Nucleic acid aptamers as stabilizers of proteins: the stability of tetanus toxoid

Roles of Nucleic Acids in Protein Folding, Aggregation, and Disease

The role of nucleic acids in protein folding and aggregation is an area of continued research, with relevance to understanding both basic biological processes and disease. In this review, we provide an overview of the trajectory of research on both nucleic acids as chaperones and their roles in several protein misfolding diseases. We highlight key questions that remain on the biophysical and biochemical specifics of how nucleic acids have large effects on multiple proteins' folding and aggregation behavior and how this pertains to multiple protein misfolding diseases.

Science and art of protein formulation development

Protein pharmaceuticals have become a significant class of marketed drug products and are expected to grow steadily over the next decade. Development of a commercial protein product is, however, a rather complex process. A critical step in this process is formulation development, enabling the final product configuration. A number of challenges still exist in the formulation development process. This review is intended to discuss these challenges, to illustrate the basic formulation development processes, and to compare the options and strategies in practical formulation development.

Stability of Vaccines

Vaccines are considered the most economical and effective preventive measure against most deadly infectious diseases. Vaccines help protect around three million lives every year, but hundreds of thousands of lives are lost due to the instability of vaccines. This review discusses the various types of instability observed, while manufacturing, storing, and distributing vaccines. It describes the specific stability problems associated with each type of vaccine. This review also discusses the various measures adopted to overcome these instability problems. Vaccines are classified based on their components, and this review discusses how these preventive measures relate to each type of vaccine. This review also includes certain case studies that illustrate various approaches to improve vaccine stability. Last, this review provides insight on prospective methods for developing more stable vaccines.

Tighter Ligand Binding Can Compensate for Impaired Stability of an RNA-Binding Protein

It has been widely shown that ligand-binding residues, by virtue of their orientation, charge, and solvent exposure, often have a net destabilizing effect on proteins that is offset by stability conferring residues elsewhere in the protein. This structure-function trade-off can constrain possible adaptive evolutionary changes of function and may hamper protein engineering efforts to design proteins with new functions. Here, we present evidence from a large randomized mutant library screen that, in the case of PUF RNA-binding proteins, this structural relationship may be inverted and that active-site mutations that increase protein activity are also able to compensate for impaired stability. We show that certain mutations in RNA-protein binding residues are not necessarily destabilizing and that increased ligand-binding can rescue an insoluble, unstable PUF protein. We hypothesize that these mutations restabilize the protein via thermodynamic coupling of protein folding and RNA binding.

Specific detection of tetanus toxoid using an aptamer-based matrix

Batch-to-batch variation of therapeutic proteins produced by biological means requires rigorous monitoring at all stages of the production process. A large number of animals are employed for risk assessment of biologicals, which has low ethical and economic acceptability. Research is now focussed on the validation of in vitro and ex vivo tests to replace live challenges. Among in vitro methods, enzyme-linked immunosorbent assay (ELISA) is considered to be the gold standard for estimation of integrity of tetanus toxoid. ELISA utilizes antibodies for detection, which, because of their biological origin and limited modifiability, may have low stability and result in irreproducibility. We have developed a method using highly specific and selective RNA aptamers for detection of tetanus toxoid. Using displacement assay, we first identified aptamers which bind to different aptatopes on the surface of the toxoid. Pairs of these aptamers were employed as capture-detection ligands in a sandwich-ALISA (aptamer-linked immobilized sorbent assay) format. The binding efficiency was confirmed by the fluorescence intensity in each microtire plate well. Using aptamers alone, detection of tetanus toxoid was possible with the same level of sensitivity as antibody. Aptamers were also used in the capture ALISA format. Adjuvanted tetanus toxoid was subjected to accelerated stress testing, including thermal, mechanical and freeze-thawing stress conditions. The loss in antigenicity of the preparation determined by ALISA in each case was found to be similar to that determined by conventional ELISA. Thus, it is possible to replace antibodies with aptamers to develop a more robust detection tool for tetanus toxoid.

Challenges with osmolytes as inhibitors of protein aggregation: Can nucleic acid aptamers provide an answer?

Protein aggregation follows some common motifs. Whether in the formation of inclusion bodies in heterologous overexpression systems or inclusions in protein conformational diseases, or aggregation during storage or transport of protein formulations, aggregates form cross beta-sheet structures and stain with amyloidophilic dyes like Thioflavin T and Congo Red, irrespective of the concerned protein. Traditionally, osmolytes are used to stabilize proteins against stress conditions. They are employed right from protein expression, through production and purification, to formulation and administration. As osmolytes interact with the solvent, the differential effect of the stress condition on the solvent mostly determines the effect of the osmolyte on protein stability. Nucleic acid aptamers, on the other hand, are highly specific for their targets. When selected against monomeric, natively folded proteins, they bind to them with very high affinity. This binding inhibits the unfolding of the protein and/or monomer-monomer interaction which are the initial common steps of protein aggregation. Thus, by changing the approach to a protein-centric model, aptamers are able to function as universal stabilizers of proteins. The review discusses cases where osmolytes were unable to provide stabilization to proteins against different stress conditions, a gap which the aptamers seem to be able to fill.

Do nucleic acids moonlight as molecular chaperones?

Organisms use molecular chaperones to combat the unfolding and aggregation of proteins. While protein chaperones have been widely studied, here we demonstrate that DNA and RNA exhibit potent chaperone activity in vitro Nucleic acids suppress the aggregation of classic chaperone substrates up to 300-fold more effectively than the protein chaperone GroEL. Additionally, RNA cooperates with the DnaK chaperone system to refold purified luciferase. Our findings reveal a possible new role for nucleic acids within the cell: that nucleic acids directly participate in maintaining proteostasis by preventing protein aggregation.

Nucleic acid aptamers stabilize proteins against different types of stress conditions

It has been observed that the same osmolyte cannot provide protection to a protein exposed to more than one stress condition. We wanted to study the effect of nucleic acid aptamers on the stabilization of proteins against a variety of stress conditions. Adjuvanted tetanus toxoid was exposed to thermal, freeze-thawing, and agitation stress. The stability and antigenicity of the toxoid were measured. Using nucleic acid aptamers selected against tetanus toxoid, we show that these specific RNA sequences were able to stabilize alumina-adsorbed tetanus toxoid against thermal-, agitation-, and freeze-thawing-induced stress. Binding affinity of the aptamer-protein complex did not show any significant change at elevated temperature as compared with that at room temperature, indicating that the aptamer protected the protein by remaining bound to it under stress conditions and did not allow either the protein to unfold or to promote protein-protein interaction. Thus, we show that by changing the stabilization strategy from a solvent-centric to a protein-centric approach, the same molecule can be employed as a stabilizer against more than one stress condition and thus probably reduce the cost of the product during its formulation.

Injectable biodegradable hydrogels: progress and challenges

Over the past decades, injectable hydrogels have emerged as promising biomaterials because of their biocompatibility, excellent permeability, minimal invasion, and easy integration into surgical procedures. These systems provide an effective and convenient way to administer a wide variety of bioactive agents such as proteins, genes, and even living cells. Additionally, they can be designed to be degradable and eventually cleared from the body after completing their missions. Given their unique characteristics, injectable biodegradable hydrogels have been actively explored as drug reservoir systems for sustained release of bioactive agents and temporary extracellular matrices for tissue engineering. This review provides an overview of state-of-the-art strategies towards constructing a rational design of injectable biodegradable hydrogels for protein drug delivery and tissue engineering. We also discuss the use of injectable hydrogels for gene delivery systems and biomedical adhesives.

Stabilization of bovine insulin against agitation-induced aggregation using RNA aptamers

Stabilization of monomeric insulin is a primary requirement for preserving the efficacy of the final formulation. Degraded and/or aggregated protein as well as the presence of any of the conventional excipients can result in immunogenic or anaphylactic reactions, and reduced bioavailability of the protein drug. The aim of this work was to select novel RNA-based stabilizers of bovine insulin which would recognize and bind to the monomeric protein and help retain its bioactivity. RNA aptamers were selected by an in vitro selection method. They were screened for their ability to inhibit insulin fibrillation using agitation as a stress condition. The in vitro activity of insulin was determined by phosphorylation of downstream proteins in the cell. In vivo bioactivity was determined in a diabetic rat model. RNA aptamers, which bound to insulin with very low dissociation constants and high specificity, were selected. These sequences were aligned and consensus regions were found. The RNA sequences had no effect on the signalling cascade initiated by insulin. The bioactivity of insulin, as measured by its ability to lower plasma glucose level in a diabetic rat model, also remained unchanged. RNA aptamers are a novel class of protein stabilizers which have the ability to disrupt protein-protein interactions and hence inhibit protein aggregation. Their non-toxic and non-immunogenic nature makes such formulations safe for use.