the conformation selection mechanism in flexible antibody-antigen binding. We recently highlighted the success and warning signs of antibody epitope predictions, including linear and conformation epitope predictions. While deep learning-based models gradually outperform traditional feature-based machine learning, sequence and structure features still provide insight into antibody-antigen recognition problems.

The Dawn of a New Era: Targeting the "Undruggables" with Antibody-Based Therapeutics

The high selectivity and affinity of antibodies toward their antigens have made them a highly valuable tool in disease therapy, diagnosis, and basic research. A plethora of chemical and genetic approaches have been devised to make antibodies accessible to more "undruggable" targets and equipped with new functions of illustrating or regulating biological processes more precisely. In this Review, in addition to introducing how naked antibodies and various antibody conjugates (such as antibody-drug conjugates, antibody-oligonucleotide conjugates, antibody-enzyme conjugates, etc.) work in therapeutic applications, special attention has been paid to how chemistry tools have helped to optimize the therapeutic outcome (i.e., with enhanced efficacy and reduced side effects) or facilitate the multifunctionalization of antibodies, with a focus on emerging fields such as targeted protein degradation, real-time live-cell imaging, catalytic labeling or decaging with spatiotemporal control as well as the engagement of antibodies inside cells. With advances in modern chemistry and biotechnology, well-designed antibodies and their derivatives via size miniaturization or multifunctionalization together with efficient delivery systems have emerged, which have gradually improved our understanding of important biological processes and paved the way to pursue novel targets for potential treatments of various diseases.

Click Bioconjugation - Modifying Proteins using Click-Like Chemistry

Bioconjugation is dealing with the chemical modification of proteins. The reactions used exploit either the intrinsic chemical reactivity of the biomolecule or introduce functionalities that can then be subsequently reacted without interfering with other functional groups of the biological entity. Perfectly selective, high yielding chemical transformations are needed that can be run in aqueous environment at mild pH conditions. Requirements that have an obvious overlap with the definition of click chemistry. This review shows a selection of successfully applied click-type reactions in bioconjugation as well as some recent developments to broaden the chemical toolbox to meet the challenge of a selective, bioorthogonal modification of biomolecules.

In vivo targeted delivery of antibodies into cancer cells with pH-responsive cell-penetrating poly(disulfide)s

Cell-penetrating poly(disulfide)s (CPDs) are promising vehicles for cytosolic delivery of proteins. However, currently available arginine-rich CPD has rarely been reported for systemic delivery due to its "always" positive charge. Herein, we developed pH-responsive CPDIMD that executes tumor targeting delivery via protonation of imidazole groups within the acidic tumor microenvironment.

Real-time imaging of cell-surface proteins with antibody-based fluorogenic probes

Cell-surface proteins, working as key agents in various diseases, are the targets for around 66% of approved human drugs. A general strategy to selectively detect these proteins in a real-time manner is expected to facilitate the development of new drugs and medical diagnoses. Although brilliant successes were attained using small-molecule probes, they could cover a narrow range of targets due to the lack of suitable ligands and some of them suffer from selectivity issues. We report herein an antibody-based fluorogenic probe prepared via a two-step chemical modification under physiological conditions, to fulfill the selective recognition and wash-free imaging of membrane proteins, establishing a modular strategy with broad implications for biochemical research and for therapeutics.

Herding cats: Label-based approaches in protein translocation through nanopore sensors for single-molecule protein sequence analysis

Proteins carry out life's essential functions. Comprehensive proteome analysis technologies are thus required for a full understanding of the operating principles of biological systems. While current proteomics techniques suffer from limitations in sensitivity and/or throughput, nanopore technology has the potential to enable de novo protein identification through single-molecule sequencing. However, a significant barrier to achieving this goal is controlling protein/peptide translocation through the nanopore sensor for processive strand analysis. Here, we review recent approaches that use a range of techniques, from oligonucleotide conjugation to molecular motors, aimed at driving protein strands and peptides through protein nanopores. We further discuss site-specific protein conjugation chemistry that could be combined with these translocation approaches as future directions to achieve single-molecule protein detection and sequencing of native proteins.

Intracellular delivery of therapeutic proteins through N-terminal site-specific modification

A versatile strategy for the intracellular delivery of functional proteins/antibodies was developed using N-terminal site-specific modification. Adopting orthogonal dual-labeling strategies, a cell-permeable RNase A prodrug was designed complementing N-terminal site-specific modification with lysine labeling. Upon successful cytosolic uptake, the prodrug showed reactive oxygen species (ROS)-dependent targeted cancer therapy.

Site-specific conjugation of native antibody

Traditionally, non-specific chemical conjugations, such as acylation of amines on lysine or alkylation of thiols on cysteines, are widely used; however, they have several shortcomings. First, the lack of site-specificity results in heterogeneous products and irreproducible processes. Second, potential modifications near the complementarity-determining region may reduce binding affinity and specificity. Conversely, site-specific methods produce well-defined and more homogenous antibody conjugates, ensuring developability and clinical applications. Moreover, several recent side-by-side comparisons of site-specific and stochastic methods have demonstrated that site-specific approaches are more likely to achieve their desired properties and functions, such as increased plasma stability, less variability in dose-dependent studies (particularly at low concentrations), enhanced binding efficiency, as well as increased tumor uptake. Herein, we review several standard and practical site-specific bioconjugation methods for native antibodies, i.e., those without recombinant engineering. First, chemo-enzymatic techniques, namely transglutaminase (TGase)-mediated transamidation of a conserved glutamine residue and glycan remodeling of a conserved asparagine N-glycan (GlyCLICK), both in the Fc region. Second, chemical approaches such as selective reduction of disulfides (ThioBridge) and N-terminal amine modifications. Furthermore, we list site-specific antibody–drug conjugates in clinical trials along with the future perspectives of these site-specific methods.

Targeting B7-H3 Immune Checkpoint With Chimeric Antigen Receptor-Engineered Natural Killer Cells Exhibits Potent Cytotoxicity Against Non-Small Cell Lung Cancer

Chimeric antigen receptor (CAR)-modified natural killer (NK) cell therapy represents a kind of promising anti-cancer treatment because CAR renders NK cells activation and recognition specificity toward tumor cells. An immune checkpoint molecule, B7-H3, plays an inhibitory role in modulation of NK cells. To enhance NK cell functions, we generated NK-92MI cells carrying anti-B7-H3 CAR by lentiviral transduction. The expression of anti-B7-H3 CAR significantly enhanced the cytotoxicity of NK-92MI cells against B7-H3-positive tumor cells. In accordance with enhanced cytotoxicity, the secretions of perforin/granzyme B and expression of CD107a were highly elevated in anti-B7-H3 CAR-NK-92MI cells. Moreover, compared to unmodified NK-92MI cells, anti-B7-H3 CAR-NK-92MI cells effectively limited tumor growth in mouse xenografts of non-small cell lung cancer and significantly prolonged the survival days of mice. This study provides the rationale and feasibility of B7-H3-specific CAR-NK cells for application in adoptive cancer immunotherapy.

Triazolecarbaldehyde Reagents for One-Step N-Terminal Protein Modification

Site-specific modification of peptides and proteins is a key aspect of protein engineering. We developed a method for modification of the N terminus of proteins using 1H-1,2,3-triazole-4-carbaldehyde (TA4C) derivatives, which can be prepared in one step. The N-terminal specific labeling of bioactive peptides and proteins with the TA4C derivatives proceeds under mild reaction conditions in excellent conversion (angiotensin I: 92 %, ribonuclease A: 90 %). This method enables site-specific conjugation of various functional molecules such as fluorophores, biotin, and polyethylene glycol attached to the triazole ring to the N terminus. Furthermore, a functional molecule modified with a primary amine moiety can be directly converted into a TA4C derivative through a Dimroth rearrangement reaction with 1-(4-nitrophenyl)-1H-1,2,3-triazole-4-carbaldehyde. This method can be used to obtain N-terminal-modified proteins via only two steps: 1) convenient preparation of a TA4C derivative with a functional group and 2) modification of the N terminus of the protein with the TA4C derivative.

Targeting immune checkpoint B7-H3 antibody-chlorin e6 bioconjugates for spectroscopic photoacoustic imaging and photodynamic therapy

In this study, we constructed bioconjugates of targeting immune checkpoint B7-H3 antibody and chlorin e6 to treat non-small cell lung cancer under the guidance of spectroscopic photoacoustic and fluorescence imaging. The B7-H3-Ce6 conjugates could display effective tumor diagnosis and therapy and provide a novel approach for immunotherapy.

Building Potent Chimeric Antigen Receptor T Cells With CRISPR Genome Editing

Chimeric antigen receptor (CAR) T cells have shown great promise in the treatment of hematological and solid malignancies. However, despite the success of this field, there remain some major challenges, including accelerated T cell exhaustion, potential toxicities, and insertional oncogenesis. To overcome these limitations, recent advances in CRISPR technology have enabled targetable interventions of endogenous genes in human CAR T cells. These CRISPR genome editing approaches have unleashed the therapeutic potential of CAR T cell therapy. Here, we summarize the potential benefits, safety concerns, and difficulties in the generation of gene-edited CAR T cells using CRISPR technology.

Array of multifunctional polymers for localized immobilization of biomolecules on microarray substrates

The performance of microarray assays results from the optimization of several parameters: in particular, the physical-chemical properties of the surface play a pivotal role in determining the robustness of the technology. Usually, microarray substrates are entirely modified with coatings able to bind, covalently or not, bioprobes. Here we present a new, fully automated approach for the immobilization of biomolecules, based on the deposition of pL amounts of water solutions of DMA based copolymers on an uncoated surface, followed by the deposition, on the same spot, of the probe. Starting from a common precursor, polymers with different characteristics and functionalities are obtained by post-polymerization modification and by combining different monomers during the synthesis. This strategy, allows to functionalize and tailor the surface properties of discrete areas of the same array with different chemistries, that coexist on a single substrate. As a consequence, probes with different functionalities are bound simultaneously to neutral, positively, negatively charged, hydrophobic, hydrophilic polymers, in micrometer-sized spots. The proposed polymer array, applicable to both DNA or protein, offers advantages in terms of time and costs reduction, since pretreatment and coating steps are totally avoided, and the requested polymer amount is extremely low. Moreover, it provides a strategy perfectly suitable for miniaturization applicable to integrated biosensors or Lab-on-a-chip devices.

pH-sensitive loaded retinal/indocyanine green micelles as an “all-in-one” theranostic agent for multi-modal imaging in vivo guided cellular senescence-photothermal synergistic therapy

pH-sensitive loaded retinal/indocyanine green (ICG) micelles were developed for cellular senescence-photothermal synergistic therapy.