Antibody mimetics: promising complementary agents to animal-sourced antibodies

Comprehensive approaches to preclinical evaluation of monoclonal antibodies and their next-generation derivatives

Biotherapeutics hold great promise for the treatment of several diseases and offer innovative possibilities for new treatments that target previously unaddressed medical needs. Despite successful transitions from preclinical to clinical stages and regulatory approval, there are instances where adverse reactions arise, resulting in product withdrawals. As a result, it is essential to conduct thorough evaluations of safety and effectiveness on an individual basis. This article explores current practices, challenges, and future approaches in conducting comprehensive preclinical assessments to ensure the safety and efficacy of biotherapeutics including monoclonal antibodies, toxin-conjugates, bispecific antibodies, single-chain antibodies, Fc-engineered antibodies, antibody mimetics, and siRNA-antibody/peptide conjugates.

Chimerism of avian IgY-scFv and truncated IgG-Fc: A novel strategy in cross-species antibody generation and enhancement

Chicken single-chain fragment variable (IgY-scFv) is a functional fragment and an emerging development in genetically engineered antibodies with a wide range of biomedical applications. However, scFvs have considerably shorter serum half-life due to the absence of antibody Fc region compared with the full-length antibody, and usually requires continuous intravenous administration for efficacy. A promising approach to overcome this limitation is to fuse scFv with immunoglobulin G (IgG) Fc region, for better recognition and mediation by the neonatal Fc receptor (FcRn) in the host. In this study, engineered mammalian ΔFc domains (CH2, CH3, and intact Fc region) were fused with anti-canine parvovirus-like particles avian IgY-scFv to produce chimeric antibodies and expressed in the HEK293 cell expression system. The obtained scFv-CH2, scFv-CH3, and scFv-Fc can bind with antigen specifically and dose-dependently. Surface plasmon resonance investigation confirmed that scFv-CH2, scFv-CH3, and scFv-Fc had different degrees of binding to FcRn, with scFv-Fc showing the highest affinity. scFv-Fc had a significantly longer half-life in mice compared with the unfused scFv. The identified ΔFcs are promising for the development of engineered Fc-based therapeutic antibodies and proteins with longer half-lives. The avian IgY-scFv-mammalian IgG Fc region opens up new avenues for antibody engineering, and it is a novel strategy to enhance the rapid development and screening of functional antibodies in veterinary and human medicine.

Antibody mimetics: The next generation antibody engineering, a retrospective and prospective analysis

Antibody mimetics represent the fourth generation of antibody engineering, following polyclonal antibodies, monoclonal antibodies, and genetically engineered antibody fragments. Despite cumulative studies highlighting the advantages of antibody mimetics, including enhanced recognition properties, superior affinity, stability, penetrability, and cost-effectiveness, a comprehensive review of this evolving field is notably absent. In this study, spanning 1986-2023 and analyzing 24,318 publications, we undertake a retrospective and prospective analysis to elucidate the evolution roadmap of antibody mimetics, providing insights into the current landscape, global contributions, and future trajectories. Concurrently, our aim is to establish standardized terminology and delineate the research scope within the realm of antibody mimetics. These endeavors not only chart the trajectory and scope of antibody mimetics research but also underscore its potential to revolutionize medicine, technology, and science.

Paper-based multiplex biosensors for inexpensive healthcare diagnostics: a comprehensive review

Multiplex detection is a smart and an emerging approach in point-of-care testing as it reduces analysis time and testing cost by detecting multiple analytes or biomarkers simultaneously which are crucial for disease detection at an early stage. Application of inexpensive substrate such as paper has immense potential and matter of research interest in the area of point of care testing for multiplexed analysis as it possesses several unique advantages. This study presents the use of paper, strategies adopted to refine the design created on paper and lateral flow strips to enhance the signal, increase the sensitivity and specificity of multiplexed biosensors. An overview of different multiplexed detection studies performed using biological samples has also been reviewed along with the challenges and advantages offered by multiplexed analysis.

Specific anti-SARS-CoV-2 S1 IgY-scFv is a promising tool for recognition of the virus

As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread globally, a series of vaccines, antibodies and drugs have been developed to combat coronavirus disease 2019 (COVID-19). High specific antibodies are powerful tool for the development of immunoassay and providing passive immunotherapy against SARS-CoV-2 and expected with large scale production. SARS-CoV-2 S1 protein was expressed in E. coli BL21 and purified by immobilized metal affinity chromatography, as antigen used to immunize hens, the specific IgY antibodies were extracted form egg yolk by PEG-6000 precipitation, and the titer of anti-S1 IgY antibody reached 1:10,000. IgY single chain variable fragment antibody (IgY-scFv) was generated by using phage display technology and the IgY-scFv showed high binding sensitivity and capacity to S1 protein of SARS-CoV-2, and the minimum detectable antigen S1 protein concentration was 6 ng/µL. The docking study showed that the multiple epitopes on the IgY-scFv interacted with multiple residues on SARS-CoV-2 S1 RBD to form hydrogen bonds. This preliminary study suggests that IgY and IgY-scFv are suitable candidates for the development of immunoassay and passive immunotherapy for COVID-19 to humans and animals.

The mosaic puzzle of the therapeutic monoclonal antibodies and antibody fragments - A modular transition from full-length immunoglobulins to antibody mimetics

The use of monoclonal antibodies represents an important and efficient diagnostic and therapeutic tool in disease management and modern science but remains limited by several factors including the uneven distribution in diseased tissues as well as undesired activation of side immune reactions. Major scientific advancements including Recombinant DNA Technology, Hybridoma Technology, and Polymerase Chain Reaction have considerably impacted the use of monoclonal antibodies providing technical and effective solutions to overcome the shortcomings encountered with conventional antibodies. Initially, the introduction of antibody fragments allowed a more uniform and deeper penetration of the targeted tissue and reduced unwanted activation of Fc-mediated immune reactions. On another level, the immunogenicity of murine-derived antibodies was overcome by humanizing their encoding genes with specific sequences of human origin andtransgenic mice able to synthesize fully human antibodies were successfully created. Moreover, the advancement of genetic engineering techniques supported by the modular structure of antibody coding genes paved the way for the development of a new generation of antibody fragments with a wide spectrum of monospecific and bispecific agents. These later could be monovalent, bivalent, or multivalent, and either expressed as a single chain, assembled in multimeric forms or stringed in tandem. This has conferred improved affinity, stability, and solubility to antibody targetting. Lately, a new array of monoclonal antibody fragments was introduced with the engineering of nanobody and antibody mimetics as non-immunoglobulin-derived fragments with promising diagnostic and therapeutic applications. In this review, we decipher the molecular basis of monoclonal antibody engineering with a detailed screening of the antibody derivatives that provides new perspectives to expand the use of monoclonal fragments into previously unexplored fields.

Development of an Enzyme-Inhibitor Reaction Using Cellular Retinoic Acid Binding Protein II for One-Pot Megamolecule Assembly

This paper presents an enzyme building block for the assembly of megamolecules. The system is based on the inhibition of the human-derived cellular retinoic acid binding protein II (CRABP2) domain. We synthesized a synthetic retinoid bearing an arylfluorosulfate group, which uses sulfur fluoride exchange click chemistry to covalently inhibit CRABP2. We conjugated both the inhibitor and a fluorescein tag to an oligo(ethylene glycol) backbone and measured a second-order rate constant for the protein inhibition reaction of approximately 3,600 M^-1 s^-1 . We used this new enzyme-inhibitor pair to assemble multi-protein structures in one-pot reactions using three orthogonal assembly chemistries to demonstrate exact control over the placement of protein domains within a single, homogeneous molecule. This work enables a new dimension of control over specificity, orientation, and stoichiometry of protein domains within atomically precise nanostructures.

Extending traditional antibody therapies: Novel discoveries in immunotherapy and clinical applications

Immunotherapy has been well regarded as one of the safer and antigen-specific anti-cancer treatments compared to first-generation chemotherapy. Since Coley's discovery, researchers focused on engineering novel antibody-based therapies. Including artificial and modified antibodies, such as antibody fragments, antibody-drug conjugates, and synthetic mimetics, the variety of immunotherapy has been rapidly expanding in the last few decades. Genetic and chemical modifications to monoclonal antibody have been brought into academia, in vivo trials, and clinical applications. Here, we have looked around antibodies overall. First, we elucidate the antibody structure and its cytotoxicity mechanisms. Second, types of therapeutic antibodies are presented. Additionally, there is a summarized list of US Food and Drug Administration (FDA)-approved therapeutic antibodies and recent clinical trials. This review provides a comprehensive overview of both the general function of therapeutic antibodies and a few main variations in development, including recent advent with the proposed mechanism of actions, and we introduce types of therapeutic antibodies, clinical trials, and approved commercial immunotherapeutic drugs.

Generation and evaluation of IgY-scFv based mimetics against canine parvovirus

Antibody mimetics may be used for various biomedical applications, especially those for which conventional antibodies are ineffective. In this study, we developed a smaller molecular chicken IgY mimetic peptide (IgY-peptide) based on the complementarity-determining regions (CDRs) of the anti-canine parvovirus (CPV) IgY-scFv prepared previously. The mimetic peptide showed no cross-reactivity with canine distemper virus (CDV) and canine coronavirus (CCV) and showed excellent protective properties for Crandell-Rees Feline Kidney (CRFK) cells against CPV. This study is the first attempt to develop a mimetic IgY-peptide and demonstrates the ease and feasibility in generating such a novel antibody-like functional molecule for biomedical purposes.

Therapeutic potential of HIV-1 entry inhibitor peptidomimetics

Human immunodeficiency virus 1 (HIV-1) infection remains a public health concern globally. Although great strides in the management of HIV-1 have been achieved, current highly active antiretroviral therapy is limited by multidrug resistance, prolonged use-related effects, and inability to purge the HIV-1 latent pool. Even though novel therapeutic options with HIV-1 broadly neutralizing antibodies (bNAbs) are being explored, the scalability of bNAbs is limited by economic cost of production and obligatory requirement for parenteral administration. However, these limitations can be addressed by antibody mimetics/peptidomimetics of HIV-1 bNAbs. In this review we discuss the limitations of HIV-1 bNAbs as HIV-1 entry inhibitors and explore the potential therapeutic use of antibody mimetics/peptidomimetics of HIV-1 entry inhibitors as an alternative for HIV-1 bNAbs. We highlight the reduced cost of production, high specificity, and oral bioavailability of peptidomimetics compared to bNAbs to demonstrate their suitability as candidates for novel HIV-1 therapy and conclude with some perspectives on future research toward HIV-1 novel drug discovery.

Reconstitution of an Anti-HER2 Antibody Paratope by Grafting Dual CDR-Derived Peptides onto a Small Protein Scaffold

Target-binding small proteins are promising alternatives to conventional monoclonal antibodies (mAbs), offering advantages in terms of tissue penetration and manufacturing costs. Recently, a design strategy to create small proteins called fluctuation-regulated affinity proteins (FLAPs) consisting of a structurally immobilized peptide from the complementarity-determining region (CDR) loops of mAbs (CDR-derived peptide) and a protein scaffold was developed. Because mAb paratopes are usually composed of multiple CDRs, FLAPs with multiple binding peptides may have an enhanced target-binding capability. Here, a strategy to create FLAPs bearing dual CDR-derived peptides (D-FLAPs) using the anti-human epithelial growth factor receptor type 2 (HER2) mAb trastuzumab as a basis is developed. Computationally selected CDR-derived peptides are first grafted onto two adjacent loops of the fibronectin type III domain (FN3) scaffold, yielding 80 D-FLAP candidates. After computational screening based on their similarity to the parental mAb with regard to the conformation of paratope residues, two candidates are selected. After further evaluation with ELISA, one D-FLAP with HYTTPP and GDGFYA peptides from CDR-L3 and CDR-H3 of the parental mAb, respectively, is found to bind HER2 with a dissociation constant of 58 nm. This method applies to various mAb drugs and allows the rational design of small protein alternatives.

Derivative of Extremophilic 50S Ribosomal Protein L35Ae as an Alternative Protein Scaffold

Small antibody mimetics, or alternative binding proteins (ABPs), extend and complement antibody functionality with numerous applications in research, diagnostics and therapeutics. Given the superiority of ABPs, the last two decades have witnessed development of dozens of alternative protein scaffolds (APSs) for the design of ABPs. Proteins from extremophiles with their high structural stability are especially favorable for APS design. Here, a 10X mutant of the 50S ribosomal protein L35Ae from hyperthermophilic archaea Pyrococcus horikoshii has been probed as an APS. A phage display library of L35Ae 10X was generated by randomization of its three CDR-like loop regions (repertoire size of 2×108). Two L35Ae 10X variants specific to a model target, the hen egg-white lysozyme (HEL), were isolated from the resulting library using phage display. The affinity of these variants (L4 and L7) to HEL ranges from 0.10 μM to 1.6 μM, according to surface plasmon resonance data. While L4 has 1-2 orders of magnitude lower affinity to HEL homologue, bovine α-lactalbumin (BLA), L7 is equally specific to HEL and BLA. The reference L35Ae 10X is non-specific to both HEL and BLA. L4 and L7 are more resistant to denaturation by guanidine hydrochloride compared to the reference L35Ae 10X (mid-transition concentration is higher by 0.1-0.5 M). Chemical crosslinking experiments reveal an increased propensity of L4 and L7 to multimerization. Overall, the CDR-like loop regions of L35Ae 10X represent a proper interface for generation of functional ABPs. Hence, L35Ae is shown to extend the growing family of protein scaffolds dedicated to the design of novel binding proteins.

Extremophilic 50S Ribosomal RNA-Binding Protein L35Ae as a Basis for Engineering of an Alternative Protein Scaffold

Due to their remarkably high structural stability, proteins from extremophiles are particularly useful in numerous biological applications. Their utility as alternative protein scaffolds could be especially valuable in small antibody mimetic engineering. These artificial binding proteins occupy a specific niche between antibodies and low molecular weight substances, paving the way for development of innovative approaches in therapeutics, diagnostics, and reagent use. Here, the 50S ribosomal RNA-binding protein L35Ae from the extremophilic archaea Pyrococcus horikoshii has been probed for its potential to serve as a backbone in alternative scaffold engineering. The recombinant wild type L35Ae has a native-like secondary structure, extreme thermal stability (mid-transition temperature of 90°C) and a moderate resistance to the denaturation by guanidine hydrochloride (half-transition at 2.6 M). Chemical crosslinking and dynamic light scattering data revealed that the wild type L35Ae protein has a propensity for multimerization and aggregation correlating with its non-specific binding to a model cell surface of HEK293 cells, as evidenced by flow cytometry. To suppress these negative features, a 10-amino acid mutant (called L35Ae 10X) was designed, which lacks the interaction with HEK293 cells, is less susceptible to aggregation, and maintains native-like secondary structure and thermal stability. However, L35Ae 10X also shows lowered resistance to guanidine hydrochloride (half-transition at 2.0M) and is more prone to oligomerization. This investigation of an extremophile protein’s scaffolding potential demonstrates that lowered resistance to charged chemical denaturants and increased propensity to multimerization may limit the utility of extremophile proteins as alternative scaffolds.