Structural elucidation of the mesothelin-mucin-16/CA125 interaction

Mesothelin (MSLN) is a cell-surface glycoprotein expressed at low levels on normal mesothelium but overexpressed in many cancers. Mesothelin has been implicated to play role/s in cell adhesion and multiple signaling pathways. Mucin-16/CA125 is an enormous cell-surface glycoprotein, also normally expressed on mesothelium and implicated in the progression and metastasis of several cancers, and directly binds mesothelin. However, the precise biological function/s of mesothelin and mucin-16/CA125 remain mysterious. We report protein engineering and recombinant production, qualitative and quantitative binding studies, and a crystal structure determination elucidating the molecular-level details governing recognition of mesothelin by mucin-16/CA125. The interface is small, consistent with the ∼micromolar binding constant and is free of glycan-mediated interactions. Sequence comparisons and modeling suggest that multiple mucin-16/CA125 modules can interact with mesothelin through comparable interactions, potentially generating a high degree of avidity at the cell surface to overcome the weak affinity, with implications for functioning and therapeutic interventions.

Effects of HLA single chain trimer design on peptide presentation and stability

MHC class I "single-chain trimer" molecules, coupling MHC heavy chain, β₂-microglobulin, and a specific peptide into a single polypeptide chain, are widely used in research. To more fully understand caveats associated with this design that may affect its use for basic and translational studies, we evaluated a set of engineered single-chain trimers with combinations of stabilizing mutations across eight different classical and non-classical human class I alleles with 44 different peptides, including a novel human/murine chimeric design. While, overall, single-chain trimers accurately recapitulate native molecules, care was needed in selecting designs for studying peptides longer or shorter than 9-mers, as single-chain trimer design could affect peptide conformation. In the process, we observed that predictions of peptide binding were often discordant with experiment and that yields and stabilities varied widely with construct design. We also developed novel reagents to improve the crystallizability of these proteins and confirmed novel modes of peptide presentation.

Abstract 1043: Advances in cystine-dense peptide (CDP) screening and therapeutic applications

Cystine-dense peptides (CDPs) are a class of drug-like miniproteins that marry many of the advantages of biologics (high affinity and specificity) and small molecule therapeutics (high tissue permeability and low immunogenicity). The beneficial properties of CDPs, and miniproteins in general, have driven interest in therapeutic applications. However, CDP diversity is vast from every clade of life, and properly interrogating “CDP space” requires specialized screening and modeling tools.

With this in mind, we have created an optimized mammalian surface display platform to screen for CDPs of clinical interest using libraries of structurally-diverse native scaffolds optimized for stability. These native CDPs can be structurally modeled, which we did in determining the structures of over 4200 native CDPs. This modeling permits further selection in silico as well as targeted mutagenesis for favorable target-binding capabilities. Hits from these screens are routinely matured to sub-nM affinity. These CDPs can play numerous roles in a drug design pipeline, from an independent drug candidate to a delivery agent for tissue-targeting to a module in a polyspecific biologic. Recent novel CDP candidates have shown promise in immune-oncology space as part of a bispecific T-cell engager targeting PD-L1, where a single 2-week treatment was capable of eliminating subcutaneous PC3 prostate cancer xenograft tumors in 27/30 mice.

Besides bispecifics, future directions for the platform include exploring targeted protein degradation. Additionally, we are expanding upon our previous work on CDPs to explore CNS or tumor delivery of therapeutic cargo. The versatility of CDPs and novel screening tools to rapidly identify and mature candidates of interest can facilitate rapid advancement of CDP therapeutics to address difficult targets in oncology.

Citation Format: Zachary R. Crook, Emily J. Girard, Gregory P. Sevilla, Mi-Youn Brusniak, Peter B. Rupert, Della J. Friend, Mesfin M. Gewe, Midori Clarke, Ida Lin, Raymond Ruff, Doan Phi, Ashok Bandaranayake, Colin E. Correnti, Andrew J. Mhyre, Natalie W. Nairn, Roland K. Strong, James M. Olson. Advances in cystine-dense peptide (CDP) screening and therapeutic applications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1043.

Ex silico engineering of cystine-dense peptides yielding a potent bispecific T cell engager

Cystine-dense peptides (CDPs) are a miniprotein class that can drug difficult targets with high affinity and low immunogenicity. Tools for their design, however, are not as developed as those for small-molecule and antibody drugs. CDPs have diverse taxonomic origins, but structural characterization is lacking. Here, we adapted Iterative Threading ASSEmbly Refinement (I-TASSER) and Rosetta protein modeling software for structural prediction of 4298 CDP scaffolds and performed in silico prescreening for CDP binders to targets of interest. Mammalian display screening of a library of docking-enriched, methionine and tyrosine scanned (DEMYS) CDPs against PD-L1 yielded binders from four distinct CDP scaffolds. One was affinity-matured, and cocrystallography yielded a high-affinity (K_D = 202 pM) PD-L1-binding CDP that competes with PD-1 for PD-L1 binding. Its subsequent incorporation into a CD3-binding bispecific T cell engager produced a molecule with pM-range in vitro T cell killing potency and which substantially extends survival in two different xenograft tumor-bearing mouse models. Both in vitro and in vivo, the CDP-incorporating bispecific molecule outperformed a comparator antibody-based molecule. This CDP modeling and DEMYS technique can accelerate CDP therapeutic development.

Computational protein design using flexible backbone remodeling and resurfacing: case studies in structure-based antigen design

Computational protein design has promise for vaccine design and other applications. We previously transplanted the HIV 4E10 epitope onto non-HIV protein scaffolds for structural stabilization and immune presentation. Here, we developed two methods to optimize the structure of an antigen, flexible backbone remodeling and resurfacing, and we applied these methods to a 4E10 scaffold. In flexible-backbone remodeling, an existing backbone segment is replaced by a de novo designed segment of prespecified length and secondary structure. With remodeling, we replaced a potentially immunodominant domain on the scaffold with a helix-loop segment that made intimate contact to the protein core. All three domain trim designs tested experimentally had improved thermal stability and similar binding affinity for the 4E10 antibody compared to the parent scaffold. A crystal structure of one design had a 0.8 Å backbone RMSD to the computational model in the rebuilt region. Comparison of parent and trimmed scaffold reactivity to anti-parent sera confirmed the deletion of an immunodominant domain. In resurfacing, the surface of an antigen outside a target epitope is redesigned to obtain variants that maintain only the target epitope. Resurfaced variants of two scaffolds were designed in which 50 positions amounting to 40% of the protein sequences were mutated. Surface-patch analyses indicated that most potential antibody footprints outside the 4E10 epitope were altered. The resurfaced variants maintained thermal stability and binding affinity. These results indicate that flexible-backbone remodeling and resurfacing are useful tools for antigen optimization and protein engineering generally.

A single amino acid difference between human and monkey interleukin (IL)-1beta dictates effective binding to soluble type II IL-1 receptor

Soluble type II interleukin (IL)-1 receptor (sIL1R-II) binds human IL-1beta with high affinity and neutralizes its activity. Recombinant sIL1R-II is considered a potentially useful anti-IL-1 therapeutic, and preclinical studies have been undertaken with this molecule in primates. To better understand the cytokine-receptor interactions occurring in this nonhuman context, monkey IL-1 and IL1R-II were cloned, and their binding abilities were examined in vitro. IL-1beta from cynomolgus monkey was capable of binding and activating the human type I IL-1 receptor. However, unlike human IL-1beta, it was unable to effectively bind and become neutralized by sIL1R-II. Human and cynomolgus IL-1beta proteins are 96% identical, differing by only six amino acids. Structural and mutational analysis revealed that the unique sIL1R-II binding ability of human IL-1beta is due to a single amino acid difference compared with monkey IL-1beta.

Identification and cloning of a novel IL-15 binding protein that is structurally related to the alpha chain of the IL-2 receptor

Interleukin-15 (IL-15) is a novel cytokine of the four-helix bundle family which shares many biological activities with IL-2, probably due to its interaction with the IL-2 receptor beta and gamma (IL-2R beta and gamma c) chains. We report here the characterization and molecular cloning of a distinct murine IL-15R alpha chain. IL-15R alpha alone displays an affinity of binding for IL-15 equivalent to that of the heterotrimeric IL-2R for IL-2. A biologically functional heteromeric IL-15 receptor complex capable of mediating IL-15 responses was generated through reconstruction experiments in a murine myeloid cell line. IL-15R alpha is structurally similar to IL-2R alpha; together they define a new cytokine receptor family. The distribution of IL-15 and IL-15R alpha mRNA suggests that IL-15 may have biological activities distinct from IL-2.

Oncostatin M and leukemia inhibitory factor trigger overlapping and different signals through partially shared receptor complexes

Leukemia inhibitory factor (LIF) and oncostatin M (OSM) both bind to the same receptor with high affinity and thus mediate an overlapping spectrum of biological activities, the signal transduction mechanisms for which are unclear. We show that mitogen-activated protein kinases are involved in both the LIF and OSM signal transduction pathways. However, we found that OSM is a much more potent inducer of both mitogen-activated protein kinase activity and biological response, both of which correlate with the expression of a second OSM receptor that does not bind LIF. In addition, different patterns of tyrosine-phosphorylated proteins were stimulated by OSM and LIF. We therefore suggest that the two receptors for OSM can be coupled to different signal transduction events.

Identification of a novel low-affinity receptor for human interleukin-7

Human recombinant interleukin-7 (IL-7) was labeled with biotin and used to examine IL-7 receptor (IL-7R) expression and regulation on human primary hematopoietic cells, the monocytoid line THP1, and a range of B- and pre-B-celi lines by flow cytometry. A strong intensity of staining was observed using relatively high (greater than 1 x 10(-7) mol/L) concentrations of biotinylated IL-7 on the majority of cell types examined. This reactivity, which could be effectively competed with excess unlabeled IL-7, did not correlate with either mRNA levels for the cloned receptor or with estimates of IL-7R expression determined by [125I]IL-7 binding. Staining of cells with a titration of biotinylated IL-7 showed, at concentrations greater than 1 x 10(-7) mol/L binding with a Ka in the range of 1 x 10(6) mol/L-1, to 1 x 10(7) mol/L-1, an affinity 100 to 1,000 times lower than that reported for the cloned IL-7 receptor. Further data suggesting the existence of a distinct low- affinity IL-7R were provided by two antibodies specific for the cloned IL-7R. Staining with these monoclonal antibodies (MoAbs) correlated with both IL-7R mRNA levels and receptor expression determined by [125I]IL-7 binding, but was not compatible with the distribution of reactivity seen with biotinylated IL-7. Using tritiated biotin to label IL-7, it was estimated that the total number of IL-7 binding sites on the cell lines examined ranged from 1 x 10(4) to at least 5 x 10(5)/cell. Cross-linking studies showed that [125I]IL-7 associated with two major proteins of approximately 62 Kd and 70 Kd on the surface of RPMI 1788 and THP1 cells, in contrast to the 75- to 80 Kd molecule characteristic of the previously cloned receptor, expressed on the surface of Daudi cells. Proliferation of THP1 cells, expressing only the low-affinity form of IL-7R and lacking detectable IL-7R mRNA, could be inhibited by the addition of IL-7 in a concentration-dependent fashion, indicating that, at least on this cell line, binding of IL-7 with a Ka of 1 x 10(6) mol/L-1 to 1 x 10(7) mol/L-1 can transduce a biological signal. Taken together, the data contained in this report demonstrate the existence of a low-affinity IL-7R, expressed in high numbers on hematopoietic cells of different lineages, which is the product of a gene distinct from that encoding the cloned IL-7R.

The IL-6 signal transducer, gp130: an oncostatin M receptor and affinity converter for the LIF receptor

Leukemia inhibitory factor (LIF) and interleukin-6 (IL-6) are multifunctional cytokines with many similar activities. LIF is structurally and functionally related to another cytokine, Oncostatin M (OSM), that binds to the high-affinity LIF receptor but not to the low-affinity LIF receptor. A complementary DNA was isolated that encodes the high-affinity converting subunit of the LIF receptor. The converter conferred high-affinity binding of both LIF and OSM when expressed with the low-affinity LIF receptor and is identical to the signal transducing subunit of the IL-6 receptor, gp130. The gp130 subunit alone confers low-affinity binding of OSM when expressed in COS-7 cells. This receptor system resembles the high-affinity receptors for granulocyte-macrophage colony-stimulating factor, IL-3, and IL-5, which share a common subunit.

Murine interleukin 7 (IL-7) receptor. Characterization on an IL-7-dependent cell line

A murine cell line (IxN/2b) absolutely dependent upon exogenous IL-7 for continued growth has been obtained that expresses lymphoid precursor and class I MHC antigens and also contains a rearranged mu heavy chain. This cell line has been used to define the binding and structural characteristics of the murine IL-7 receptor using 125I-labeled recombinant murine IL-7. 125I-IL-7 binding to IxN/2b cell was rapid and saturable at both 4 degrees and 37 degrees C. Equilibrium binding studies produced curvilinear Scatchard plots at both temperatures with high and low affinity Ka values of approximately 1 x 10(10) M-1 and 4 x 10(8) M-1, respectively, and a total of 2,000-2,500 IL-7 binding sites expressed per cell. Experiments measuring inhibition of binding of 125I-IL-7 by unlabeled IL-7 also produced data consistent with the existence of two classes of IL-7 receptors. Evidence concerning the possible molecular nature of two classes of IL-7 receptors was provided by dissociation kinetics and affinity crosslinking experiments. The dissociation rate of 125I-IL-7 was markedly increased when measured in the presence of unlabeled IL-7 at both 37 degrees and 4 degrees C, which is diagnostic of a receptor population displaying negative cooperativity. Crosslinking studies showed that under both reducing and nonreducing conditions, the major crosslinked species observed corresponded to a receptor size of 75-79 kD while a less intense higher molecular mass crosslinked species was also seen which corresponded to a receptor size approximately twice as large (159-162 kD). Both types of experiments suggest that the IL-7 receptor may form noncovalently associated dimers in the membrane. The IL-7 receptor was expressed on pre-B cells, but not detected on several murine B cell lines or primary mature B cells. It was also expressed on murine thymocytes, some T lineage cell lines, and on bone marrow-derived macrophage. All cells binding 125I-IL-7 exhibited curvilinear Scatchard plots. No cytokines or growth factors tested were able to inhibit binding of 125I-IL-7 to its receptor. These results define the initial binding and structural characteristics, and the cellular distribution, of the murine IL-7 receptor.

Photosynthetic and leaf morphological characteristics in Leucaena leucocephala as affected by growth under different neutral shade levels

Morphological and physiological measurements on individual leaves of Leucaena leucocephala seedlings were used to study acclimation to neutral shading. The light-saturated photosynthetic rate (Pn max) ranged from 19.6 to 6.5 μmol CO2 m(-2) s(-1) as photosynthetic photon flux density (PPFD) during growth decreased from 27 to 1.6 mol m(-2) s(-1). Stomatal density varied from 144 mm(-2) in plants grown in high PPFD to 84 mm(-2) in plants grown in low PPFD. Average maximal stomatal conductance for H2O was 1.1 in plants grown in high PPFD and 0.3 for plants grown in low PPFD. Plants grown in low PPFD had a greater total chlorophyll content than plants grown in high PPFD (7.2 vs 2.9 mg g(-1) on a unit fresh weight basis, and 4.3 vs 3.7 mg dm(-2) on a unit leaf area basis). Leaf area was largest when plants were grown under the intermediate PPFDs. Leaf density thickness was largest when plants were grown under the largest PPFDs. It is concluded that L. leucocephala shows extensive ability to acclimate to neutral shade, and could be considered a facultative shade plant.

Shade adaptation of photosynthesis in Coffea arabica

The effect of irradiance on the rate of net photosynthesis was measured for mature leaves of coffee grown under five levels of radiation from 100% to 5% daylight. The rate of light-saturated photosynthesis per unit leaf area (PNmax) increased from 2 μmol CO2 m(-2) s(-1) under 5% daylight to 4.4 μmol CO2 m(-2) s(-1) under 100% daylight. The photon flux density (PAR, photosynthetically active radiation) needed for 50% saturation of photosynthesis, as well as the light compensation point, also increased with increasing levels of irradiation during growth. The quantum efficiency of photosynthesis (α), measured by the initial slope of the photosynthetic response to increasing irradiance, was greater under shaded growth conditions. The rate of dark respiration was greatest for plants grown in full daylight. On the basis of the increase in the quantal efficiency of photosynthesis and the low light compensation point when grown under shaded conditions, coffee shows high shade adaptation. Plants adjusted to shade by an increased ability to utilize short-term increases in irradiance above the level of the growth irradiance (measured by the difference between photosynthesis at the growth irradiance, PNg, and PNmax).

Promotion of Flowering in Brassica campestris L. cv Ceres by Sucrose

Flower initiation of the quantitative long-day plant Brassica campestris cv Ceres was earlier and at a lower final leaf number when sucrose was added to the medium in which plants were grown in sterile culture. The optimal concentration of sucrose was 40 to 80 millimolar. This flower-promoting effect of sucrose was not osmotic, as mannitol, sodium chloride, and polyethylene glycol were not effective at equal osmotic potentials.Seedlings grown heterotrophically after treatment with 4-chloro-5-(dimethylamino)-2-phenyl-3-(2H)-pyridazinone to prevent chlorophyll accumulation were also induced to form flower primordia earlier as the sucrose concentration in the medium was increased up to 80 millimolar. Inclusion of 4 millimolar sodium nitrate in the culture medium of green plants did not reduce the flower-promoting effects of sucrose but delayed initiation in plants grown without added sucrose.Removal of CO(2) during a single main or supplementary light period, or both, greatly reduced flower initiation. It is concluded that sucrose may be an important controlling factor determining floral initiation in Brassica.

Participation of Photosynthesis in Floral Induction of the Long Day Plant Anagallis arvensis L

The saturating photon flux density (400 to 700 nanometers) for induction of flowering of the long day plant Anagallis arvensis L. was 1,900 micromoles per square meter per second (6,000 foot-candles) when an 8-hour daylength was extended to 24 hours by a single period of supplementary irradiation. The saturating photon flux density for photosynthetic CO(2) uptake during the same single supplementary light period was lower, at about 1,000 to 650 micromoles per square meter per second (3,000 to 2,000 foot-candles).The per cent flowering and mean number of floral buds per plant were significantly reduced when the light extension treatment was given in CO(2)-free air, and glucose (10 kilograms per cubic meter in water) relieved this effect. Glucose solution also significantly increased flowering of plants given supplementary light treatment in atmospheric air under a photon flux density of 80 micromoles per square meter per second. Increasing the CO(2) concentration to 1.27 grams per cubic meter of CO(2) in air during the supplementary light period did not increase flowering.It is concluded that high photon flux densities promote flowering of Anagallis through both increased photosynthesis and the photomorphogenic action of high irradiance.

Brassica campestris L.: Floral Induction by One Long Day

A strain of Brassica campestris L. responds to a single photoinductive cycle 4 days after sowing. Extending the photoperiod from 8 to 22 or 24 hours, with incandescent light of 538-lux intensity, induced inflorescence in 90 percent of the plants. Inflorescence development was visible on dissection 5 or 6 days after photoinduction. Floral induction increased with duration and intensity of the supplementary light.