Polymer-enhanced biomacromolecules

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.

Glycerol- and diglycerol-based polyesters: Evaluation of backbone alterations upon nano-formulation performance

Despite the success of polyethylene glycol-based (PEGylated) polyesters in the drug delivery and biomedical fields, concerns have arisen regarding PEG's immunogenicity and limited biodegradability. In addition, inherent limitations, including limited chemical handles as well as highly hydrophobic nature, can restrict their effectiveness in physiological conditions of the polyester counterpart. To address these matters, an increasing amount of research has been focused towards identifying alternatives to PEG. One promising strategy involves the use of bio-derived polyols, such as glycerol. In particular, glycerol is a hydrophilic, non-toxic, untapped waste resource and as other polyols, can be incorporated into polyesters via enzymatic catalysis routes. In the present study, a systematic screening is conducted focusing on the incorporation of 1,6-hexanediol (Hex) (hydrophobic diol) into both poly(glycerol adipate) (PGA) and poly(diglycerol adipate) (PDGA) at different (di)glycerol:hex ratios (30:70; 50:50 and 70:30 mol/mol) and its effect on purification upon NPs formation. By varying the amphiphilicity of the backbone, we demonstrated that minor adjustments influence the NPs formation, NPs stability, drug encapsulation, and degradation of these polymers, despite the high chemical similarity. Moreover, the best performing materials have shown good biocompatibility in both in vitro and in vivo (whole organism) tests. As preliminary result, the sample containing diglycerol and Hex in a 70:30 ratio, named as PDGA-Hex 30%, has shown to be the most promising candidate in this small library analysed. It demonstrated comparable stability to the glycerol-based samples in various media but exhibited superior encapsulation efficiency of a model hydrophobic dye. This in-depth investigation provides new insights into the design and modification of biodegradable (di)glycerol-based polyesters, potentially paving the way for more effective and sustainable PEG-free drug delivery nano-systems in the pharmaceutical and biomedical fields.

Ribonuclease A-polymer conjugates via in situ growth for cancer treatment

Efficient delivery of therapeutic proteins is a critical aspect for protein-based cancer treatment. Herein, an in situ growth approach was employed to prepare ribonuclease A (RNase A)-polymer conjugates by incorporating a cationic polymer, poly(N,N'-dimethylamino-2-ethyl methacrylate) (P(DMAEMA)), and a hydrophobic polymer, poly(N-isopropylacrylamide) (P(NIPAM)), through atom transfer radical polymerization (ATRP). The synthesized RNase A-polymer conjugates (namely R-P(D-b-N)) could preserve the integrity of RNase A and exhibit a unique combination of cationic and hydrophobic properties, leading to enhanced intracellular delivery efficiency. The successful delivery of RNase A by R-P(D-b-N) conjugates effectively triggered the cell apoptosis through the mitochondria-dependent signaling pathway to achieve the anti-proliferative response. Additionally, the conjugates could inhibit cell migration and thus possess the potential for the suppression of tumor metastasis. Overall, our findings highlight that the introduction of cationic and hydrophobic moieties via ATRP provides a versatile platform for the intracellular delivery of therapeutic proteins, offering a new avenue for treating diverse diseases.

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.

Construction of molecular enrichment accelerators via assembly of enzyme surface grafted polymer and cyclodextrin achieving rapid and stable ester catalysis for biodiesel synthesis

Efficient and stable catalysis has always been the core concept of enzyme catalysis in industrial processes for manufacturing. Here, we constructed molecular enrichment accelerators to synergistically enhance enzyme activity and stability by assembling enzyme surface grafted polymer and cyclodextrin. At 40 °C, the enzyme activity of CalB-PNIPAM212/β-CD was 2.9 times that of CalB-PNIPAM212. The enzyme activity of CalB-PNIPAM428/γ-CD had reached 1.61 times that of CalB. At the same time, the stability of CalB-PNIPAM212/β-CD and CalB-PNIPAM428/γ-CD are slightly better than that of CalB under high temperature, organic solution and extreme pH conditions. The synergistic increase in activity and stability of the lipase-polymer assembly was achieved due to the structure of assembly, in which the role of cyclodextrin could enrich substrate affecting molecular diffusion. In addition, the lipase-polymer assembly proved to be an efficient catalyst for biodiesel synthesis, with a biodiesel conversion 1.4 times that of CalB at 60 °C. Therefore, this simple and low-cost lipase-polymer assembly provides new possibilities for the construction of high-efficiency industrial biocatalytic catalysts.

Molecular Sieving with PEGylated Dendron-Protein Conjugates

A series of generation 3-5 dendrons based on a bis(2,2-hydroxymethylpropionic acid) (bis-MPA) scaffold bearing three respective lengths of linear poly(ethylene glycol) at their periphery and a dibenzocyclooctyne unit at their core was prepared. These dendrons were appended to the surface of azide-decorated α-chymotrypsin (α-CT) via strain-promoted azide-alkyne cycloaddition to yield a library of dendron-protein conjugates. These conjugates were characterized by FT-IR and NMR spectroscopy and were imaged using cryo-electron microscopy. The activity of the PEGylated α-CT-dendron conjugates was investigated using a small molecule (benzoyl-l-tyrosine p-nitroanilide) as well as different proteins of different sizes and crystallinities (casein and bovine serum albumin) as substrates. It was found that the activity of the conjugates toward the small molecule was largely retained, while the activity toward the proteins was significantly diminished. Furthermore, the results indicate that for most of the conjugates the PEG length had a more pronounced impact on enzyme activity than the dendron generation. Overall, the highest sieving ratios were found for α-CT-dendron conjugates decorated with G3-PEG2000, G4-PEG2000, and G5-PEG1000, with the latter two structures offering the best combination of sieving ratio and small molecule activity.

Synthesis of Multifunctional Protein-Polymer Conjugates via Oxygen-tolerant, Aqueous Copper-Mediated Polymerization, and Bioorthogonal Click Chemistry

Oxygen-tolerant, aqueous copper-mediated polymerization approaches are combined with click chemistry in either a sequential or a simultaneous manner, to enable the synthesis of multifunctional protein-polymer conjugates. Propargyl acrylate (PgA) and propargyl methacrylate (PgMA) grafting from a bovine serum albumin (BSA) macroinitiator is thoroughly optimized to synthesize chemically addressable BSA-poly(propargyl acrylate) and BSA-poly(propargyl methacrylate) respectively. The produced multifunctional bioconjugates bear pendant terminal 1-alkynes which can be readily post-functionalized via both [3+2] Huisgen cycloaddition and thiol-yne click chemistry under mild reaction conditions. Simultaneous oxygen-tolerant, aqueous copper-catalyzed polymerization, and click chemistry mediate the in situ multiple chemical tailoring of biomacromolecules in excellent yields.

Carbon-Centered Radicals in Protein Manipulation

Methods to directly post-translationally modify proteins are perhaps the most straightforward and operationally simple ways to create and study protein post-translational modifications (PTMs). However, precisely altering or constructing the C-C scaffolds pervasive throughout biology is difficult with common two-electron chemical approaches. Recently, there has been a surge of new methods that have utilized single electron/radical chemistry applied to site-specifically "edit" proteins that have started to create this potential-one that in principle could be near free-ranging. This review provides an overview of current methods that install such "edits", including those that generate function and/or PTMs, through radical C-C bond formation (as well as C-X bond formation via C• where illustrative). These exploit selectivity for either native residues, or preinstalled noncanonical protein side-chains with superior radical generating or accepting abilities. Particular focus will be on the radical generation approach (on-protein or off-protein, use of light and photocatalysts), judging the compatibility of conditions with proteins and cells, and novel chemical biology applications afforded by these methods. While there are still many technical hurdles, radical C-C bond formation on proteins is a promising and rapidly growing area in chemical biology with long-term potential for biological editing.

Visible-Light-Mediated Controlled Radical Branching Polymerization in Water

Hyperbranched polymethacrylates were synthesized by green-light-induced atom transfer radical polymerization (ATRP) under biologically relevant conditions in the open air. Sodium 2-bromoacrylate (SBA) was prepared in situ from commercially available 2-bromoacrylic acid and used as a water-soluble inibramer to induce branching during the copolymerization of methacrylate monomers. As a result, well-defined branched polymethacrylates were obtained in less than 30 min with predetermined molecular weights (36 000<M_n <170 000), tunable degree of branching, and low dispersity values (1.14≤Đ≤1.33). Moreover, the use of SBA inibramer enabled the synthesis of bioconjugates with a well-controlled branched architecture.

Universal Method for Label-Free Detection of Pathogens and Biomolecules by Surface-Enhanced Raman Spectroscopy Based on Gold Nanoparticles

The detection of biomolecules is the key to basic molecular research, diagnostics, drug screening, and other biomedical applications. However, the existing detection techniques can only detect single classes of biomolecules, which warrant the development of a versatile biomolecule detection platform. Here, we developed a universal method for label-free detection of biomolecules via surface-enhanced Raman spectroscopy (SERS) by using sulfhydryl-modified gold nanoparticles as the substrate. The biomolecules can be adsorbed on the surface of gold nanoparticles cleaned by bromide ions to obtain initially enhanced Raman signals, and the aggregator (calcium ion) was further added to form a "hot spot", which enhanced the biomolecular signal again. Through the "two-step enhancement method", we were able to obtain fingerprints of DNA, RNA, amino acids, peptides, proteins, viruses, bacteria, and lipid molecules. This low-toxic, highly sensitive, and widely applicable technique has potential applications in biomedical research, clinical testing, and disease diagnosis and lays the foundation for the development of SERS technology in various fields.

Polynorbornene-based bioconjugates by aqueous grafting-from ring-opening metathesis polymerization reduce protein immunogenicity

Protein-polymer conjugates (PPCs) improve therapeutic efficacy of proteins and have been widely used for the treatment of various diseases such as cancer, diabetes, and hepatitis. PEGylation is considered as the "gold standard" in bioconjugation, although in practice its clinical applications are becoming limited because of extensive evidence of immunogenicity induced by pre-existing anti-PEG antibodies in patients. Here, optimized reaction conditions for living aqueous grafting-from ring-opening metathesis polymerization (ROMP) are utilized to synthesize water-soluble polynorbornene (PNB)-based PPCs of lysozyme (Lyz-PPCs) and bacteriophage Qβ (Qβ-PPCs) as PEG alternatives. Lyz-PPCs retain nearly 100% bioactivity and Qβ-PPCs exhibit up to 35% decrease in protein immunogenicity. Qβ-PPCs derived from NB-PEG show no reduction in recognition by anti-PEG antibodies while Qβ-PPCs derived from NB-Zwit show >95% reduction as compared with Qβ-PEG. This work demonstrates a new method for PPC synthesis and the utility of grafting from PPCs to evade immune recognition.

Rapid Oxygen-Tolerant Synthesis of Protein-Polymer Bioconjugates via Aqueous Copper-Mediated Polymerization

The synthesis of protein-polymer conjugates usually requires extensive and costly deoxygenation procedures, thus limiting their availability and potential applications. In this work, we report the ultrafast synthesis of polymer-protein bioconjugates in the absence of any external deoxygenation via an aqueous copper-mediated methodology. Within 10 min and in the absence of any external stimulus such as light (which may limit the monomer scope and/or disrupt the secondary structure of the protein), a range of hydrophobic and hydrophilic monomers could be successfully grafted from a BSA macroinitiator, yielding well-defined polymer-protein bioconjugates at quantitative yields. Our approach is compatible with a wide range of monomer classes such as (meth) acrylates, styrene, and acrylamides as well as multiple macroinitiators including BSA, BSA nanoparticles, and beta-galactosidase from Aspergillus oryzae. Notably, the synthesis of challenging protein-polymer-polymer triblock copolymers was also demonstrated, thus significantly expanding the scope of our strategy. Importantly, both lower and higher scale polymerizations (from 0.2 to 35 mL) were possible without compromising the overall efficiency and the final yields. This simple methodology paves the way for a plethora of applications in aqueous solutions without the need of external stimuli or tedious deoxygenation.

Toward Green Atom Transfer Radical Polymerization: Current Status and Future Challenges

Reversible-deactivation radical polymerizations (RDRPs) have revolutionized synthetic polymer chemistry. Nowadays, RDRPs facilitate design and preparation of materials with controlled architecture, composition, and functionality. Atom transfer radical polymerization (ATRP) has evolved beyond traditional polymer field, enabling synthesis of organic-inorganic hybrids, bioconjugates, advanced polymers for electronics, energy, and environmentally relevant polymeric materials for broad applications in various fields. This review focuses on the relation between ATRP technology and the 12 principles of green chemistry, which are paramount guidelines in sustainable research and implementation. The green features of ATRP are presented, discussing the environmental and/or health issues and the challenges that remain to be overcome. Key discoveries and recent developments in green ATRP are highlighted, while providing a perspective for future opportunities in this area.

Gallic acid functionalized polylysine for endowing cotton fiber with antibacterial, antioxidant, and drug delivery properties

In recent years, the serious influence of infectious diseases on public health and economy development has raised global awareness of the importance of medical textiles for preventing and curing injuries and diseases. The application of biomass molecules is a feasible and sustainable approach to design multipurpose medical materials. In this work, a novel cotton fiber with antibacterial, antioxidant, and drug delivery properties was prepared using gallic acid functionalized polylysine (GA-PL). GA-PL was synthesized by immobilizing GA onto PL using the carbodiimide coupling method. The content of GA immobilized onto PL was 117.9 mg/g. The as-prepared GA-PL was grafted onto oxidized cotton by means of the Schiff base reaction between the amino groups of GA-PL and the aldehyde groups of oxidized cotton. The content of GA-PL grafted onto cotton fiber was 205.1 mg/g. GA-PL grafted cotton fiber exhibited not only durable antibacterial and antioxidant activities but also good drug loading and releasing properties for acetylsalicylic acid. This work presents a novel, cleaner, and sustainable approach to prepare medical cotton fibers with bioactive and drug delivery properties.

Molecular Simulations of Zwitterlation-induced Conformation and Dynamics Variation of Glucagon-like Peptide-1 and Insulin

Zwitterionic materials have shown their ability to improve the circulation time and stability of proteins. Zwitterionic peptides present unique potential because genetic technology can fuse them to any wild-type protein....

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.

Asynchronous parallel Bayesian optimization for AI-driven cloud laboratories

Motivation

The recent emergence of cloud laboratories—collections of automated wet-lab instruments that are accessed remotely, presents new opportunities to apply Artificial Intelligence and Machine Learning in scientific research. Among these is the challenge of automating the process of optimizing experimental protocols to maximize data quality.

Results

We introduce a new deterministic algorithm, called PaRallel OptimizaTiOn for ClOud Laboratories (PROTOCOL), that improves experimental protocols via asynchronous, parallel Bayesian optimization. The algorithm achieves exponential convergence with respect to simple regret. We demonstrate PROTOCOL in both simulated and real-world cloud labs. In the simulated lab, it outperforms alternative approaches to Bayesian optimization in terms of its ability to find optimal configurations, and the number of experiments required to find the optimum. In the real-world lab, the algorithm makes progress toward the optimal setting.

Data availability and implementation

PROTOCOL is available as both a stand-alone Python library, and as part of a R Shiny application at https://github.com/clangmead/PROTOCOL. Data are available at the same repository.

Supplementary information

Supplementary data are available at Bioinformatics online.

Thermoresponsive Poly(N,N-diethylacrylamide-co-glycidyl methacrylate) Copolymers and Its Catalytically Active α-Chymotrypsin Bioconjugate with Enhanced Enzyme Stability

Responsive (smart, intelligent, adaptive) polymers have been widely explored for a variety of advanced applications in recent years. The thermoresponsive poly(N,N-diethylacrylamide) (PDEAAm), which has a better biocompatibility than the widely investigated poly(N,N-isopropylacrylamide), has gained increased interest in recent years. In this paper, the successful synthesis, characterization, and bioconjugation of a novel thermoresponsive copolymer, poly(N,N-diethylacrylamide-co-glycidyl methacrylate) (P(DEAAm-co-GMA)), obtained by free radical copolymerization with various comonomer contents and monomer/initiator ratios are reported. It was found that all the investigated copolymers possess LCST-type thermoresponsive behavior with small extent of hysteresis, and the critical solution temperatures (CST), i.e., the cloud and clearing points, decrease linearly with increasing GMA content of these copolymers. The P(DEAAm-co-GMA) copolymer with pendant epoxy groups was found to conjugate efficiently with α-chymotrypsin in a direct, one-step reaction, leading to enzyme-polymer nanoparticle (EPNP) with average size of 56.9 nm. This EPNP also shows reversible thermoresponsive behavior with somewhat higher critical solution temperature than that of the unreacted P(DEAAm-co-GMA). Although the catalytic activity of the enzyme-polymer nanoconjugate is lower than that of the native enzyme, the results of the enzyme activity investigations prove that the pH and thermal stability of the enzyme is significantly enhanced by conjugation the with P(DEAAm-co-GMA) copolymer.

Mechanistic Understanding From Molecular Dynamics Simulation in Pharmaceutical Research 1: Drug Delivery

In this review, we outline the growing role that molecular dynamics simulation is able to play as a design tool in drug delivery. We cover both the pharmaceutical and computational backgrounds, in a pedagogical fashion, as this review is designed to be equally accessible to pharmaceutical researchers interested in what this new computational tool is capable of and experts in molecular modeling who wish to pursue pharmaceutical applications as a context for their research. The field has become too broad for us to concisely describe all work that has been carried out; many comprehensive reviews on subtopics of this area are cited. We discuss the insight molecular dynamics modeling has provided in dissolution and solubility, however, the majority of the discussion is focused on nanomedicine: the development of nanoscale drug delivery vehicles. Here we focus on three areas where molecular dynamics modeling has had a particularly strong impact: (1) behavior in the bloodstream and protective polymer corona, (2) Drug loading and controlled release, and (3) Nanoparticle interaction with both model and biological membranes. We conclude with some thoughts on the role that molecular dynamics simulation can grow to play in the development of new drug delivery systems.

Effect of conjugated (EK)10 peptide on structural and dynamic properties of ubiquitin protein: a molecular dynamics simulation study

Peptide conjugation modulates the stability and biological acitivty of proteins via the allosteric effect.