Mutagenic analysis of a receptor contact site on interleukin-2: preparation of an IL-2 analog with increased potency

New therapeutic strategies based on biasing IL-2 mutants for cancers and autoimmune diseases

Interleukin-2 (IL-2) is an immunomodulatory multifunctional cytokine. High-dose IL-2 was first approved by the U.S. Food and Drug Administration (FDA) in the 1990s for the treatment of metastatic renal cell carcinoma and metastatic melanoma. However, the short half-life of IL-2 and its toxicity caused by high-dose IL-2 limit the clinical use of IL-2. Recently, the development of cell-type-selective engineered IL-2 products become a hot research filed, mainly because IL-2 stimulates both regulatory T cells (Treg) and effector T cells (Teff) in vivo. The selective effect of IL-2 on Treg and Teff can be improved by designing biased IL-2 mutants, which showed reduced toxicity while being more effective in stimulating anti-tumor effector immunity or ameliorating autoimmune diseases. In this review we summarize the biological properties of IL-2 mutants reported so far. The design process and principle of IL-2 mutants, IL-2 mutant antibody complexes and IL-2 fusion proteins were discussed, which provided research basis for the design and application of IL-2 mutants in the future.

Modeling cell-specific dynamics and regulation of the common gamma chain cytokines

The γ-chain receptor dimerizes with complexes of the cytokines interleukin-2 (IL-2), IL-4, IL-7, IL-9, IL-15, and IL-21 and their corresponding "private" receptors. These cytokines have existing uses and future potential as immune therapies because of their ability to regulate the abundance and function of specific immune cell populations. Here, we build a binding reaction model for the ligand-receptor interactions of common γ-chain cytokines, which includes receptor trafficking dynamics, enabling quantitative predictions of cell-type-specific response to natural and engineered cytokines. We then show that tensor factorization is a powerful tool to visualize changes in the input-output behavior of the family across time, cell types, ligands, and concentrations. These results present a more accurate model of ligand response validated across a panel of immune cell types as well as a general approach for generating interpretable guidelines for manipulation of cell-type-specific targeting of engineered ligands.

Insights into cytokine-receptor interactions from cytokine engineering

Cytokines exert a vast array of immunoregulatory actions critical to human biology and disease. However, the desired immunotherapeutic effects of native cytokines are often mitigated by toxicity or lack of efficacy, either of which results from cytokine receptor pleiotropy and/or undesired activation of off-target cells. As our understanding of the structural principles of cytokine-receptor interactions has advanced, mechanism-based manipulation of cytokine signaling through protein engineering has become an increasingly feasible and powerful approach. Modified cytokines, both agonists and antagonists, have been engineered with narrowed target cell specificities, and they have also yielded important mechanistic insights into cytokine biology and signaling. Here we review the theory and practice of cytokine engineering and rationalize the mechanisms of several engineered cytokines in the context of structure. We discuss specific examples of how structure-based cytokine engineering has opened new opportunities for cytokines as drugs, with a focus on the immunotherapeutic cytokines interferon, interleukin-2, and interleukin-4.

Multifarious determinants of cytokine receptor signaling specificity

Cytokines play crucial roles in regulating immune homeostasis. Two important characteristics of most cytokines are pleiotropy, defined as the ability of one cytokine to exhibit diverse functionalities, and redundancy, defined as the ability of multiple cytokines to exert overlapping activities. Identifying the determinants for unique cellular responses to cytokines in the face of shared receptor usage, pleiotropy, and redundancy will be essential in order to harness the potential of cytokines as therapeutics. Here, we discuss the biophysical (ligand-receptor geometry and affinity) and cellular (receptor trafficking and intracellular abundance of signaling molecules) parameters that contribute to the specificity of cytokine bioactivities. Whereas the role of extracellular ternary complex geometry in cytokine-induced signaling is still not completely elucidated, cytokine-receptor affinity is known to impact signaling through modulation of the stability and kinetics of ternary complex formation. Receptor trafficking also plays an important and likely underappreciated role in the diversification of cytokine bioactivities but it has been challenging to experimentally probe trafficking effects. We also review recent efforts to quantify levels of intracellular signaling components, as second messenger abundance can affect cytokine-induced bioactivities both quantitatively and qualitatively. We conclude by discussing the application of protein engineering to develop therapeutically relevant cytokines with reduced pleiotropy and redirected biological functionalities.

pH Dependence of structural stability of interleukin-2 and granulocyte colony-stimulating factor

After a cytokine binds to its receptor on the cell surface (pH approximately 7), the complex is internalized into acidic endosomal compartments (pH approximately 5-6), where partially unfolded intermediates can form. The nature of these structural transitions was studied for wild-type interleukin-2 (IL-2) and wild-type granulocyte colony-stimulating factor (G-CSF). A noncoincidence of denaturation transitions in the secondary and tertiary structure of IL-2 and tertiary structural perturbations in G-CSF suggest the presence of an intermediate state for each, a common feature of this structural family of four-helical bundle proteins. Unexpectedly, both IL-2 and G-CSF display monotonic increases in stability as the pH is decreased from 7 to 4. We hypothesize that such cytokines with cell-based clearance mechanisms in vivo may have evolved to help stabilize endosomal complexes for sorting to lysosomal degradation. We show that mutants of both IL-2 and G-CSF have differential stabilities to their wild-type counterparts as a function of pH, and that these differences may explain the differences in ligand trafficking and depletion. Further understanding of the structural changes accompanying unfolding may help guide cytokine design with respect to ligand binding, endocytic trafficking, and, consequently, therapeutic efficacy.

Mutational analysis of chicken interleukin 2

Chicken interleukin 2 (chIL-2) has low, but significant, homology to both mammalian IL-2 and mammalian IL-15. In view of its unique phylogenetic position and potential use as a vaccine adjuvant, a detailed mutational analysis for critical functional sites was undertaken. It was found that Asp17 is a critical N terminal contact site for binding to the putative chIL-2 receptor, which is similar to results obtained for mammalian IL-2 and IL-15. Analysis of the C terminus did not reveal a single critical amino acid. However, deletion mutant studies demonstrated that removal of C terminal amino acids yielded proteins with decreased bioactivity and that this decrease was a function of the number and kind of amino acids removed. This study is the first non-mammalian IL-2 mutational analysis and proposes a model for the interaction between chIL-2 and its receptor.

Improving the refolding yield of interleukin-4 through the optimization of local interactions

Interleukin-4 (IL-4) is a multifunctional cytokine that plays an important role in the regulation of various immune responses. However, the development of IL-4 or IL-4 variants into potential therapeutic drugs is hindered by the low efficiency of the in vitro refolding process of this protein. In this work, we have investigated the improvement of the refolding yield of IL-4 using two different rational design approaches. The first one is based on the so-called inverse hydrophobic effect and involved the replacement of a solvent exposed, non-conserved, hydrophobic residue (W91) by serine. This led to an increase in stability of 1.4 kcal mol(-1) and shifted the midpoint transition temperature (Tm) from 62 to 70 degrees C. The second approach is based on the stabilization of alpha-helices through the introduction of favorable local interactions. This strategy resulted in the following helix sequence for helix C of IL-4, 68ASAAEANRHKQLIRFLKRLDRNLWGLAG95. The mutant protein was stabilized by 0.5 kcal mol(-1), the Tm shifted to 68 degrees C, and a two-fold increase in the refolding yield was consistently observed. Our results make the large-scale production of IL-4 derivatives economically more viable, suggest that a similar approach can be applied to other related proteins, and may represent a general strategy to improve in vitro refolding yields through the selective optimization of the stability of alpha-helices.

Increased endosomal sorting of ligand to recycling enhances potency of an interleukin-2 analog

An interleukin-2 (IL-2) variant containing adjacent point mutations (L18M/L19S, termed 2D1) displaying binding affinity to the heterotrimeric IL-2 receptor similar to that of wild-type IL-2 (WT) had been previously found to surprisingly exhibit increased bioactivity in a peripheral blood lymphocyte proliferation assay. In order to provide an explanatory mechanism for this unexpected potency enhancement, we hypothesize that altered endocytic trafficking of the 2D1 variant might be responsible by increasing the number of ligand-receptor complexes. We demonstrate here that the internalization kinetics of 2D1 via the high affinity IL-2 receptor are equivalent to those of WT but that a significantly increased fraction of internalized 2D1 is sorted to recycling instead of to lysosomal degradation. We further find a reduced pH sensitivity of binding to IL-2 receptor alpha relative to IL-2 receptor beta compared with WT, which could be responsible for the altered sorting behavior of 2D1 in the acidic endosomal compartment. Accordingly, the 2D1 variant displays a half-life 36 h longer than that of IL-2 in T-lymphocyte culture at concentrations equal to the K(D) of the IL-2 receptor. The extended half-life of intact 2D1 provides enhanced mitogenesis as compared with IL-2. In addition, 2D1 stimulates natural killer cells to a lesser degree than IL-2 at equal concentrations. We conclude that this IL-2 variant provides increased mitogenic stimulation that could not be easily predicted from its cell surface receptor binding affinity while minimizing undesired stimulation of natural killer cells. This concept of altering trafficking dynamics may offer a generalizable approach to generating improvements in the pharmacological efficacy of therapeutic cytokines.

Scratching the (cell) surface: cytokine engineering for improved ligand/receptor trafficking dynamics

Cytokines can be engineered for greater potency in stimulating cellular functions. An obvious test criterion for an improved cytokine is receptor-binding affinity, but this does not always correlate with improved biological response. By combining protein-engineering techniques with studies of receptor trafficking and signaling, it might be possible to identify the ligand receptor-binding properties that should be sought.

Exploring the cellulose/xylan specificity of the beta-1,4-glycanase cex from Cellulomonas fimi through crystallography and mutation

The retaining beta-1,4-glycanase Cex from Cellulomonas fimi, a family 10 glycosyl hydrolase, hydrolyzes xylan 40-fold more efficiently than cellulose. To gain insight into the nature of its preference for xylan, we determined the crystal structure of the Cex catalytic domain (Cex-cd) trapped as its covalent 2-deoxy-2-fluoroxylobiosyl-enzyme intermediate to 1.9 A resolution. Together with the crystal structure of unliganded Cex-cd [White, A., et al. (1994) Biochemistry 33, 12546-12552] and the previously determined crystal structure of the covalent 2-deoxy-2-fluorocellobiosyl-Cex-cd intermediate [White, A., et al. (1996) Nat. Struct. Biol. 3, 149-154], this structure provides a convincing rationale for the observed substrate specificity in Cex. Two active site residues, Gln87 and Trp281, are found to sterically hinder the binding of glucosides and must rearrange to accommodate these substrates. Such rearrangements are not necessary for the binding of xylobiosides. The importance of this observation was tested by examining the catalytic behavior of the enzyme with Gln87 mutated to Met. This mutation had no measurable effect on substrate affinity or turnover number relative to the wild type enzyme, indicating that the Met side chain could accommodate the glucoside moiety as effectively as the wild type Gln residue. Subsequent mutagenesis studies will address the role of entropic versus enthalpic contributions to binding by introducing side chains that might be more rigid in the unliganded enzyme.

Partial signaling by cytokines: cytokine regulation of cell cycle and Fas-dependent, activation-induced death in CD4+ subsets

Fas-dependent, activation-induced death (AID) of T cells has been implicated in the regulation of peripheral T cell populations. We have previously reported that IL-2 plays a unique role in regulating sensitivity to AID in primary CD4+ cells. In this report we have compared the capacity of IL-2, IL-4, and IL-7 to increase entry into cell cycle vs their capacity to increase sensitivity to AID. Our data indicate that IL-2 plays a unique role in the regulation of AID in both Th1 and Th2 subsets and that with a given AID stimulus, cell cycle progression is necessary, but not sufficient, for AID. Interestingly, induction of cell cycle entry and sensitivity to AID can be dissociated (partial signaling) not only with different cytokines, but even with point mutations in IL-2 itself. This provides the first evidence that cytokine variants or pharmacological agents that mimic their action will be useful in enhancing selective elements of pleiotropic cytokine actions.

The functional display of interleukin-2 on filamentous phage

We report the novel display of interleukin-2 (IL-2) and an IL-2 analog, D126, on the surface of filamentous bacteriophage using a phagemid vector system. A synthetic human IL-2 gene and its D126 analog were fused to the carboxyl-terminal domain of the gene III minor phage coat protein. Expression of IL-2 and D126 was verified by their reactivity with an IL-2-specific antibody. Biological response of IL-2 phage on murine CTLL-2 cells was comparable to that of recombinant soluble IL-2, while the D126 phage displayed a reduced biological response similar to that previously measured by soluble D126 protein. Biosensor surface plasmon resonance was employed to verify binding of the IL-2 and D126 phage to the IL-2 alpha beta cc receptor complex. A 41-fold enrichment of IL-2 phage over R408 helper phage was demonstrated in biopanning affinity selection studies employing biotinylated alpha beta cc receptor complex. These biopanning studies are the first reports of affinity selection of IL-2 phage and demonstrate a novel use for the alpha beta cc receptor complex. Together, these studies confirm that the structural integrity of IL-2 and D126 is maintained when they are displayed as a gIIIp fusion protein on phage particles and provide the foundation for further selection studies employing IL-2 analog phage libraries.

Identification and characterization of two alternative splice variants of human interleukin-2

Our previous work showed that alternative splicing is used to make an inhibitory variant of human interleukin (IL)-4. Because of homology between IL-4 and IL-2 proteins and receptors, we tested whether alternative splicing is used to generate similar inhibitory variants of human IL-2. Messenger RNA from peripheral blood mononuclear cells was subjected to reverse transcription-polymerase chain reaction using IL-2 exon 1- and exon 4-specific primers. Two amplification products, named IL-2delta2 and IL-2delta3, were found in addition to the native IL-2 product. The IL-2delta2 cDNA sequence was identical to IL-2 cDNA throughout the entire coding region, except exon 2 was omitted by alternative splicing. In IL-2delta3 cDNA, the third exon of IL-2 was omitted by alternative splicing. Unlike IL-2, IL-2delta2 and IL-2delta3 did not stimulate T cell proliferation. However, both inhibited IL-2 costimulation of T cell proliferation, and both inhibited cellular binding of rhIL-2 to high affinity IL-2 receptors. Thus, IL-2 is the second cytokine that uses alternative splicing to generate variants that are competitive inhibitors.

An IgG3-IL-2 fusion protein has higher affinity than hrIL-2 for the IL-2R alpha subunit: real time measurement of ligand binding

The alpha subunit of the interleukin-2 (IL-2) receptor (IL-2R alpha)3 has the highest individual affinity for IL-2 and is the only subunit not known to bind other cytokines. The interactions between IL-2 and IL-2R alpha studied in cell binding assays have revealed a number of factors which may vary significantly in different cell lines used for these assays in different laboratories. In order to avoid the problems associated with cellular assays we used an optical biosensor to examine the interaction between IL-2R alpha and hrIL-2. Real-time measurement of association and dissociation resulted in a calculated KD of 1.9 x 10(-7) M for this interaction. We then examined the IL-2R alpha binding of a potentially bivalent IgG3-IL2 fusion protein previously shown to have a higher affinity than hrIL-2 for the high affinity IL-2R but not the intermediate affinity IL-2R. Biosensor measurements of association and dissociation of IgG3-IL2 to IL-2R alpha yielded a similar association rate but a decreased dissociation rate compared to hrIL-2, resulting in a KD of 5.3 x 10(-8) M. This system is applicable to the numerous IL-2 mutants with different affinities and activities and is generalizable to other cytokine/receptor interactions.

DAB389 interleukin-2 receptor binding domain mutations. Cytotoxic probes for studies of ligand-receptor interactions

Site-directed mutagenesis was used to generate point mutations in the diphtheria toxin-related fusion protein, DAB389 interleukin-2 (IL-2). Thr-439, in the IL-2 receptor binding domain of the fusion toxin, was changed to a Pro residue. The resultant fusion toxin, DAB389 IL-2(T439P), was 300-fold less cytotoxic than wild type DAB389 IL-2, partially as the result of a 100-fold decrease in binding affinity for the high affinity form of the IL-2 receptor. However, DAB389 IL-2(T439P) stimulated DNA synthesis to a greater extent than expected. Studies of intoxication kinetics indicated that the increased stimulation might result from an increased contact time between the mutated IL-2 receptor binding domain and the receptor, perhaps due to a decreased internalization rate. Another mutant, DAB389 IL-2(Q514D), in which a Gln residue at position 514 was changed to an Asp, was 2000-fold less cytotoxic than wild type DAB389 IL-2. This mutant had a 50-fold decrease in binding affinity, did not stimulate DNA synthesis and also had a reduced rate of intoxication. Gln-514 appears to play a role in receptor binding and activation, whereas Thr-439 appears to be involved with receptor binding and signaling internalization of the fusion toxin-receptor complex.

Interleukin-2 as a neuroregulatory cytokine

Interleukin-2 (IL-2), the cytokine also known as T-cell growth factor, has multiple immunoregulatory functions and biological properties not only related to T-cells. In the past decade, substantial evidence accumulated to suggest that IL-2 is also a modulator of neural and neuroendocrine functions. First, extremely potent effects of IL-2 on neural cells were discovered, including activities related to cell growth and survival, transmitter and hormone release and the modulation of bioelectric activities. IL-2 may be involved in the regulation of sleep and arousal, memory function, locomotion and the modulation of the neuroendocrine axis. Second, the concept that IL-2 could act as a neuroregulatory cytokine has been supported by reports on the presence in rodent and human brain tissues of IL-2-like bioactivity, IL-2-like immunoreactivity, IL-2-like mRNA, IL-2 binding sites, IL-2 receptor (IL-2R alpha) and beta chain mRNA and IL-2R immunoreactivity. IL-2 and/or IL-2R molecules mainly localize to the frontal cortex, septum, striatum, hippocampal formation, hypothalamus, locus coeruleus, cerebellum, the pituitary and fiber tracts, such as the corpus callosum, where they are likely expressed by both neuronal and glial cells. Although the molecular biology of the brain IL-2/IL-2R system (including its relation to IL-15/IL-15R alpha) is not yet fully established by cloning and complete sequencing of all respective components, similarities (and to some extent differences) to peripheral counterparts are now apparent. The ability of IL-2 to readily penetrate the blood-brain barrier further suggests that this cytokine could regulate interactions between peripheral tissues and the central nervous system. Taken together, these data suggest that IL-2 of either immune and CNS origin can have access to functional IL-2R molecules on neurons and glia under normal conditions. Additionally, dysregulation of the IL-2/IL-2 receptor system could lead or contribute to functional and pathological alterations in the brain as in the immune system. Understanding the neurobiology of the IL-2/IL-2 receptor system should also help to explain neurologic, neuropsychiatric and neuroendocrine side effects occurring during IL-2 treatment of peripheral and brain tumors. Immunopharmacological manipulation either aiming at the activation or suppression of IL-2 signaling should consider functional interference with constitutive and inducible IL-2 receptors on brain cells in order to fulfil the high expectations associated with the use of this cytokine as a promising agent in immunotherapies, especially of brain tumors.

Characterization of a monoclonal antibody directed against the NH2 terminal area of interleukin-2 (IL-2) and inhibiting specifically the binding of IL-2 to IL-2 receptor beta chain (IL-2R beta)

An anti-human IL-2 mAb (19B11/beta) was found to selectively block the binding of IL-2 to TS1 beta cells expressing the interleukin-2 receptor beta (IL-2R beta) without affecting binding to TS1 alpha cells expressing the IL-2R alpha receptor. It also specifically inhibits the IL-2 driven cell proliferation in TS1 beta cells. These observations have lead to the hypothesis that its epitope is related to an IL-2 area involved in binding with IL-2R beta chain. This epitope was identified using various peptides covering the N-terminal half (including alpha helix A) of the 133 amino acids of IL-2. MAb 19B11/beta does not recognize peptides 30-54 and 44-54 but recognizes peptides 1-22 and 1-30 with a good affinity. Furthermore, threonine in position no. 3 was found to be critical for the binding of mAb 19B11/beta. A relationship between the epitope of mAb 19B11/beta and the glycosylation of the IL-2 molecule was observed. This further demonstrates that the NH2 terminal area of IL-2 is critical for IL-2/IL-2R beta interactions. Two other mAbs were studied during the course of this work. They served as control for the study of mAb 19B11/beta and provide some additional insight concerning the question of IL-2/IL-2R structure-function. MAb 16F11/alpha selectively blocks the IL-2 binding to TS1 alpha cells. The epitope of mAb 16F11 is conformational and it was not possible to study the corresponding IL-2/IL-2R alpha region of interaction. Epitope of mAb 3H9 is localized between residues 30 and 54 and does not affect the binding of IL-2 to IL-2R alpha.

Ligand binding analysis of soluble interleukin-2 receptor complexes by surface plasmon resonance

Knowledge of the kinetic binding characteristics is often critical to the development of ligand/receptor structure-activity relationships. To better understand the contribution of each of the subunits to ligand binding in the multimeric interleukin-2 receptor system, we have previously prepared stable solution complexes of the alpha- and beta-subunits. In this study, we have employed surface plasmon resonance biosensor methodology (BIAcore) to evaluate both the kinetic and equilibrium binding constants for these complexes. The structural nature of the complexes facilitated immobilization on the sensor surfaces in a manner that minimized interference with ligand interactions. The interleukin-2 receptor complex surfaces displayed excellent binding capacity and stability toward regeneration. In all cases where the binding constants were measurable, the values determined for interleukin-2 were in good agreement with those previously determined by other methods. When interleukin-2 analogs with receptor subunit specific mutations were employed, the binding parameters were consistent with the nature of the mutations. The combination of coiled-coil-mediated solution assembly and surface plasmon resonance analysis of ligand binding provides a powerful approach to the study of multimeric cytokine receptor systems.