Viara P. Grantcharova

Experiment and theory highlight role of native state topology in SH3 folding

We use a combination of experiments, computer simulations and simple model calculations to characterize, first, the folding transition state ensemble of the src SH3 domain, and second, the features of the protein that determine its folding mechanism. Kinetic analysis of mutations at 52 of the 57 residues in the src SH3 domain revealed that the transition state ensemble is even more polarized than suspected earlier: no single alanine substitution in the N-terminal 15 residues or the C-terminal 9 residues has more than a two-fold effect on the folding rate, while such substitutions at 15 sites in the central three-stranded β-sheet cause significant decreases in the folding rate. Molecular dynamics (MD) unfolding simulations and ab initio folding simulations on the src SH3 domain exhibit a hierarchy of folding similar to that observed in the experiments. The similarity in folding mechanism of different SH3 domains and the similar hierarchy of structure formation observed in the experiments and the simulations can be largely accounted for by a simple native state topology-based model of protein folding energy landscapes.

Mechanisms of protein folding

The strong correlation between protein folding rates and the contact order suggests that folding rates are largely determined by the topology of the native structure. However, for a given topology, there may be several possible low free energy paths to the native state and the path that is chosen (the lowest free energy path) may depend on differences in interaction energies and local free energies of ordering in different parts of the structure. For larger proteins whose folding is assisted by chaperones, such as the Escherichia coli chaperonin GroEL, advances have been made in understanding both the aspects of an unfolded protein that GroEL recognizes and the mode of binding to the chaperonin. The possibility that GroEL can remove non-native proteins from kinetic traps by unfolding them either during polypeptide binding to the chaperonin or during the subsequent ATP-dependent formation of folding-active complexes with the co-chaperonin GroES has also been explored.

Therapeutically Targeting ErbB3: A Key Node in Ligand-Induced Activation of the ErbB Receptor–PI3K Axis

Computational modeling of the ErbB signaling network affirms ErbB3 as a therapeutic target. Zooming In on ErbB3 Aberrant signaling involving the ErbB family of receptors, which can signal as homo- or heterodimers to activate the phosphatidylinositol 3-kinase (PI3K) signaling pathway, has been implicated as contributing to various cancers. Using a systems approach, Schoeberl et al. implicated ErbB3—a member of the ErbB family that is catalytically inactive—as critical to signaling stimulated by ligands that bind either ErbB1 or ErbB3. Computational analysis suggested that inhibiting ligand binding to ErbB3 might represent a more successful approach to treating cancers associated with ligand-induced stimulation of ErbB-PI3K signaling mediated by combinatorial receptor activation than do current therapies that target overexpressed or mutationally activated ErbB-family receptors. Moreover, experimental analysis revealed that a monoclonal antibody developed on the basis of this strategy could stop the growth of tumors grafted into immunodeficient mice. The signaling network downstream of the ErbB family of receptors has been extensively targeted by cancer therapeutics; however, understanding the relative importance of the different components of the ErbB network is nontrivial. To explore the optimal way to therapeutically inhibit combinatorial, ligand-induced activation of the ErbB–phosphatidylinositol 3-kinase (PI3K) axis, we built a computational model of the ErbB signaling network that describes the most effective ErbB ligands, as well as known and previously unidentified ErbB inhibitors. Sensitivity analysis identified ErbB3 as the key node in response to ligands that can bind either ErbB3 or EGFR (epidermal growth factor receptor). We describe MM-121, a human monoclonal antibody that halts the growth of tumor xenografts in mice and, consistent with model-simulated inhibitor data, potently inhibits ErbB3 phosphorylation in a manner distinct from that of other ErbB-targeted therapies. MM-121, a previously unidentified anticancer therapeutic designed using a systems approach, promises to benefit patients with combinatorial, ligand-induced activation of the ErbB signaling network that are not effectively treated by current therapies targeting overexpressed or mutated oncogenes.

Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain

Experimental and theoretical studies on the folding of small proteins such as the chymotrypsin inhibitor 2 (CI-2) and the P22 Arc repressor suggest that the folding transition state is an expanded version of the native state with most interactions partially formed. Here we report that this picture does not hold generally: a hydrogen bond network involving two β-turns and an adjacent hydrophobic cluster appear to be formed in the folding transition state of the src SH3 domain, while the remainder of the polypeptide chain is largely unstructured. Comparison with data on other small proteins suggests that this structural polarization is a consequence of the topology of the SH3 domain fold. The non-uniform distribution of structure in the folding transition state provides a challenging test for computational models of the folding process.

Simplified proteins: minimalist solutions to the 'protein folding problem'.

Recent research has suggested that stable, native proteins may be encoded by simple sequences of fewer than the full set of 20 proteogenic amino acids. Studies of the ability of simple amino acid sequences to encode stable, topologically complex, native conformations and to fold to these conformations in a biologically relevant time frame have provided insights into the sequence determinants of protein structure and folding kinetics. They may also have important implications for protein design and for theories of the origins of protein synthesis itself.

A systematic, family-wide investigation reveals that ~30% of mammalian PDZ domains engage in PDZ-PDZ interactions

PDZ domains are independently folded modules that typically mediate protein-protein interactions by binding to the C termini of their target proteins. However, in a few instances, PDZ domains have been reported to dimerize with other PDZ domains. To investigate this noncanonical-binding mode further, we used protein microarrays comprising virtually every mouse PDZ domain to systematically query all possible PDZ-PDZ pairs. We then used fluorescence polarization to retest and quantify interactions and coaffinity purification to test biophysically validated interactions in the context of their full-length proteins. Overall, we discovered 37 PDZ-PDZ interactions involving 46 PDZ domains (~30% of all PDZ domains tested), revealing that dimerization is a more frequently used binding mode than was previously appreciated. This suggests that many PDZ domains evolved to form multiprotein complexes by simultaneously interacting with more than one ligand.

Systems biology driving drug development: from design to the clinical testing of the anti-ErbB3 antibody seribantumab (MM-121)

The ErbB family of receptor tyrosine kinases comprises four members: epidermal growth factor receptor (EGFR/ErbB1), human EGFR 2 (HER2/ErbB2), ErbB3/HER3, and ErbB4/HER4. The first two members of this family, EGFR and HER2, have been implicated in tumorigenesis and cancer progression for several decades, and numerous drugs have now been approved that target these two proteins. Less attention, however, has been paid to the role of this family in mediating cancer cell survival and drug tolerance. To better understand the complex signal transduction network triggered by the ErbB receptor family, we built a computational model that quantitatively captures the dynamics of ErbB signaling. Sensitivity analysis identified ErbB3 as the most critical activator of phosphoinositide 3-kinase (PI3K) and Akt signaling, a key pro-survival pathway in cancer cells. Based on this insight, we designed a fully human monoclonal antibody, seribantumab (MM-121), that binds to ErbB3 and blocks signaling induced by the extracellular growth factors heregulin (HRG) and betacellulin (BTC). In this article, we present some of the key preclinical simulations and experimental data that formed the scientific foundation for three Phase 2 clinical trials in metastatic cancer. These trials were designed to determine if patients with advanced malignancies would derive benefit from the addition of seribantumab to standard-of-care drugs in platinum-resistant/refractory ovarian cancer, hormone receptor-positive HER2-negative breast cancer, and EGFR wild-type non-small cell lung cancer (NSCLC). From preclinical studies we learned that basal levels of ErbB3 phosphorylation correlate with response to seribantumab monotherapy in mouse xenograft models. As ErbB3 is rapidly dephosphorylated and hence difficult to measure clinically, we used the computational model to identify a set of five surrogate biomarkers that most directly affect the levels of p-ErbB3: HRG, BTC, EGFR, HER2, and ErbB3. Preclinically, the combined information from these five markers was sufficient to accurately predict which xenograft models would respond to seribantumab, and the single-most accurate predictor was HRG. When tested clinically in ovarian, breast and lung cancer, HRG mRNA expression was found to be both potentially prognostic of insensitivity to standard therapy and potentially predictive of benefit from the addition of seribantumab to standard of care therapy in all three indications. In addition, it was found that seribantumab was most active in cancers with low levels of HER2, consistent with preclinical predictions. Overall, our clinical studies and studies of others suggest that HRG expression defines a drug-tolerant cancer cell phenotype that persists in most solid tumor indications and may contribute to rapid clinical progression. To our knowledge, this is the first example of a drug designed and clinically tested using the principles of Systems Biology.

Abstract LB-243: The ErbB3-targeting antibody MM-121 (seribantumab) reverses heregulin-driven resistance to multiple chemotherapies on tumor cell growth

Purpose: Heregulin-mediated activation of the human epidermal growth factor receptor 3 (HER3/ErbB3) is required for the growth and survival of many epithelial cancers. This signaling pathway is also emerging as a mechanism of resistance to targeted agents and chemotherapies. MM-121 (seribantumab) is an investigational human monoclonal anti-ErbB3 antibody that has previously been shown to effectively block ligand-dependent activation of ErbB3 in a range of tumors, and has demonstrated clinical activity in biomarker positive patients in several Phase II trials. The purpose of this study was to examine in three indications of interest, the ability of heregulin to induce resistance to standard chemotherapies and the reversal of this effect by MM-121. Such systematic evaluation of different combinations can serve as a guide for the future clinical development of MM-121. Methods: To assess the effect of heregulin and MM-121 on chemotherapies in cancer cells, we conducted a high throughput proliferation screen in 3D cultures. A panel of 60 cell lines of relevant clinical indications (ovarian, breast and lung cancer) was selected and tested for the sensitivity to respective standard-of-care chemotherapies in the absence or presence of exogenously added heregulin. Using these data, we analyzed the rescuing capacity of heregulin and the MM-121 combination9s sensitivity, and selected representative combinations for in vivo models. Results: We show that in a large panel of cancer cell lines the presence of heregulin can induce resistance to multiple chemotherapies with very different mechanisms of action. The combination of MM-121 with any one of these chemotherapies can reverse the heregulin-meditated rescue and provide an additive treatment effect at therapeutically relevant doses achieved in the clinic. These results were further validated in xenograft mouse models of all three indications, using representative chemotherapies and doses. In addition, biomarker analysis revealed that ErbB3 receptor levels largely determine responsiveness to heregulin and MM-121. Conclusions: MM-121 is an anti-ErbB3 antibody designed to block ligand-mediated signaling, and currently in clinical development. The results presented here demonstrate the role of heregulin in reducing the sensitivity of tumors to standard-of-care chemotherapies, and the effect of ErbB3 pathway inhibition across indications. Citation Format: Kristina Masson, Viara Grantcharova, Olga Burenkova, Marisa Wainszelbaum, Sergio Iadevaia, Sharlene Adams, Andreas Raue, Akos Czibere, Birgit Schoeberl, Gavin MacBeath. The ErbB3-targeting antibody MM-121 (seribantumab) reverses heregulin-driven resistance to multiple chemotherapies on tumor cell growth. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-243. doi:10.1158/1538-7445.AM2015-LB-243

Abstract 3756: Prediction of xenograft response to MM-121, an anti-ErbB3 inhibitor, using computational modeling and measurements of five biomarkers

Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC One of the challenges faced by targeted therapeutics currently in the clinic is the relatively small population of patients who derive significant benefit from their use. We report the development of a preclinical classifier which can correctly predict xenograft response to MM-121, an anti-ErbB3 antibody, based on the measurement of a few key biomarkers in cell lysates. Deregulation of the ErbB family receptors is common in many cancers. Using a combination of computational modeling and quantitative experiments we identified ErbB3 as a key mediator of mitogenic signaling downstream of the ErbB receptors. Based on these results, we developed MM-121, a first in class anti-ErbB3 monoclonal antibody that blocks heregulin-induced signaling and inhibits tumor growth in multiple xenograft models of human cancer. Here we present our efforts to derive a predictive biomarker signature that identifies tumors that are responsive to MM-121. Using our computational model of the ErbB signaling pathway we identified the five most critical proteins for predicting activation of phospho-AKT - a key mediator of cell survival and apoptosis. These proteins include MM-121s target, ErbB3, and its ligand, heregulin. We profiled these biomarkers in a large panel of cancer cell lines, and using the measured effect of MM-121 on inhibiting tumor growth in eight xenograft tumor models, we determined a classification rule for predicting xenograft response. We subsequently used this classification rule to correctly predict a priori MM-121 response in 11 xenograft models. These results suggest that our computationally-derived biomarker signature is sufficient for predicting response to MM-121 in xenografts, and could offer significant clinical benefit by helping select patients for MM-121 treatment. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3756.

Abstract 1806: Efficacy of MM121 in ER+ and triple negative breast cancer studies

In women, breast cancer is among the most common cancers and the fifth most common cause of cancer deaths. Due to the heterogeneity of the disease, 10-year progression free survival can vary widely with stage and type from 98% to 10%. We present data showing that MM-121, a fully human monoclonal anti-ErbB3 antibody, is efficacious in studies of both hormone dependent (ER+) and triple negative (ER-,PR-, Low Erb2) breast cancer lines that express the molecular profile consistent with MM-121 response (co-expression of ErbB3 and HRG). Using a combination of computational and experimental approaches, ErbB3 was identified as a critical transducer of oncogenic signaling leading to the development of MM-121, a first in class anti-ErbB3 antibody. We have previously demonstrated that MM-121, when used as a single agent, inhibits heregulin-induced signaling events in human cancer cell lines. Moreover, MM-121 caused dose-dependent inhibition of tumor growth in multiple xenograft models of human cancer, including ovarian, renal cell, pancreatic, lung, and prostate cancer. Estrogen dependent, or ER+ breast cancers, make up about 80% of breast cancers. A standard treatment for ER+ breast cancer includes hormone therapy; however a substantial number of ER+ breast cancers eventually develop resistance requiring additional treatments. Here we show that in ER+ breast cancer cells, MM-121 can block HRG induced ErbB3 activation and VEGF secretion as well as HGF induced pErbB3 in vitro. Additionally, in ER+ breast cancer xenograft models, MM121 is effective in combination with both chemotherapy agents and targeted therapies and may be effective in ER+ breast cancers that are refractory to hormone treatment. The triple negative breast cancers are characterized by poor prognosis, aggressiveness, and reduced responsiveness to standard treatments. MM-121 used as a single agent therapy was able to suppress tumor growth in triple negative primary human tumors, when grown as xenografts suggesting that MM-121 monotherapy may be clinically efficacious in triple negative breast cancers. Together, these data suggest that MM-121, when used as a single agent or in combination with other therapies, could offer significant clinical benefit to both ER+ and triple negative breast cancer patients. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1806.