Tailoring Site Specificity of Bioconjugation Using Step-Wise Atom-Transfer Radical Polymerization on Proteins

Artificial Zymogen Based on Protein-Polymer Hybrids

This study explores the synthesis and application of artificial zymogens using protein-polymer hybrids to mimic the controlled enzyme activation observed in natural zymogens. Pro-trypsin (pro-TR) and pro-chymotrypsin (pro-CT) hybrids were engineered by modifying the surfaces of trypsin (TR) and chymotrypsin (CT) with cleavable peptide inhibitors utilizing surface-initiated atom transfer radical polymerization. These hybrids exhibited 70 and 90% reductions in catalytic efficiency for pro-TR and pro-CT, respectively, due to the inhibitory effect of the grafted peptide inhibitors. The activation of pro-TR by CT and pro-CT by TR resulted in 1.5- and 2.5-fold increases in enzymatic activity, respectively. Furthermore, the activated hybrids triggered an enzyme activation cascade, enabling amplification of activity through a dual pro-protease hybrid system. This study highlights the potential of artificial zymogens for therapeutic interventions and biodetection platforms by harnessing enzyme activation cascades for precise control of catalytic activity.

Sequence-encoded bioactive protein-multiblock polymer conjugates via quantitative one-pot iterative living polymerization

Protein therapeutics are essential in treating various diseases, but their inherent biological instability and short circulatory half-lives in vivo pose challenges. Herein, a quantitative one-pot iterative living polymerization technique is reported towards precision control over the molecular structure and monomer sequence of protein-polymer conjugates, aiming to maximize physicochemical properties and biological functions of proteins. Using this quantitative one-pot iterative living polymerization technique, we successfully develop a series of sequence-controlled protein-multiblock polymer conjugates, enhancing their biostability, pharmacokinetics, cellular uptake, and in vivo biodistribution. All-atom molecular dynamics simulations are performed to disclose the definite sequence-function relationship of the bioconjugates, further demonstrating their sequence-encoded cellular uptake behavior and in vivo biodistribution in mice. Overall, this work provides a robust approach for creating precision protein-polymer conjugates with defined sequences and advanced functions as a promising candidate in disease treatment.

Aqueous photo-RAFT polymerization under ambient conditions: synthesis of protein-polymer hybrids in open air

A photoinduced reversible addition-fragmentation chain-transfer (photo-RAFT) polymerization technique in the presence of sodium pyruvate (SP) and pyruvic acid derivatives was developed. Depending on the wavelength of light used, SP acted as a biocompatible photoinitiator or promoter for polymerization, allowing rapid open-to-air polymerization in aqueous media. Under UV irradiation (370 nm), SP decomposes to generate CO2 and radicals, initiating polymerization. Under blue (450 nm) or green (525 nm) irradiation, SP enhances the polymerization rate via interaction with the excited state RAFT agent. This method enabled the polymerization of a range of hydrophilic monomers in reaction volumes up to 250 mL, eliminating the need to remove radical inhibitors from the monomers. In addition, photo-RAFT polymerization using SP allowed for the facile synthesis of protein-polymer hybrids in short reaction times (<1 h), low organic content (≤16%), and without rigorous deoxygenation and the use of transition metal photocatalysts. Enzymatic studies of a model protein (chymotrypsin) showed that despite a significant loss of protein activity after conjugation with RAFT chain transfer agents, the grafting polymers from proteins resulted in a 3-4-fold recovery of protein activity.

Tailored Branched Polymer-Protein Bioconjugates for Tunable Sieving Performance

Protein-polymer conjugates combine the unique properties of both proteins and synthetic polymers, making them important materials for biomedical applications. In this work, we synthesized and characterized protein-branched polymer bioconjugates that were precisely designed to retain protein functionality while preventing unwanted interactions. Using chymotrypsin as a model protein, we employed a controlled radical branching polymerization (CRBP) technique utilizing a water-soluble inibramer, sodium 2-bromoacrylate. The green-light-induced atom transfer radical polymerization (ATRP) enabled the grafting of branched polymers directly from the protein surface in the open air. The resulting bioconjugates exhibited a predetermined molecular weight, well-defined architecture, and high branching density. Conformational analysis by SEC-MALS validated the controlled grafting of branched polymers. Furthermore, enzymatic assays revealed that densely grafted polymers prevented protein inhibitor penetration, and the resulting conjugates retained up to 90% of their enzymatic activity. This study demonstrates a promising strategy for designing protein-polymer bioconjugates with tunable sieving behavior, opening avenues for applications in drug delivery and biotechnology.

Integrating Enzymes with Supramolecular Polymers for Recyclable Photobiocatalytic Catalysis

Chemical modifications of enzymes excel in the realm of enzyme engineering due to its directness, robustness, and efficiency; however, challenges persist in devising versatile and effective strategies. In this study, we introduce a supramolecular modification methodology that amalgamates a supramolecular polymer with Candida antarctica lipase B (CalB) to create supramolecular enzymes (SupEnzyme). This approach features the straightforward preparation of a supramolecular amphiphilic polymer (β-CD@SMA), which was subsequently conjugated to the enzyme, resulting in a SupEnzyme capable of self-assembly into supramolecular nanoparticles. The resulting SupEnzyme nanoparticles can form micron-scale supramolecular aggregates through supramolecular and electrostatic interactions with guest entities, thus enhancing catalyst recycling. Remarkably, these aggregates maintain 80 % activity after seven cycles, outperforming Novozym 435. Additionally, they can effectively initiate photobiocatalytic cascade reactions using guest photocatalysts. As a consequence, our SupEnzyme methodology exhibits noteworthy adaptability in enzyme modification, presenting a versatile platform for various polymer, enzyme, and biocompatible catalyst pairings, with potential applications in the fields of chemistry and biology.

Molecular Dynamics Simulations for Rationalizing Polymer Bioconjugation Strategies: Challenges, Recent Developments, and Future Opportunities

The covalent modification of proteins with polymers is a well-established method for improving the pharmacokinetic properties of therapeutically valuable biologics. The conjugated polymer chains of the resulting hybrid represent highly flexible macromolecular structures. As the dynamics of such systems remain rather elusive for established experimental techniques from the field of protein structure elucidation, molecular dynamics simulations have proven as a valuable tool for studying such conjugates at an atomistic level, thereby complementing experimental studies. With a focus on new developments, this review aims to provide researchers from the polymer bioconjugation field with a concise and up to date overview of such approaches. After introducing basic principles of molecular dynamics simulations, as well as methods for and potential pitfalls in modeling bioconjugates, the review illustrates how these computational techniques have contributed to the understanding of bioconjugates and bioconjugation strategies in the recent past and how they may lead to a more rational design of novel bioconjugates in the future.

Design and Application of Hybrid Polymer-Protein Systems in Cancer Therapy

Polymer-protein systems have excellent characteristics, such as non-toxic, non-irritating, good water solubility and biocompatibility, which makes them very appealing as cancer therapeutics agents. Inspiringly, they can achieve sustained release and targeted delivery of drugs, greatly improving the effect of cancer therapy and reducing side effects. However, many challenges, such as reducing the toxicity of materials, protecting the activities of proteins and controlling the release of proteins, still need to be overcome. In this review, the design of hybrid polymer-protein systems, including the selection of polymers and the bonding forms of polymer-protein systems, is presented. Meanwhile, vital considerations, including reaction conditions and the release of proteins in the design process, are addressed. Then, hybrid polymer-protein systems developed in the past decades for cancer therapy, including targeted therapy, gene therapy, phototherapy, immunotherapy and vaccine therapy, are summarized. Furthermore, challenges for the hybrid polymer-protein systems in cancer therapy are exemplified, and the perspectives of the field are covered.

Moving Protein PEGylation from an Art to a Data Science

PEGylation is a well-established and clinically proven half-life extension strategy for protein delivery. Protein modification with amine-reactive poly(ethylene glycol) (PEG) generates heterogeneous and complex bioconjugate mixtures, often composed of several PEG positional isomers with varied therapeutic efficacy. Laborious and costly experiments for reaction optimization and purification are needed to generate a therapeutically useful PEG conjugate. Kinetic models which accurately predict the outcome of so-called “random” PEGylation reactions provide an opportunity to bypass extensive wet lab experimentation and streamline the bioconjugation process. In this study, we propose a protein tertiary structure-dependent reactivity model that describes the rate of protein-amine PEGylation and introduces “PEG chain coverage” as a tangible metric to assess the shielding effect of PEG chains. This structure-dependent reactivity model was implemented into three models (linear, structure-based, and machine-learned) to gain insight into how protein-specific molecular descriptors (exposed surface areas, pK_a, and surface charge) impacted amine reactivity at each site. Linear and machine-learned models demonstrated over 75% prediction accuracy with butylcholinesterase. Model validation with Somavert, PEGASYS, and phenylalanine ammonia lyase showed good correlation between predicted and experimentally determined degrees of modification. Our structure-dependent reactivity model was also able to simulate PEGylation progress curves and estimate “PEGmer” distribution with accurate predictions across different proteins, PEG linker chemistry, and PEG molecular weights. Moreover, in-depth analysis of these simulated reaction curves highlighted possible PEG conformational transitions (from dumbbell to brush) on the surface of lysozyme, as a function of PEG molecular weight.

Hydrolytically Stable Maleimide-End-Functionalized Polymers for Site-Specific Protein Conjugation

Site-specific conjugation to cysteines of proteins often uses ester groups to link maleimide or alkene groups to polymers. However, the ester group is susceptible to hydrolysis, potentially losing the benefits gained through bioconjugation. Here, we present a simple conjugation strategy that utilizes the amide bond stability of traditional 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide/N-hydroxysuccinimide coupling while introducing site specificity. Hydrolytically stable maleimide-end-functionalized polymers for site-specific conjugation to free cysteines of proteins were synthesized using reversible addition-fragmentation chain-transfer (RAFT) polymerization. The alpha terminus of the polymers was amidated with a furan-protected aminoethyl maleimide using carbodiimide-based chemistry. Finally, the maleimide was exposed by a retro Diels-Alder reaction to yield the maleimide group, allowing for thiol-maleimide click chemistry for bioconjugation. A thermophilic cellulase from Fervidobacterium nodosum (FnCel5a) was conjugated using various strategies, including random 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC)/N-hydroxysuccinimide (NHS) coupling, site-specific hydroxyethyl maleimide (HEMI) end-functionalized coupling, hydroxyethyl acrylate (HEA) end-functionalized coupling, and amidoethyl maleimide (AEMI) end-functionalized coupling. Only the polymers conjugated by EDC and AEMI remained conjugated a week after attachment. This indicates that hydrolytically stable amide-based maleimides are an important bioconjugation strategy for conjugates that require long-term stability, while esters are better suited for systems that require debonding of polymers over time.

A comprehensive analysis in one run - in-depth conformation studies of protein-polymer chimeras by asymmetrical flow field-flow fractionation

Polymer-based protein engineering has enabled the synthesis of a variety of protein-polymer conjugates that are widely applicable in therapeutic, diagnostic and biotechnological industries. Accurate characterizations of physical-chemical properties, in particular, molar masses, sizes, composition and their dispersities are critical parameters that determine the functionality and conformation of protein-polymer conjugates and are important for creating reproducible manufacturing processes. Most of the current characterization techniques suffer from fundamental limitations and do not provide an accurate understanding of a sample's true nature. In this paper, we demonstrate the advantage of asymmetrical flow field-flow fractionation (AF4) coupled with multiple detectors for the characterization of a library of complex, zwitterionic and neutral protein-polymer conjugates. This method allows for determination of intrinsic physical properties of protein-polymer chimeras from a single, rapid measurement.

Nanohybrids as Protein-Polymer Conjugate Multimodal Therapeutics

Protein therapeutic formulations are being widely explored as multifunctional nanotherapeutics. Challenges in ensuring susceptibility and efficacy of nanoformulation still prevail owing to various interactions with biological fluids before reaching the target site. Smart polymers with the capability of masking drugs, ease of chemical modification, and multi-stimuli responsiveness can assist controlled delivery. An active moiety like therapeutic protein has started to be known as an important biological formulation with a diverse medicinal prospect. The delivery of proteins and peptides with high target specificity has however been tedious, due to their tendency to aggregate formation in different environmental conditions. Proteins due to high chemical reactivity and poor bioavailability are being researched widely in the field of nanomedicine. Clinically, multiple nano-based formulations have been explored for delivering protein with different carrier systems. A biocompatible and non-toxic polymer-based delivery system serves to tailor the polymer or drug better. Polymers not only aid delivery to the target site but are also responsible for proper stearic orientation of proteins thus protecting them from internal hindrances. Polymers have been shown to conjugate with proteins through covalent linkage rendering stability and enhancing therapeutic efficacy prominently when dealing with the systemic route. Here, we present the recent developments in polymer-protein/drug-linked systems. We aim to address questions by assessing the properties of the conjugate system and optimized delivery approaches. Since thorough characterization is the key aspect for technology to enter into the market, correlating laboratory research with commercially available formulations will also be presented in this review. By examining characteristics including morphology, surface properties, and functionalization, we will expand different hybrid applications from a biomaterial stance applied in in vivo complex biological conditions. Further, we explore understanding related to design criteria and strategies for polymer-protein smart nanomedicines with their potential prophylactic theranostic applications. Overall, we intend to highlight protein-drug delivery through multifunctional smart polymers.

Self-assembly of protein-polymer conjugates for drug delivery

Protein-polymer conjugates are a class of molecules that combine the stability of polymers with the diversity, specificity, and functionality of biomolecules. These bioconjugates can result in hybrid materials that display properties not found in their individual components and can be particularly relevant for drug delivery applications. Engineering amphiphilicity into these bioconjugate materials can lead to phase separation and the assembly of high-order structures. The assembly, termed self-assembly, of these hierarchical structures entails multiple levels of organization: at each level, new properties emerge, which are, in turn, influenced by lower levels. Here, we provide a critical review of protein-polymer conjugate self-assembly and how these materials can be used for therapeutic applications and drug delivery. In addition, we discuss central bioconjugate design questions and propose future perspectives for the field of protein-polymer conjugate self-assembly.

Dealing with the complexity of conjugated and self-assembled polymer-nanostructures using field-flow fractionation

Broad diversity and heterogeneity are inherently showcased by both natural and synthetic macromolecular structures. The high application potential for such structures and their combinations calls for novel analytical approaches that allow for comprehensive characterization and a full understanding of their complex composition. This review gives an overview of recent advances in designing and fabricating bioconjugated and self-assembled polymer structures, and introduces adequate characterization protocols for sufficient elucidation of their specific molecular properties. Possible pitfalls in their analysis are demonstrated, and potential alternatives are discussed. The primary focus is on addressing the highlights, and future prospects of applying field-flow fractionation coupled and/or hyphenated to different detection methods as a powerful separation and analytical technique for bioconjugate and self-assembled nanostructures.

Atom Transfer Radical Polymerization for Biorelated Hybrid Materials

Proteins, nucleic acids, lipid vesicles, and carbohydrates are the major classes of biomacromolecules that function to sustain life. Biology also uses post-translation modification to increase the diversity and functionality of these materials, which has inspired attaching various other types of polymers to biomacromolecules. These polymers can be naturally (carbohydrates and biomimetic polymers) or synthetically derived and have unique properties with tunable architectures. Polymers are either grafted-to or grown-from the biomacromolecule's surface, and characteristics including polymer molar mass, grafting density, and degree of branching can be controlled by changing reaction stoichiometries. The resultant conjugated products display a chimerism of properties such as polymer-induced enhancement in stability with maintained bioactivity, and while polymers are most often conjugated to proteins, they are starting to be attached to nucleic acids and lipid membranes (cells) as well. The fundamental studies with protein-polymer conjugates have improved our synthetic approaches, characterization techniques, and understanding of structure-function relationships that will lay the groundwork for creating new conjugated biomacromolecular products which could lead to breakthroughs in genetic and tissue engineering.

Transforming protein-polymer conjugate purification by tuning protein solubility

Almost all commercial proteins are purified using ammonium sulfate precipitation. Protein-polymer conjugates are synthesized from pure starting materials, and the struggle to separate conjugates from polymer, native protein, and from isomers has vexed scientists for decades. We have discovered that covalent polymer attachment has a transformational effect on protein solubility in salt solutions. Here, protein-polymer conjugates with a variety of polymers, grafting densities, and polymer lengths are generated using atom transfer radical polymerization. Charged polymers increase conjugate solubility in ammonium sulfate and completely prevent precipitation even at 100% saturation. Atomistic molecular dynamic simulations show the impact is driven by an anti-polyelectrolyte effect from zwitterionic polymers. Uncharged polymers exhibit polymer length-dependent decreased solubility. The differences in salting-out are then used to simply purify mixtures of conjugates and native proteins into single species. Increasing protein solubility in salt solutions through polymer conjugation could lead to many new applications of protein-polymer conjugates.