Designing proteins for therapeutic applications

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Abstract

Protein design is becoming an increasingly useful tool for optimizing protein drugs and creating novel biotherapeutics. Recent progress includes the engineering of monoclonal antibodies, cytokines, enzymes and viral fusion inhibitors.

Introduction

As the use of protein and peptide drugs continues to rise, the opportunity for designing novel and optimized biotherapeutics also increases [1]. In the past 18 months alone, several new engineered protein and peptide drugs have successfully completed clinical trials, including the following: Genentech’s Somavert® (pegvisomant), an antagonistic variant of human growth hormone (hGH); Trimeris’s Fuzeon® (enfuvirtide), an inhibitor of HIV fusion derived from the viral protein gp41; Amgen’s Aranesp® (darbepoetin alfa), a hyperglycosylated variant of erythropoietin (EPO); and Abbott’s Humira® (adalimumab), a fully human monoclonal anti-TNFα antibody.

The most successful and exciting examples of therapeutic protein design highlighted below are the product of interdisciplinary insight and collaboration. The field of therapeutic protein design continues to draw from classical principles of protein design and modeling. However, application to biotherapeutics has demanded the consideration of additional issues (illustrated in Figure 1), including the pharmacokinetics (PK) and pharmacodynamics of protein drugs, the potential for deleterious side effects and immune responses, and the efficacy of different therapeutic mechanisms of action. In this review, we discuss recent progress in engineering monoclonal antibodies, cytokines and enzymes, as well as design approaches that are enabling the development of a new class of biotherapeutics: viral fusion inhibitors.

Section snippets

Monoclonal antibodies

Decades of protein engineering and clinical development have made antibodies the best-characterized class of protein drugs [2]. Despite the field’s maturity, advances continue, providing deeper insights into antibody structure and function, and guiding the development of improved therapeutics.

Cytokine engineering

Cytokines are secreted protein factors that are involved in both short- and long-range cell–cell communication. They play critical roles in the regulation of the immune system, and in the development and proliferation of various types of blood cells. Cytokines and cytokine inhibitors have proven their utility in the treatment of a wide variety of diseases. However, the efficacy of cytokine therapeutics is often limited by their rapid clearance from serum, as well as by their immunogenicity,

Engineered therapeutic enzymes

Although monoclonal antibodies and cytokines are the most widely prescribed classes of protein therapeutics, a variety of enzyme drugs are used to promote or inhibit blood clotting, replace deficient factors, combat cancer and treat infectious diseases. Engineering is being used to modify the enzymatic features of these drugs, such as their catalytic efficiency and substrate specificity, as well as their general protein properties, such as solubility and serum half-life. One excellent recent

Viral fusion inhibitors

Much of the early academic work in protein design focused on highly symmetric coiled-coil and helical-bundle proteins. The knowledge gained in these studies is currently being applied to engineer peptide inhibitors of viral fusion for the treatment of HIV and other viruses 24., 25., 26.. As shown in Figure 3, a conformational change in gp41, a subunit of the HIV surface protein Env, promotes fusion of the viral and cellular membranes. Regions of gp41 referred to as N- and C-helices (their

Conclusions

Protein design has long been a valuable tool for investigating the physico-chemical underpinnings of protein stability, folding and function. A new challenge for the protein design community is to elucidate the links between protein sequence, protein structure and therapeutically relevant parameters such as immunogenicity, nonspecific toxicity, PK and pharmacodynamics. An ultimate goal is the development of general methods that enable the design of safe and effective protein therapeutics with

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

  • of special interest

  • ••

    of outstanding interest

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