PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFold

Protein-protein interactions underlie nearly all cellular processes. With the advent of protein structure prediction methods such as AlphaFold2 (AF2), models of specific protein pairs can be built extremely accurately in most cases. However, determining the relevance of a given protein pair remains an open question. It is presently unclear how to use best structure-based tools to infer whether a pair of candidate proteins indeed interact with one another: ideally, one might even use such information to screen amongst candidate pairings to build up protein interaction networks. Whereas methods for evaluating quality of modeled protein complexes have been co-opted for determining which pairings interact (e.g., pDockQ and iPTM), there have been no rigorously benchmarked methods for this task. Here we introduce PPIscreenML, a classification model trained to distinguish AF2 models of interacting protein pairs from AF2 models of compelling decoy pairings. We find that PPIscreenML out-performs methods such as pDockQ and iPTM for this task, and further that PPIscreenML exhibits impressive performance when identifying which ligand/receptor pairings engage one another across the structurally conserved tumor necrosis factor superfamily (TNFSF). Analysis of benchmark results using complexes not seen in PPIscreenML development strongly suggest that the model generalizes beyond training data, making it broadly applicable for identifying new protein complexes based on structural models built with AF2.

Musashi-2 (MSI2) regulation of DNA damage response in lung cancer

Lung cancer is one of the most common types of cancer worldwide. Non-small cell lung cancer (NSCLC), typically caused by KRAS and TP53 driver mutations, represents the majority of all new lung cancer diagnoses. Overexpression of the RNA-binding protein (RBP) Musashi-2 (MSI2) has been associated with NSCLC progression. To investigate the role of MSI2 in NSCLC development, we compared the tumorigenesis in mice with lung-specific Kras-activating mutation and Trp53 deletion, with and without Msi2 deletion (KPM2 versus KP mice). KPM2 mice showed decreased lung tumorigenesis in comparison with KP mice. In addition, KPM2 lung tumors showed evidence of decreased proliferation, but increased DNA damage, marked by increased levels of phH2AX (S139) and phCHK1 (S345), but decreased total and activated ATM. Using cell lines from KP and KPM2 tumors, and human NSCLC cell lines, we found that MSI2 directly binds ATM mRNA and regulates its translation. MSI2 depletion impaired DNA damage response (DDR) signaling and sensitized human and murine NSCLC cells to treatment with PARP inhibitors in vitro and in vivo. Taken together, we conclude that MSI2 supports NSCLC tumorigenesis, in part, by supporting repair of DNA damage by controlling expression of DDR proteins. These results suggest that targeting MSI2 may be a promising strategy for lung cancers treated with DNA-damaging agents.

Novel Substrate Prediction for the TAM Family of RTKs Using Phosphoproteomics and Structure-Based Modeling

The TAM family of receptor tyrosine kinases is implicated in multiple distinct oncogenic signaling pathways. However, to date, there are no FDA-approved small molecule inhibitors for the TAM kinases. Inhibitor design and screening rely on tools to study the kinase activity. Our goal was to address this gap by designing a set of synthetic peptide substrates for each of the TAM family members: Tyro3, Axl, and Mer. We used an in vitro phosphoproteomics workflow to determine the substrate profile of each TAM kinase and input the identified substrates into our data processing pipeline, KINATEST-ID, producing a position-specific scoring matrix for each target kinase and generating a list of candidate synthetic peptide substrates. We synthesized and characterized a set of those substrate candidates, systematically measuring their initial phosphorylation rate with each TAM kinase by LC-MS. We also used the multimer modeling function of AlphaFold2 (AF2) to predict peptide-kinase interactions at the active site for each of the novel candidate peptide sequences against each of the TAM family kinases and observed that, remarkably, every sequence for which it predicted a putative catalytically competent interaction was also demonstrated biochemically to be a substrate for one or more of the TAM kinases. This work shows that kinase substrate design can be achieved using a combination of preference motifs and structural modeling, and it provides the first demonstration of peptide-protein interaction modeling with AF2 for predicting the likelihood of constructive catalytic interactions.

Secreted folate receptor γ drives fibrogenesis in metabolic dysfunction-associated steatohepatitis by amplifying TGFβ signaling in hepatic stellate cells

Hepatic fibrosis is the primary determinant of mortality in patients with metabolic dysfunction-associated steatohepatitis (MASH). Transforming growth factor-β (TGFβ), a master profibrogenic cytokine, is a promising therapeutic target that has not yet been translated into an effective therapy in part because of liabilities associated with systemic TGFβ antagonism. We have identified that soluble folate receptor γ (FOLR3), which is expressed in humans but not in rodents, is a secreted protein that is elevated in the livers of patients with MASH but not in those with metabolic dysfunction-associated steatotic liver disease, those with type II diabetes, or healthy individuals. Global proteomics showed that FOLR3 was the most highly significant MASH-specific protein and was positively correlated with increasing fibrosis stage, consistent with stimulation of activated hepatic stellate cells (HSCs), which are the key fibrogenic cells in the liver. Exposure of HSCs to exogenous FOLR3 led to elevated extracellular matrix (ECM) protein production, an effect synergistically potentiated by TGFβ1. We found that FOLR3 interacts with the serine protease HTRA1, a known regulator of TGFBR, and activates TGFβ signaling. Administration of human FOLR3 to mice induced severe bridging fibrosis and an ECM pattern resembling human MASH. Our study thus uncovers a role of FOLR3 in enhancing fibrosis.

Poor Generalization by Current Deep Learning Models for Predicting Binding Affinities of Kinase Inhibitors

The extreme surge of interest over the past decade surrounding the use of neural networks has inspired many groups to deploy them for predicting binding affinities of drug-like molecules to their receptors. A model that can accurately make such predictions has the potential to screen large chemical libraries and help streamline the drug discovery process. However, despite reports of models that accurately predict quantitative inhibition using protein kinase sequences and inhibitors' SMILES strings, it is still unclear whether these models can generalize to previously unseen data. Here, we build a Convolutional Neural Network (CNN) analogous to those previously reported and evaluate the model over four datasets commonly used for inhibitor/kinase predictions. We find that the model performs comparably to those previously reported, provided that the individual data points are randomly split between the training set and the test set. However, model performance is dramatically deteriorated when all data for a given inhibitor is placed together in the same training/testing fold, implying that information leakage underlies the models' performance. Through comparison to simple models in which the SMILES strings are tokenized, or in which test set predictions are simply copied from the closest training set data points, we demonstrate that there is essentially no generalization whatsoever in this model. In other words, the model has not learned anything about molecular interactions, and does not provide any benefit over much simpler and more transparent models. These observations strongly point to the need for richer structure-based encodings, to obtain useful prospective predictions of not-yet-synthesized candidate inhibitors.

An African-Specific Variant of TP53 Reveals PADI4 as a Regulator of p53-Mediated Tumor Suppression

TP53 is the most frequently mutated gene in cancer, yet key target genes for p53-mediated tumor suppression remain unidentified. Here, we characterize a rare, African-specific germline variant of TP53 in the DNA-binding domain Tyr107His (Y107H). Nuclear magnetic resonance and crystal structures reveal that Y107H is structurally similar to wild-type p53. Consistent with this, we find that Y107H can suppress tumor colony formation and is impaired for the transactivation of only a small subset of p53 target genes; this includes the epigenetic modifier PADI4, which deiminates arginine to the nonnatural amino acid citrulline. Surprisingly, we show that Y107H mice develop spontaneous cancers and metastases and that Y107H shows impaired tumor suppression in two other models. We show that PADI4 is itself tumor suppressive and that it requires an intact immune system for tumor suppression. We identify a p53-PADI4 gene signature that is predictive of survival and the efficacy of immune-checkpoint inhibitors.

SIGNIFICANCE

We analyze the African-centric Y107H hypomorphic variant and show that it confers increased cancer risk; we use Y107H in order to identify PADI4 as a key tumor-suppressive p53 target gene that contributes to an immune modulation signature and that is predictive of cancer survival and the success of immunotherapy. See related commentary by Bhatta and Cooks, p. 1518. This article is highlighted in the In This Issue feature, p. 1501.

Musashi-2 (MSI2) regulation of DNA damage response in lung cancer

Lung cancer is one of the most common types of cancers worldwide. Non-small cell lung cancer (NSCLC), typically caused by KRAS and TP53 driver mutations, represents the majority of all new lung cancer diagnoses. Overexpression of the RNA-binding protein (RBP) Musashi-2 (MSI2) has been associated with NSCLC progression. To investigate the role of MSI2 in NSCLC development, we compared the tumorigenesis in mice with lung-specific Kras -activating mutation and Trp53 deletion, with and without Msi2 deletion (KP versus KPM2 mice). KPM2 mice showed decreased lung tumorigenesis in comparison with KP mice what supports published data. In addition, using cell lines from KP and KPM2 tumors, and human NSCLC cell lines, we found that MSI2 directly binds ATM/Atm mRNA and regulates its translation. MSI2 depletion impaired DNA damage response (DDR) signaling and sensitized human and murine NSCLC cells to treatment with PARP inhibitors in vitro and in vivo . Taken together, we conclude that MSI2 supports lung tumorigenesis, in part, by direct positive regulation of ATM protein expression and DDR. This adds the knowledge of MSI2 function in lung cancer development. Targeting MSI2 may be a promising strategy to treat lung cancer.

Significance

This study shows the novel role of Musashi-2 as regulator of ATM expression and DDR in lung cancer.

Abstract 2608: Defining the function of tumor suppressor p53 arginine 181 residue in tumorigenesis

The gene Tp53 encodes for the protein p53 which has many tumor suppressive functions. Li-Fraumeni syndrome is characterized by germline Tp53 mutations that significantly increase the risk of cancer. The p53 amino acid residue arginine 181 is one such mutation site that promotes tumorigenesis by impacting a phenomenon known as p53 cooperativity. This is the ability of one p53 molecule to interact with another in order to efficiently bind specific sites on DNA to enact specific p53 functional pathways. Two p53 molecules interact with each other through the formation of a salt bridge between H1 helices found in respective DNA binding domains. The two key amino acid residues in this salt bridge are positively charged arginine (R) 181 and negatively charged glutamic acid (E) 180 which form electrostatic interactions with the residues on the opposite p53 H1 helix. Cooperativity mutants such as R181H and R181C show a hypomorphic behavior wherein much of p53’s canonical functions remain intact. Colony suppression data show that H1299 cells with p53 R181H and R181C yield a similar number of colonies as p53 wild type, which is significantly fewer than the yield of p53 hotspot mutation R175H and the absence of p53. Despite retaining some wild-type behavior, R181 mutants are found in LFS patients with cancer. Discovering the importance of the R181 residue for p53’s role in defending against tumorigenesis can lead to unique treatment opportunities for LFS patients with cooperativity mutants.

Citation Format: Renyta Moses, Gregory Kelly, Alexandra Indeglia, Sven Miller, John Karanicolas, Maureen Murphy, Kara Maxwell. Defining the function of tumor suppressor p53 arginine 181 residue in tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2608.

Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry

RNA-binding proteins (RBPs) are key post-transcriptional regulators of gene expression, and thus underlie many important biological processes. Here, we developed a strategy that entails extracting a "hotspot pharmacophore" from the structure of a protein-RNA complex, to create a template for designing small-molecule inhibitors and for exploring the selectivity of the resulting inhibitors. We demonstrate this approach by designing inhibitors of Musashi proteins MSI1 and MSI2, key regulators of mRNA stability and translation that are upregulated in many cancers. We report this novel series of MSI1/MSI2 inhibitors is specific and active in biochemical, biophysical, and cellular assays. This study extends the paradigm of "hotspots" from protein-protein complexes to protein-RNA complexes, supports the "druggability" of RNA-binding protein surfaces, and represents one of the first rationally-designed inhibitors of non-enzymatic RNA-binding proteins. Owing to its simplicity and generality, we anticipate that this approach may also be used to develop inhibitors of many other RNA-binding proteins; we also consider the prospects of identifying potential off-target interactions by searching for other RBPs that recognize their cognate RNAs using similar interaction geometries. Beyond inhibitors, we also expect that compounds designed using this approach can serve as warheads for new PROTACs that selectively degrade RNA-binding proteins.

Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry

RNA-binding proteins (RBPs) are key post-transcriptional regulators of gene expression, and thus underlie many important biological processes. Here, we developed a strategy that entails extracting a "hotspot pharmacophore" from the structure of a protein-RNA complex, to create a template for designing small-molecule inhibitors and for exploring the selectivity of the resulting inhibitors. We demonstrate this approach by designing inhibitors of Musashi proteins MSI1 and MSI2, key regulators of mRNA stability and translation that are upregulated in many cancers. We report this novel series of MSI1/MSI2 inhibitors is specific and active in biochemical, biophysical, and cellular assays. This study extends the paradigm of "hotspots" from protein-protein complexes to protein-RNA complexes, supports the "druggability" of RNA-binding protein surfaces, and represents one of the first rationally-designed inhibitors of non-enzymatic RNA-binding proteins. Owing to its simplicity and generality, we anticipate that this approach may also be used to develop inhibitors of many other RNA-binding proteins; we also consider the prospects of identifying potential off-target interactions by searching for other RBPs that recognize their cognate RNAs using similar interaction geometries. Beyond inhibitors, we also expect that compounds designed using this approach can serve as warheads for new PROTACs that selectively degrade RNA-binding proteins.

Abstract 874: MSI2 regulates VEGFR2 signaling and tumor progression in NSCLC

Lung cancer holds second place in incidence and first place in mortality among all cancers, both in men and women, with metastasis contributing to the vast majority of deaths. Recently, expression of vascular endothelial growth factor receptor-2 (VEGFR2) on both endothelial and tumor cells was demonstrated as one of the key mechanisms contributing to growth of non-small cell lung cancer (NSCLC), the most common subtype of lung cancer. VEGFR2 dependent signaling is critical both for tumor autocrine functions related to NSCLC migration, and in paracrine control of tumor angiogenesis through action on tumor-proximal endothelial cells, suggesting a potential mechanism for growth control. Several drugs targeting VEGFR2 signaling pathway demonstrated their clinical efficacy in NSCLC setting, including VEGFR2 and VEGF-A inhibitors, VEGF-A/PIGF trap. Recently our group demonstrated that RNA-binding protein Musashi-2 (MSI2) is driving progression and metastasis of NSCLC. MSI2 regulates mRNA translation of multiple targets, its expression is upregulated in the metastasis-competent murine and human lung cancer cell lines and is progressively elevated in lung cancer samples. The goal of this study is to define the role of MSI2 in sustaining VEGFR2 signaling during NSCLC progression. Using reverse RNA immunoprecipitation (RIP) qPCR analysis, we demonstrate that MSI2 directly binds VEGFR2 mRNA. Reverse protein phase array (RPPA) of several NSCLC cell line models with expression or knockdown of MSI2 and subsequent direct validation showed that MSI2 strongly and positively regulates expression of VEGFR2. Subsequent mechanistical analysis revealed that MSI2 knockdown leads to decreased VEGFR2 protein and mRNA levels expression in several NSCLC cell lines in vitro, resulting in increased apoptosis via inhibition of VEGFR2 signaling pathway. To better characterize MSI2 biology, we’ve crossed the B6/129S4-Msi2tm1.1Cjl/J (M2) mice with B6/129S/Sv-Krastm3Tyj/J;Trp53tm1Brn/J (KP) mice and generated novel B6/129S/Sv-KP;Msi2-/- (KPM2) mouse model. Induction of tumorigenesis in KP mice using Cre adenovirus leads to development of lung adenocarcinoma. Induction of lung-specific Cre resulted in tumorigenesis in both KP and KPM2 mice. Interestingly, we observed significant decrease in both total lung tumor number and total lung tumor burden in KPM2 compared to KP mice. Next, we established three novel KP and KPM2 derived cell lines from mouse lung tumors and found that KPM2 cell lines demonstrate reduced proliferation capacity and VEGFR2 mRNA level relative to KP cell lines. Additional studies to understand an impact of MSI2 deletion in KP cell lines are ongoing. Taken together, MSI2 is a promising target for NSCLC treatment, as this protein regulates VEGFR2 signaling and apoptosis in cell models and contributes to KP tumorigenesis in vivo.

Citation Format: Igor Bychkov, Alexander Deneka, Iuliia Topchu, Petr Makhov, Alexander Kudinov, Anna Nikonova, John Karanicolas, Erica Golemis, Christopher Lengner, Hossein Borghaei, Jyoti Patel, Yanis Boumber. MSI2 regulates VEGFR2 signaling and tumor progression in NSCLC [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 874.

Abstract 3718: NSD histone methyltransferases drive cell proliferation in HPV-negative head and neck squamous cell carcinoma (HNSCC)

Histone modifications play important role in regulating the function and structure of chromatin. Abnormal histone methylation is often detected during tumor development and progression. NSD1, NSD2, and NSD3 are key histone methyltransferases (HMTs) that catalyze lysine 36 dimethylation (K36me2) at histone H3. Inactivating NSD1 mutations are frequent in head neck squamous cell carcinoma (HNSCC) commonly occur in HPV-negative oropharyngeal (OP) carcinoma and laryngeal carcinomas (LC), and define a novel prognostic subtype in LC, where they associate with dramatically improved overall and progression-free survival. Here, we explored the biological impact of the loss of function of NSD1 in head neck squamous carcinoma (HNSCC). First, we discovered that HNSCC cells with a damaging mutation in NSD1 have reduced K36me2 methylation levels relative to NSD1 wild-type HNSCC cells. Second, we also found slower cell proliferation in NSD1 mutant cell line (SCC4) in comparison with other NSD1 WT cell lines. To further investigate the biologic impact of NSDs, we knocked down NSD1 and NSD2 with shRNA in different histologic subtypes of HNSCC cell lines (JHU011, JHU022, Cal27, and FaDu cell lines). We discovered that depletion of NSD1 and NSD2 results in a reduction of K36me2 and a significant decrease in cell proliferation and clonogenic formation in HNSCC, but not in lung cancer cells. Next, we performed a flow cytometry-based assay and found that NSD1/NSD2 depletion in HNSCC cells causes a significant increase in apoptosis level. We also probed for gene expression and signaling in HNSCC cells following NSD1 depletion using RNA sequencing and reverse protein phase array (RPPA) approaches. From a list of RPPA candidate targets of NSD1, we confirmed the decrease in the protein and mRNA level of Phosphatidylinositol-5-Phosphate 4-Kinase Type 2 Beta (PIP4K2B), but not other members of this family (PIP4K2A and PIP4K2C). PIP4K2B may regulate the ratio of lipid messengers PI5P and PI(4,5)P2 (substrate and reaction product, respectively). The level of phosphorylation of mitogen-activated kinase p70S6 was also decreased under NSD1 knockdown. PIP4K2B siRNA depletion has also led to a significant decrease in HNSCC proliferation. Taken together, this data supports the idea that NSD1 is required for HNSCC cell proliferation via PIP4K2B. Downstream signaling, gene expression effects, and possible cell cycle regulation by NSD enzymes remain to be investigated in more detail. Further, NSDs might be attractive targets for drug development, and targeting NSD1/NSD2 enzymes may be a new strategy for improving outcomes in HNSCC patients.

Citation Format: Iuliia Topchu, Rajendra Pangeni, Igor Bychkov, Petr Makhov, John Karanicolas, Jindan Yu, Erica Golemis, Jochen Lorch, Yanis Boumber. NSD histone methyltransferases drive cell proliferation in HPV-negative head and neck squamous cell carcinoma (HNSCC) [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 3718.

Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2)

Musashi 2 (MSI2) is an RNA binding protein (RBP) that regulates asymmetric cell division and cell fate decisions in normal and cancer stem cells. MSI2 appears to repress translation by binding to 3′ untranslated regions (3′UTRs) of mRNA, but the identity of functional targets remains unknown. Here, we used individual nucleotide resolution cross-linking and immunoprecipitation (iCLIP) to identify direct RNA binding partners of MSI2 and integrated these data with polysome profiling to obtain insights into MSI2 function. iCLIP revealed specific MSI2 binding to thousands of mRNAs largely in 3′UTRs, but translational differences were restricted to a small fraction of these transcripts, indicating that MSI2 regulation is not triggered by simple binding. Instead, the functional targets identified here were bound at higher density and contain more ‘UAG’ motifs compared to targets bound nonproductively. To further distinguish direct and indirect targets, MSI2 was acutely depleted. Surprisingly, only 50 transcripts were found to undergo translational induction on acute loss. Using complementary approaches, we determined eukaryotic translation initiation factor 3A (EIF3A) to be an immediate, direct target. We propose that MSI2 downregulation of EIF3A amplifies these effects on translation. Our results also underscore the challenges in defining functional targets of RBPs since mere binding does not imply a discernible functional interaction.

Structural Plasticity Is a Feature of Rheostat Positions in the Human Na+/Taurocholate Cotransporting Polypeptide (NTCP)

In the Na⁺/taurocholate cotransporting polypeptide (NTCP), the clinically relevant S267F polymorphism occurs at a "rheostat position". That is, amino acid substitutions at this position ("S267X") lead to a wide range of functional outcomes. This result was particularly striking because molecular models predicted the S267X side chains are buried, and thus, usually expected to be less tolerant of substitutions. To assess whether structural tolerance to buried substitutions is widespread in NTCP, here we used Rosetta to model all 19 potential substitutions at another 13 buried positions. Again, only subtle changes in the calculated stabilities and structures were predicted. Calculations were experimentally validated for 19 variants at codon 271 ("N271X"). Results showed near wildtype expression and rheostatic modulation of substrate transport, implicating N271 as a rheostat position. Notably, each N271X substitution showed a similar effect on the transport of three different substrates and thus did not alter substrate specificity. This differs from S267X, which altered both transport kinetics and specificity. As both transport and specificity may change during protein evolution, the recognition of such rheostat positions may be important for evolutionary studies. We further propose that the presence of rheostat positions is facilitated by local plasticity within the protein structure. Finally, we note that identifying rheostat positions may advance efforts to predict new biomedically relevant missense variants in NTCP and other membrane transport proteins.

Efficient Hit-to-Lead Searching of Kinase Inhibitor Chemical Space via Computational Fragment Merging

In early-stage drug discovery, the hit-to-lead optimization (or "hit expansion") stage entails starting from a newly identified active compound and improving its potency or other properties. Traditionally, this process relies on synthesizing and evaluating a series of analogues to build up structure-activity relationships. Here, we describe a computational strategy focused on kinase inhibitors, intended to expedite the process of identifying analogues with improved potency. Our protocol begins from an inhibitor of the target kinase and generalizes the synthetic route used to access it. By searching for commercially available replacements for the individual building blocks used to make the parent inhibitor, we compile an enumerated library of compounds that can be accessed using the same chemical transformations; these huge libraries can exceed many millions─or billions─of compounds. Because the resulting libraries are much too large for explicit virtual screening, we instead consider alternate approaches to identify the top-scoring compounds. We find that contributions from individual substituents are well described by a pairwise additivity approximation, provided that the corresponding fragments position their shared core in precisely the same way relative to the binding site. This key insight allows us to determine which fragments are suitable for merging into single new compounds and which are not. Further, the use of pairwise approximation allows interaction energies to be assigned to each compound in the library without the need for any further structure-based modeling: interaction energies instead can be reliably estimated from the energies of the component fragments, and the reduced computational requirements allow for flexible energy minimizations that allow the kinase to respond to each substitution. We demonstrate this protocol using libraries built from six representative kinase inhibitors drawn from the literature, which target five different kinases: CDK9, CHK1, CDK2, EGFR^T790M, and ACK1. In each example, the enumerated library includes additional analogues reported by the original study to have activity, and these analogues are successfully prioritized within the library. We envision that the insights from this work can facilitate the rapid assembly and screening of increasingly large libraries for focused hit-to-lead optimization. To enable adoption of these methods and to encourage further analyses, we disseminate the computational tools needed to deploy this protocol.

Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta

Proteolysis-targeting chimaeras (PROTACs) are molecules that combine a target-binding warhead with an E3 ligase-recruiting moiety; by drawing the target protein into a ternary complex with the E3 ligase, PROTACs induce target protein degradation. While PROTACs hold exciting potential as chemical probes and as therapeutic agents, development of a PROTAC typically requires synthesis of numerous analogs to thoroughly explore variations on the chemical linker; without extensive trial and error, it is unclear how to link the two protein-recruiting moieties to promote formation of a productive ternary complex. Here, we describe a structure-based computational method for evaluating the suitability of a given linker for ternary complex formation. Our method uses Rosetta to dock the protein components and then builds the PROTAC from its component fragments into each binding mode; complete models of the ternary complex are then refined. We apply this approach to retrospectively evaluate multiple PROTACs from the literature, spanning diverse target proteins. We find that modeling ternary complex formation is sufficient to explain both activity and selectivity reported for these PROTACs, implying that other cellular factors are not key determinants of activity in these cases. We further find that interpreting PROTAC activity is best approached using an ensemble of structures of the ternary complex rather than a single static conformation and that members of a structurally conserved protein family can be recruited by the same PROTAC through vastly different binding modes. To encourage adoption of these methods and promote further analyses, we disseminate both the computational methods and the models of ternary complexes.

A clinically relevant polymorphism in the Na+/taurocholate cotransporting polypeptide (NTCP) occurs at a rheostat position

Conventionally, most amino acid substitutions at “important” protein positions are expected to abolish function. However, in several soluble-globular proteins, we identified a class of nonconserved positions for which various substitutions produced progressive functional changes; we consider these evolutionary “rheostats”. Here, we report a strong rheostat position in the integral membrane protein, Na⁺/taurocholate (TCA) cotransporting polypeptide, at the site of a pharmacologically relevant polymorphism (S267F). Functional studies were performed for all 20 substitutions (S267X) with three substrates (TCA, estrone-3-sulfate, and rosuvastatin). The S267X set showed strong rheostatic effects on overall transport, and individual substitutions showed varied effects on transport kinetics (K_m and V_max) and substrate specificity. To assess protein stability, we measured surface expression and used the Rosetta software (https://www.rosettacommons.org) suite to model structure and stability changes of S267X. Although buried near the substrate-binding site, S267X substitutions were easily accommodated in the Na⁺/TCA cotransporting polypeptide structure model. Across the modest range of changes, calculated stabilities correlated with surface-expression differences, but neither parameter correlated with altered transport. Thus, substitutions at rheostat position 267 had wide-ranging effects on the phenotype of this integral membrane protein. We further propose that polymorphic positions in other proteins might be locations of rheostat positions.

Abstract PR08: African-centric p53 hypomorphs play significant roles in cancer risk and efficacy of therapy

The p53 tumor suppressor gene plays a central role in human cancer. In addition to mutation, there are genetic coding region variants of p53 that exist in different ethnic groups. In some cases, these variants have incomplete or impaired function and confer increased cancer risk. We call such variants ‘hypomorphs’. Two p53 hypomorphs exist in populations of African descent: P47S and Y107H. Our research on the P47S hypomorph of p53 revealed that this variant confers increased risk for cancer in humans and in mouse models (Jennis, Genes Dev 2016; Murphy, NPJ Breast Cancer 2017). We find that P47S protein is selectively impaired for the ability to confer sensitivity to ferroptosis (Leu, PNAS 2019); consequently, we find that human and mouse cells with this variant accumulate iron in certain tissues, and that the P47S variant is associated with iron overload in African Americans (Singh, Nat Comm 2020). We find that tumor cells containing the P47S variant are resistant to most genotoxic chemotherapies, but we have discovered that P47S tumor cells are markedly more sensitive to other therapies, including cisplatin and BRD2/4 inhibitors (Barnoud, Can Res 2018). Our current focus is on another African-centric p53 hypomorph, Y107H. We show that this variant is impaired for p53-mediated apoptosis, and is associated with cancer risk in a mouse model. We also show that Y107H is impaired for the transactivation of only a dozen p53 target genes. Notably, half of these genes are known tumor suppressor genes. Our biophysical and NMR structure of the Y107H protein explains the mechanistic basis for the impaired function of this hypomorph. Our analysis of the P47S and Y107H hypomorphs of p53 has significant potential to understand cancer risk and improve cancer therapy in populations of African descent.

Citation Format: Tim Barnoud, Jessica Leung, Keerthana Gnanapradeepan, Lei Ke, John Karanicolas, Maureen E. Murphy. African-centric p53 hypomorphs play significant roles in cancer risk and efficacy of therapy [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PR08.

Identification and Validation of an Aspergillus nidulans Secondary Metabolite Derivative as an Inhibitor of the Musashi-RNA Interaction

RNA-binding protein Musashi-1 (MSI1) is a key regulator of several stem cell populations. MSI1 is involved in tumor proliferation and maintenance, and it regulates target mRNAs at the translational level. The known mRNA targets of MSI1 include Numb, APC, and P21^WAF-1, key regulators of Notch/Wnt signaling and cell cycle progression, respectively. In this study, we aim to identify small molecule inhibitors of MSI1-mRNA interactions, which could block the growth of cancer cells with high levels of MSI1. Using a fluorescence polarization (FP) assay, we screened small molecules from several chemical libraries for those that disrupt the binding of MSI1 to its consensus RNA. One cluster of hit compounds is the derivatives of secondary metabolites from Aspergillus nidulans. One of the top hits, Aza-9, from this cluster was further validated by surface plasmon resonance and nuclear magnetic resonance spectroscopy, which demonstrated that Aza-9 binds directly to MSI1, and the binding is at the RNA binding pocket. We also show that Aza-9 binds to Musashi-2 (MSI2) as well. To test whether Aza-9 has anti-cancer potential, we used liposomes to facilitate Aza-9 cellular uptake. Aza-9-liposome inhibits proliferation, induces apoptosis and autophagy, and down-regulates Notch and Wnt signaling in colon cancer cell lines. In conclusion, we identified a series of potential lead compounds for inhibiting MSI1/2 function, while establishing a framework for identifying small molecule inhibitors of RNA binding proteins using FP-based screening methodology.

Machine learning classification can reduce false positives in structure-based virtual screening

With the recent explosion in the size of libraries available for screening, virtual screening is positioned to assume a more prominent role in early drug discovery's search for active chemical matter. In typical virtual screens, however, only about 12% of the top-scoring compounds actually show activity when tested in biochemical assays. We argue that most scoring functions used for this task have been developed with insufficient thoughtfulness into the datasets on which they are trained and tested, leading to overly simplistic models and/or overtraining. These problems are compounded in the literature because studies reporting new scoring methods have not validated their models prospectively within the same study. Here, we report a strategy for building a training dataset (D-COID) that aims to generate highly compelling decoy complexes that are individually matched to available active complexes. Using this dataset, we train a general-purpose classifier for virtual screening (vScreenML) that is built on the XGBoost framework. In retrospective benchmarks, our classifier shows outstanding performance relative to other scoring functions. In a prospective context, nearly all candidate inhibitors from a screen against acetylcholinesterase show detectable activity; beyond this, 10 of 23 compounds have IC₅₀ better than 50 μM. Without any medicinal chemistry optimization, the most potent hit has IC₅₀ 280 nM, corresponding to K_i of 173 nM. These results support using the D-COID strategy for training classifiers in other computational biology tasks, and for vScreenML in virtual screening campaigns against other protein targets. Both D-COID and vScreenML are freely distributed to facilitate such efforts.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http://www.rosettacommons.org.

Target-Based Design of Promysalin Analogues Identifies a New Putative Binding Cleft in Succinate Dehydrogenase

Promysalin is a small-molecule natural product that specifically inhibits growth of the Gram-negative pathogen Pseudomonas aeruginosa (PA). This activity holds promise in the treatment of multidrug resistant infections found in immunocompromised patients with chronic illnesses, such as cystic fibrosis. In 2015, our lab completed the first total synthesis; subsequent analogue design and SAR investigation enabled identification of succinate dehydrogenase (Sdh) as the biological target in PA. Herein, we report the target-guided design of new promysalin analogues with varying alkyl chains, one of which is on par with our most potent analogue to date. Computational docking revealed that some analogues have a different orientation in the Sdh binding pocket, placing the terminal carbon proximal to a tryptophan residue. This inspired the design of an extended side chain analogue bearing a terminal phenyl moiety, providing a basis for the design of future analogues.

Impact of antibiotic treatment and host innate immune pressure on enterococcal adaptation in the human bloodstream

Multidrug-resistant enterococcal strains emerged in the early 1980s and are now among the leading causes of drug-resistant bacterial infection worldwide. We used functional genomics to study an early bacterial outbreak in patients in a Wisconsin hospital between 1984 and 1988 that was caused by multidrug-resistant Enterococcus faecalis The goal was to determine how a clonal lineage of E. faecalis became adapted to growth and survival in the human bloodstream. Genome sequence analysis revealed a progression of increasingly fixed mutations and repeated independent occurrences of mutations in a relatively small set of genes. Repeated independent mutations suggested selection within the host during the course of infection in response to pressures such as host immunity and antibiotic treatment. We observed repeated independent mutations in a small number of loci, including a little studied polysaccharide utilization pathway and the cydABDC locus. Functional studies showed that mutating these loci rendered E. faecalis better able to withstand antibiotic pressure and innate immune defenses in the human bloodstream. We also observed a shift in mutation pattern that corresponded to the introduction of carbapenem antibiotics in 1987. This work identifies pathways that allow enterococci to survive the transition from the human gut into the bloodstream, enabling them to cause severe bacteremia associated with high mortality.

Computational Design of an Allosteric Antibody Switch by Deletion and Rescue of a Complex Structural Constellation

Therapeutic monoclonal antibodies have transformed medicine, especially with regards to treating cancers and disorders of the immune system. More than 50 antibody-derived drugs have already reached the clinic, the majority of which target cytokines or cell-surface receptors. Unfortunately, many of these targets have pleiotropic functions: they serve multiple different roles, and often not all of these roles are disease-related. This can be problematic because antibodies act throughout the body, and systemic neutralization of such targets can lead to safety concerns. To address this, we have developed a strategy whereby an antibody's ability to recognize its antigen is modulated by a second layer of control, relying on addition of an exogenous small molecule. In previous studies, we began to explore this idea by introducing a deactivating tryptophan-to-glycine mutation in the domain-domain interface of a single-chain variable fragment (scFv), and then restoring activity by adding back indole to fit the designed cavity. Here, we now describe a novel computational strategy for enumerating larger cavities that can be formed by simultaneously introducing multiple adjacent large-to-small mutations; we then carry out a complementary virtual screen to identify druglike compounds to match each candidate cavity. We first demonstrate the utility of this strategy in a fluorescein-binding single-chain variable fragment (scFv) and experimentally characterize a triple mutant with reduced antigen-binding (Rip-3) that can be rescued using a complementary ligand (Stitch-3). Because our design is built upon conserved residues in the antibody framework, we then show that the same mutation/ligand pair can also be used to modulate antigen-binding in an scFv build from a completely unrelated framework. This set of residues is present in many therapeutic antibodies as well, suggesting that this mutation/ligand pair may serve as a general starting point for introducing ligand-dependence into many clinically relevant antibodies.

Abstract 3059: Identification and validation of an Aspergillus nidulanssecondary metabolite derivative as an inhibitor of the Musashi1-RNA interaction

RNA-binding protein Musashi-1 (MSI1) is a key regulator of several stem cell populations. It is involved in tumor proliferation and maintenance, and it regulates target mRNAs at the translational level. The known mRNA targets of MSI1 include Numb, APC and P21WAF-1, key regulators of Notch, Wnt signaling and cell cycle progression, respectively. In this study, we aim to identify small molecule inhibitors of MSI1-mRNA interaction thus blocking the growth of cancer cells with high levels of MSI1. Using a fluorescence polarization (FP) assay, we screened small molecules from several chemical libraries for those that disrupt the binding of MSI1 to its consensus RNA binding site. Two clusters of hit compounds have been identified, one of which is composed of derivatives of secondary metabolites from Aspergillus nidulans. The top hit, Aza-9, from this cluster was further validated by surface plasmon resonance and nuclear magnetic resonance which revealed that Aza-9 binds to MSI1 directly, in the RNA binding pocket. Next, we tested whether Aza-9 has anti-cancer potential in cells and whether such activities work through MSI1. Due to poor cellular uptake, we used PEGylated liposomes to facilitate Aza-9 entry into the cells. Aza-9-lipo inhibits colon cancer cell proliferation, induces apoptosis and autophagy, and down-regulates Notch/Wnt signaling in colon cancer cell lines. In conclusion, we identified a series of potential lead compounds for inhibiting MSI1 function while establishing a framework for identifying small molecule inhibitors of RNA binding proteins using FP-based screening methodology.

Citation Format: Lan Lan, Jiajun Liu, Amber Amith, Carl Appelman, Xiaoqing Wu, Ke Li, Anuradha Roy, Ragul Gowthaman, John Karanicolas, Amber Somoza, Clay Wang, Berl Oakley, Roberto De Guzman, Kristi Neufeld, Liang Xu. Identification and validation of an Aspergillus nidulanssecondary metabolite derivative as an inhibitor of the Musashi1-RNA interaction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3059.

Abstract 1235: Targeting RNA-binding protein HuR to inhibit human breast cancer invasion and metastasis

The majority of breast cancer-related mortality is due to metastasis. Patients diagnosed with metastatic breast cancer have a dismal 5-year survival rate of only 24%. The RNA-binding protein Hu antigen R (HuR) is overexpressed in breast cancer. Cytoplasmic HuR accumulation correlates with high-grade malignancy, poor distant disease-free survival and serves as a prognostic factor for poor clinical outcome in breast cancer. HuR promotes tumorigenesis by regulating numerous proto-oncogenes, growth factors and cytokines that implicate major tumor hallmarks including invasion and metastasis. Knocking out HuR by CRISPR/CAS9 technology inhibits cell invasion in breast cancer cells. Therefore, HuR is an emerging target for breast cancer therapy, especially the lethal metastatic breast cancer. RNA-binding proteins had previously been considered “undruggable” due to lack of a well-defined binding pocket for target RNAs. Using high throughput screening followed by structure-based rational design and lead optimization, we have identified small molecules that inhibit HuR-mRNA interaction at nM to sub-µM potency. Our lead compound, KH-3, potently inhibits breast cancer cell growth and decreases cell invasion in vitro similar to HuR knockout, as well as increasing the expression of epithelial marker E-cadherin. In the study of mechanism of action, a transcription factor, FOXQ1, which is recently revealed to implicate in breast cancer invasion and metastasis processes, is found for the first time to be a direct mRNA target of HuR and one of the top genes that are reduced by KH-3 treatment. Exogenous introduction of FOXQ1 can rescue cell invasive capability impaired by HuR knockout and abolish the effect of KH-3 on inhibiting cell invasion in breast cancer cells. Moreover, KH-3 disrupts HuR-FOXQ1 interaction in RNP-IP, RNA pull down and FOXQ1 3′-UTR luciferase reporter assays. In vivo efficacy studies show that KH-3 not only exhibits potent antitumor efficacy in an orthotopic xenograft model of breast cancer, but also efficiently inhibits lung metastasis and improves mouse survival in an experimental metastasis model. Our data provide a proof-of-principle that HuR inhibition by KH-3 may be developed as a promising molecular therapy for inhibiting progression and metastasis of breast cancer with high HuR.

Citation Format: Xiaoqing Wu, Gulhumay Gardashova, Lan Lan, Shuang Han, Cuncong Zhong, Ragul Gowthaman, John Karanicolas, Dan A. Dixon, Danny R. Welch, Ling Li, Min Ji, Jeffrey Aubé, Liang Xu. Targeting RNA-binding protein HuR to inhibit human breast cancer invasion and metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1235.

Leveraging a Low-Affinity Diazaspiro Orthosteric Fragment to Reduce Dopamine D3 Receptor (D3R) Ligand Promiscuity across Highly Conserved Aminergic G-Protein-Coupled Receptors (GPCRs)

Previously, we reported a 3-(2-methoxyphenyl)-9-(3-((4-methyl-5-phenyl-4 H-1,2,4-triazol-3-yl)thio)propyl)-3,9-diazaspiro[5.5]undecane (1) compound with excellent dopamine D₃ receptor (D₃R) affinity (D₃R K_i = 12.0 nM) and selectivity (D₂R/D₃R ratio = 905). Herein, we present derivatives of 1 with comparable D₃R affinity (32, D₃R K_i = 3.2 nM, D₂R/D₃R ratio = 60) and selectivity (30, D₃R K_i = 21.0 nM, D₂R/D₃R ratio = 934). Fragmentation of 1 revealed orthosteric fragment 5a to express an unusually low D₃R affinity ( K_i = 2.7 μM). Compared to piperazine congener 31, which retains a high-affinity orthosteric fragment (5d, D₃R K_i = 23.9 nM), 1 was found to be more selective for the D₃R among D₁- and D₂-like receptors and exhibited negligible off-target interactions at serotoninergic and adrenergic G-protein-coupled receptors (GPCRs), common off-target sites for piperazine-containing D₃R scaffolds. This study provides a unique rationale for implementing weakly potent orthosteric fragments into D₃R ligand systems to minimize drug promiscuity at other aminergic GPCR sites.

Isothermal Analysis of ThermoFluor Data can readily provide Quantitative Binding Affinities

Differential scanning fluorimetry (DSF), also known as ThermoFluor or Thermal Shift Assay, has become a commonly-used approach for detecting protein-ligand interactions, particularly in the context of fragment screening. Upon binding to a folded protein, most ligands stabilize the protein; thus, observing an increase in the temperature at which the protein unfolds as a function of ligand concentration can serve as evidence of a direct interaction. While experimental protocols for this assay are well-developed, it is not straightforward to extract binding constants from the resulting data. Because of this, DSF is often used to probe for an interaction, but not to quantify the corresponding binding constant (Kd). Here, we propose a new approach for analyzing DSF data. Using unfolding curves at varying ligand concentrations, our "isothermal" approach collects from these the fraction of protein that is folded at a single temperature (chosen to be temperature near the unfolding transition). This greatly simplifies the subsequent analysis, because it circumvents the complicating temperature dependence of the binding constant; the resulting constant-temperature system can then be described as a pair of coupled equilibria (protein folding/unfolding and ligand binding/unbinding). The temperature at which the binding constants are determined can also be tuned, by adding chemical denaturants that shift the protein unfolding temperature. We demonstrate the application of this isothermal analysis using experimental data for maltose binding protein binding to maltose, and for two carbonic anhydrase isoforms binding to each of four inhibitors. To facilitate adoption of this new approach, we provide a free and easy-to-use Python program that analyzes thermal unfolding data and implements the isothermal approach described herein ( https://sourceforge.net/projects/dsf-fitting ).

Natural product derivative Gossypolone inhibits Musashi family of RNA-binding proteins

BACKGROUND

The Musashi (MSI) family of RNA-binding proteins is best known for the role in post-transcriptional regulation of target mRNAs. Elevated MSI1 levels in a variety of human cancer are associated with up-regulation of Notch/Wnt signaling. MSI1 binds to and negatively regulates translation of Numb and APC (adenomatous polyposis coli), negative regulators of Notch and Wnt signaling respectively.

METHODS

Previously, we have shown that the natural product (-)-gossypol as the first known small molecule inhibitor of MSI1 that down-regulates Notch/Wnt signaling and inhibits tumor xenograft growth in vivo. Using a fluorescence polarization (FP) competition assay, we identified gossypolone (Gn) with a > 20-fold increase in Ki value compared to (-)-gossypol. We validated Gn binding to MSI1 using surface plasmon resonance, nuclear magnetic resonance, and cellular thermal shift assay, and tested the effects of Gn on colon cancer cells and colon cancer DLD-1 xenografts in nude mice.

RESULTS

In colon cancer cells, Gn reduced Notch/Wnt signaling and induced apoptosis. Compared to (-)-gossypol, the same concentration of Gn is less active in all the cell assays tested. To increase Gn bioavailability, we used PEGylated liposomes in our in vivo studies. Gn-lip via tail vein injection inhibited the growth of human colon cancer DLD-1 xenografts in nude mice, as compared to the untreated control (P < 0.01, n = 10).

CONCLUSION

Our data suggest that PEGylation improved the bioavailability of Gn as well as achieved tumor-targeted delivery and controlled release of Gn, which enhanced its overall biocompatibility and drug efficacy in vivo. This provides proof of concept for the development of Gn-lip as a molecular therapy for colon cancer with MSI1/MSI2 overexpression.

Abstract B03: Targeting the KIF11/KIF15/TPX2 axis to develop new therapies for ovarian cancer

Unlimited genetic and epigenetic diversity across the patient population, and within the tumor and among metastatic lesions of an individual patient, presents a challenge in developing targeted therapies to treat epithelial ovarian cancer (EOC). To find the Achilles heel of ovarian cancers, we designed an RNAi-based screen (&gt;6,000 genes) to identify points of molecular vulnerability. These screens identified KIF11 as essential to maintain tumor cell viability. KIF11 encodes kinesin Eg5 (KIF11), a motor protein required for microtubule antiparallel sliding during mitosis that has been targeted clinically. Although KIF11 inhibitors are well tolerated by EOC patients, clinical response rates were disappointing in heavily treated patients with advanced disease. We hypothesize one mechanism through which KIF11 inhibitors’ efficacy is muted is via functional compensation of mitotic spindle assembly by KIF15, a second motor kinesin. Using a synthetic lethal approach, we have shown that RNAi-mediated silencing of KIF15 has no effect on cell viability, but significantly sensitized cells by &gt;10- to 100-fold to a class of KIF11 inhibitors (KIF11is). TPX2-targeted siRNAs reduce cell viability by 5-fold alone, and sensitize cells by 100-fold in the presence of KIF11i. Based on these observations, we designed a high-throughput screening assay using Alpha Technology©. Informed by previous predictions of KIF15-TPX2 binding domains, we designed peptides corresponding to the appropriate domains of KIF15 (aa1149-1388, GST-tagged) and TPX2 (aa346-747, His-tagged), for use in the AlphaScreen© assay. Following several optimization steps (e.g., buffer selection, protein titration, TruHits© assay validation), we demonstrate that KIF15 binds TPX2, producing a signal &gt;30-fold greater than background signal. Further, peptides designed to mimic either KIF15 or TPX2 binding domains, but not scrambled controls, exhibited concentration-dependent disruption of the KIF15-TPX2 interaction. Next, we screened a FDA library (3,474 compounds) and bioactive (1,902 compounds) library and identified 122 hits; fresh compound stocks were tested at 4 concentrations (20, 10, 5, and 2.5 μM), resulting in 53 confirmed hits (28 FDA, 25 bioactive). To identify false positives that interfere with assay chemistry, we repeated the screen at 3 concentrations, replacing the His-TPX2 and GST-KIF15 proteins with a His-GST fusion. As an orthogonal screen, we performed a Homogenous Time Resolved Fluorescence© (HTRF)-based screen to reconfirm hit compounds at the aforementioned concentrations. From these combined data, we have identified 4 hit compounds (KU-P001 to KU-P004) that disrupt KIF15/TPX2 protein-protein interactions. To further prioritize our hits, we developed in vitro (EOC cell lines were exposed to increasing concentrations, up to 1 µM, of KIF11i for 4 months) and in vivo (patient-derived ascites xenograft models of EOC were treated with 3 cycles of either 5 mg/kg or 10 mg/kg of a KIF11i and were serially passaged and treated for 3 additional generations) models of KIF11i-resistance to evaluate their activities. In resistant EOC cells we observed a 3-fold increase in KIF15 protein expression as compared with parental cells; TPX2 protein expression remained unchanged. In vivo, both KIF15 (68% increase) and TPX2 (2-fold) protein expression was increased in resistant versus untreated PDX tumor cells. Combination studies of KU-P004 and ispinesib (KIF11i) in vitro revealed a 2- to 64-fold increase in cell death for both responsive and resistant EOC cells compared with KIF11i treatment alone. In summary, we have developed a high-throughput screening assay platform to identify inhibitors of the KIF15-TPX2 interaction and are using iterative medicinal chemistry to guide optimization and functional evaluation of hits and lead compounds to develop new combination therapies for women with ovarian cancer.

Citation Format: Rebecca J. Wates, Anuradha Roy, Frank Schoenen, John Karanicolas, Scott Weir, Andrew Godwin. Targeting the KIF11/KIF15/TPX2 axis to develop new therapies for ovarian cancer. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr B03.

Abstract 2952: Targeting CDK9 reactivates epigenetically silenced genes in cancer

In cancer, the epigenome is aberrantly reprogrammed leading to a wide range of heritable changes in gene expression, such as silencing of tumor suppressor genes (TSG). Altered epigenetic marks in cancer involve DNA methylation and histone post-translational modifications, and these come about as a result of aging and acquisition of genetic and epigenetic changes in readers/writers/editors of the epigenome. Given the reversible nature of epigenetic modifications, one goal of epigenetic therapy of cancer is to induce TSG reactivation, leading to cancer cell differentiation and cancer cell death.

To identify novel targets that can reactivate epigenetically silenced genes, we developed a phenotypic-based system, YB5. YB5 is a colon cancer cell line generated by stably transfecting SW48 cells with a vector containing GFP driven by a methylated and silenced CMV promoter. GFP re-expression can be achieved by known epigenetic drugs that lead to demethylation or induce active chromatin marks in the CMV promoter.

We screened a natural compound library for GFP activation in YB5 and identified a novel drug class that shares an aminothiazole core structure, and has epigenetic effects that are equivalent to DNA methyltransferase inhibitor (DNMTi). Target deconvolution identified CDK9 as the target of these drugs, which reactivate gene expression without affecting DNA methylation. It is well established that CDK9, the catalytic subunit of p-TEFb, is a transcriptional activator. CDK9 in complex with its regulatory subunit, Cyclin T1 or T2, is recruited by multiple mechanisms to promote RNAPII promoter-proximal pause release by phosphorylating negative elongation factors (DSIF and NELF). In addition, phosphorylation of the C-terminal domain (CTD) of RNAPII on Serine-2 allows recruitment of RNA processing factors, which work on the nascent RNA as it emerges from RNAPII. Our new data show that long-term CDK9 inhibition can reactivate epigenetically silenced genes with minimal downregulation effects, effects which are the opposite of the canonical role of CDK9-mediated transcriptional elongation. Mechanistically, we showed that CDK9 inhibition dephosphorylates the SWI/SNF protein SMARCA4 and represses HP1α expression, both of which contribute to gene reactivation. Based on gene activation, we developed the highly selective and potent CDK9 inhibitor MC180295 (IC50 =5nM) that has broad anti-cancer activity in-vitro and is effective in in-vivo cancer models. Additionally, CDK9 inhibition sensitizes with the immune checkpoint inhibitor α-PD-1 in vivo, making it an excellent target for epigenetic therapy of cancer. This is the first study that links CDK9 to maintaining gene silencing at epigenetically repressed loci in mammals. Excitingly, this is also the first example of kinase inhibitors as potential drugs that reverse epigenetic silencing.

Citation Format: Hanghang Zhang, Somnath Pandey, Meghan Travers, Jittasak Khowsathit, George Morton, Hongxing Sum, Carlos A. Barrero, Carmen Merali, Yasuyuki Okamoto, Takahiro Sato, Judit Garriga, Natarajan V. Bhanu, Johayra Simithy, Bela Patel, Jozef Madzo, Noël Raynal, Benjamin A. Garcia, Marlene A. Jacobson, Salim Merali, Yi Zhang, Wayne Childers, Magid Abou-Gharbia, John Karanicolas, Stephen B. Baylin, Cynthia A. Zahnow, Jaroslav Jelinek, Xavier Graña, Jean-Pierre J. Issa. Targeting CDK9 reactivates epigenetically silenced genes in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2952.

Contribution of an unusual CDR2 element of a single domain antibody in ricin toxin binding affinity and neutralizing activity

Ricin toxin's enzymatic subunit (RTA) has been subjected to intensive B cell epitope mapping studies using a combination of competition ELISAs, hydrogen exchange-mass spectrometry and X-ray crystallography. Those studies identified four spatially distinct clusters (I-IV) of toxin-neutralizing epitopes on the surface of RTA. Here we describe A9, a new single domain camelid antibody (VHH) that was proposed to recognize a novel epitope on RTA that straddles clusters I and III. The X-ray crystal structure of A9 bound to RTA (2.6 Å resolution) revealed extensive antibody contact with RTA's β-strand h (732 Å2 buried surface area; BSA), along with limited engagement with α-helix D (90 Å2) and α-helix C (138 Å2). Collectively, these contacts explain the overlap between epitope clusters I and III, as identified by competition ELISA. However, considerable binding affinity, and, consequently, toxin-neutralizing activity of A9 is mediated by an unusual CDR2 containing five consecutive Gly residues that interact with α-helix B (82 Å2), a known neutralizing hotspot on RTA. Removal of a single Gly residue from the penta-glycine stretch in CDR2 reduced A9's binding affinity by 10-fold and eliminated toxin-neutralizing activity. Computational modeling indicates that removal of a Gly from CDR2 does not perturb contact with RTA per se, but results in the loss of an intramolecular hydrogen bond network involved in stabilizing CDR2 in the unbound state. These results reveal a novel configuration of a CDR2 element involved in neutralizing ricin toxin.

Modulating Antibody Structure and Function through Directed Mutations and Chemical Rescue

Monoclonal antibody therapeutics have revolutionized the treatment of diseases such as cancer and autoimmune disorders, and also serve as research reagents for diverse and unparalleled applications. To extend their utility in both contexts, we have begun development of tunable antibodies, whose activity can be controlled by addition of a small molecule. Conceptually, we envision that incorporating cavity-forming mutations into an antibody can disrupt its structure, thereby reducing its affinity for antigen; addition of a small molecule may then restore the active structure, and thus rescue antigen binding. As a first proof of concept toward implementing this strategy, we have incorporated individual tryptophan to glycine mutations into FITC-E2, an anti-fluorescein single-chain variable fragment (scFv). We find that these can disrupt the protein structure and diminish antigen binding, and further that both structure and function can be rescued by addition of indole to complement the deleted side chain. While the magnitude of the affinity difference triggered by indole is modest in this first model system, it nonetheless provides a framework for future mutation/ligand pairs that may induce more dramatic responses. Disrupting and subsequently rescuing antibody activity, as exemplified by this first example, may represent a new approach to "design in" fine-tuned control of antibody activity for a variety of future applications.

Promysalin Elicits Species-Selective Inhibition of Pseudomonas aeruginosa by Targeting Succinate Dehydrogenase

Natural products have served as an inspiration to scientists both for their complex three-dimensional architecture and exquisite biological activity. Promysalin is one such Pseudomonad secondary metabolite that exhibits narrow-spectrum antibacterial activity, originally isolated from the rhizosphere. We herein utilize affinity-based protein profiling (AfBPP) to identify succinate dehydrogenase (Sdh) as the biological target of the natural product. The target was further validated in silico, in vitro, in vivo, and through the selection, and sequencing, of a resistant mutant. Succinate dehydrogenase plays an essential role in primary metabolism of Pseudomonas aeruginosa as the only enzyme that is involved both in the tricarboxylic acid cycle (TCA) and in respiration via the electron transport chain. These findings add credence to other studies that suggest that the TCA cycle is an understudied target in the development of novel therapeutics to combat P. aeruginosa, a significant pathogen in clinical settings.

Using homology modeling to interrogate binding affinity in neutralization of ricin toxin by a family of single domain antibodies

In this report we investigated, within a group of closely related single domain camelid antibodies (V_H Hs), the relationship between binding affinity and neutralizing activity as it pertains to ricin, a fast-acting toxin and biothreat agent. The V1C7-like V_H Hs (V1C7, V2B9, V2E8, and V5C1) are similar in amino acid sequence, but differ in their binding affinities and toxin-neutralizing activities. Using the X-ray crystal structure of V1C7 in complex with ricin's enzymatic subunit (RTA) as a template, Rosetta-based homology modeling coupled with energetic decomposition led us to predict that a single pairwise interaction between Arg29 on V5C1 and Glu67 on RTA was responsible for the difference in ricin toxin binding affinity between V1C7, a weak neutralizer, and V5C1, a moderate neutralizer. This prediction was borne out experimentally: substitution of Arg for Gly at position 29 enhanced V1C7's binding affinity for ricin, whereas the reverse (ie, Gly for Arg at position 29) diminished V5C1's binding affinity by >10 fold. As expected, the V5C1_R29G mutant was largely devoid of toxin-neutralizing activity (TNA). However, the TNA of the V1C7_G29R mutant was not correspondingly improved, indicating that in the V1C7 family binding affinity alone does not account for differences in antibody function. V1C7 and V5C1, as well as their respective point mutants, recognized indistinguishable epitopes on RTA, at least at the level of sensitivity afforded by hydrogen-deuterium mass spectrometry. The results of this study have implications for engineering therapeutic antibodies because they demonstrate that even subtle differences in epitope specificity can account for important differences in antibody function.

Abstract 3878: Musashi-2 (MSI2) regulation of ERBB family proteins in non-small cell lung cancer (NSCLC)

The purpose of this study is to establish whether a new signaling axis we recently described can be targeted to improve patient survival in lung cancer, one of the leading causes of death worldwide, with over 1.6 million deaths annually. Non-small cell lung cancer (NSCLC) is the most common form of lung cancer. A small number of targeted therapies have been shown to be useful in lung cancer, including inhibitors of EGFR, but these are typically only active in a subset of tumors that maintain epithelial characteristics. Musashi-2 (MSI2), an RNA-binding protein that regulates mRNA translation, has been linked to maintenance of a stem cell state in multiple hematologic and solid tumor malignancies. We recently established (Kudinov et al, PNAS 2016, PMID:27274057) that MSI2 is elevated in a subset of NSCLC tumor upon progression and drives NSCLC metastasis, in part based on activity supporting a TGF-beta/SMAD3/claudin signaling cascade that enhances epithelial-mesenchymal transition (EMT). Using reverse phase protein array (RPPA) analysis of MSI2-depleted versus control KrasLA1/+;P53R172HΔG/+ murine NSCLC cell line models identified a significant 2.7-fold upregulation of HER3 upon MSI2 depletion. Negative MSI2-dependent regulation of ERBB3 protein expression was confirmed in multiple additional murine and human KRAS-dependent NSCLC models, based on analysis of MSI2 depletion or overexpression. In contrast, MSI2 positively regulated expression of the EGFR/ERBB1 protein in the same models. In detailed analysis, we have addressed the mechanism by which MSI2 regulates expression of the ERBB group of receptor tyrosine kinases. In addition, these data suggested the hypothesis that MSI2 expression might predict response to EGFR-targeted inhibitors, and that dual targeting of MSI2 and EGFR might be therapeutically valuable. We will present data on the activity of EGFR inhibitors in the context of depleted or elevated MSI2 expression, and the effect of combining inhibition of EGFR with recently developed MSI2 inhibitors. In summary, these results for the first time indicate a role of MSI2 in supporting EGFR expression in NSCLC and suggest that MSI2 may drive NSCLC development and progression in part via EGFR, and may modulate response to EGFR-targeted agents.

Citation Format: Alexander Kudinov, Alexander Deneka, Anna N. Nikonova, Emmanuelle Nicolas, Vladislav A. Korobeynikov, Ilya G. Serebriiskii, John Karanicolas, Erica A. Golemis, Yanis Boumber. Musashi-2 (MSI2) regulation of ERBB family proteins in non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3878. doi:10.1158/1538-7445.AM2017-3878

Abstract 1133: Discovery of novel small molecule inhibitors of RNA-binding protein Musashi-1

1) Background and Objective: Musashi-1(Msi1) is an RNA-binding protein that negatively regulates translation by binding to the 3′-UTRs of target mRNAs including Numb, APC and p21WAF-1, key regulators of Notch, Wnt signaling and cell cycle progression, respectively. We aim to identify small molecule inhibitors of Msi1’s mRNA-binding activity thus blocking the growth of a broad range of cancer cells.

2) Methods: Fluorescence polarization assay was used to screen for small molecules that disrupt the binding of Msi1 to its consensus RNA binding site. Hits were validated by surface plasmon resonance, amplified luminescent proximity homogeneous assay and nuclear magnetic resonance.

3) Results: Among ~2,000 small molecules we screened, we found several clusters of compounds that disrupt the Msi1-numb RNA binding potently, including natural products, herbal extracts and fungal metabolites. One of the clusters is the derivatives of the secondary metabolites from Aspergillus nidulans. The top hit, Aza-9, from this cluster was validated by amplified luminescent proximity homogeneous assay. Further validation by surface plasmon resonance and nuclear magnetic resonance indicate that Aza-9 binds to Msi1 directly, in the RNA binding pocket.

4) Discussion and Conclusions: Our study supports the hypothesis that Msi1 inhibition is a viable and effective anti-cancer strategy. More target validation assays will be carried out for the compounds from other clusters.

Citation Format: Lan Lan, Amber Smith, Xiaoqing Wu, Anuradha Roy, Ragul Gowthaman, John Karanicolas, Amber D. Somoza, Clay C.C. Wang, Berl Oakley, Roberto De Guzman, Kristi Neufeld, Liang Xu. Discovery of novel small molecule inhibitors of RNA-binding protein Musashi-1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1133. doi:10.1158/1538-7445.AM2017-1133

Optimal allosteric stabilization sites using contact stabilization analysis

Proteins can be destabilized by a number of environmental factors such as temperature, pH, and mutation. The ability to subsequently restore function under these conditions by adding small molecule stabilizers, or by introducing disulfide bonds, would be a very powerful tool, but the physical principles that drive this stabilization are not well understood. The first problem lies is in choosing an appropriate binding site or disulfide bond location to best confer stability to the active site and restore function. Here, we present a general framework for predicting which allosteric binding sites correlate with stability in the active site. Using the Karanicolas-Brooks Gō-like model, we examine the dynamics of the enzyme β-glucuronidase using an Umbrella Sampling method to thoroughly sample the conformational landscape. Each intramolecular contact is assigned a score termed a "stabilization factor" that measures its correlation with structural changes in the active site. We have carried out this analysis for three different scaling strengths for the intramolecular contacts, and we examine how the calculated stabilization factors depend on the ensemble of destabilized conformations. We further examine a locally destabilized mutant of β-glucuronidase that has been characterized experimentally, and show that this brings about local changes in the stabilization factors. We find that the proximity to the active site is not sufficient to determine which contacts can confer active site stability. © 2016 Wiley Periodicals, Inc.

Identification of novel small molecule Beclin 1 mimetics activating autophagy

Anti-apoptotic proteins Bcl-2 and Bcl-xL could block autophagy by binding to Beclin 1 protein, an essential inducer of autophagy. Compounds mimicking Beclin 1 might be able to disrupt Bcl-xL/2-Beclin 1 interaction, free out Beclin 1, and thus trigger autophagy. In order to identify small molecule Beclin 1 mimetics, a fluorescence polarization-based high-throughput screening of 50,316 compounds was carried out with a Z' score of 0.82 ± 0.05, and an outcome of 58 hits. After the structure analysis, three acridine analogues were unveiled and confirmed using the fluorescence polarization assay and the surface plasmon resonance assay. Moreover, a set of 17 additional acridine analogues was prepared and tested. Compound 7 showed selectivity for Bcl-xL (K_D = 6.5 μM) over Bcl-2 (K_D = 160 μM) protein, and potent cytotoxicity (nanomolar scale) in PC-3, PC-3a and DU145 prostate cancer cells. Furthermore, induction of autophagy was also demonstrated in PC-3 and PC-3a cells treated with some acridine compounds by LC3 conversion immunoblotting and LC3 fluorescence microscopy. These Beclin 1 mimetics will be invaluable tools for developing novel autophagy inducers, better understanding the roles of autophagy in cancer, and will contribute to cancer therapy.

The fungal natural product azaphilone-9 binds to HuR and inhibits HuR-RNA interaction in vitro

The RNA-binding protein Hu antigen R (HuR) binds to AU-rich elements (ARE) in the 3'-untranslated region (UTR) of target mRNAs. The HuR-ARE interactions stabilize many oncogenic mRNAs that play important roles in tumorigenesis. Thus, small molecules that interfere with the HuR-ARE interaction could potentially inhibit cancer cell growth and progression. Using a fluorescence polarization (FP) competition assay, we identified the compound azaphilone-9 (AZA-9) derived from the fungal natural product asperbenzaldehyde, binds to HuR and inhibits HuR-ARE interaction (IC50 ~1.2 μM). Results from surface plasmon resonance (SPR) verified the direct binding of AZA-9 to HuR. NMR methods mapped the RNA-binding interface of HuR and identified the involvement of critical RNA-binding residues in binding of AZA-9. Computational docking was then used to propose a likely binding site for AZA-9 in the RNA-binding cleft of HuR. Our results show that AZA-9 blocks key RNA-binding residues of HuR and disrupts HuR-RNA interactions in vitro. This knowledge is needed in developing more potent AZA-9 derivatives that could lead to new cancer therapy.

"Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics

Water engages in two important types of interactions near biomolecules: it forms ordered "cages" around exposed hydrophobic regions, and it participates in hydrogen bonds with surface polar groups. Both types of interaction are critical to biomolecular structure and function, but explicitly including an appropriate number of solvent molecules makes many applications computationally intractable. A number of implicit solvent models have been developed to address this problem, many of which treat these two solvation effects separately. Here, we describe a new model to capture polar solvation effects, called SHO ("solvent hydrogen-bond occlusion"); our model aims to directly evaluate the energetic penalty associated with displacing discrete first-shell water molecules near each solute polar group. We have incorporated SHO into the Rosetta energy function, and find that scoring protein structures with SHO provides superior performance in loop modeling, virtual screening, and protein structure prediction benchmarks. These improvements stem from the fact that SHO accurately identifies and penalizes polar groups that do not participate in hydrogen bonds, either with solvent or with other solute atoms ("unsatisfied" polar groups). We expect that in future, SHO will enable higher-resolution predictions for a variety of molecular modeling applications. © 2017 Wiley Periodicals, Inc.

Musashi RNA-Binding Proteins as Cancer Drivers and Novel Therapeutic Targets

Aberrant gene expression that drives human cancer can arise from epigenetic dysregulation. Although much attention has focused on altered activity of transcription factors and chromatin-modulating proteins, proteins that act posttranscriptionally can potently affect expression of oncogenic signaling proteins. The RNA-binding proteins (RBP) Musashi-1 (MSI1) and Musashi-2 (MSI2) are emerging as regulators of multiple critical biological processes relevant to cancer initiation, progression, and drug resistance. Following identification of Musashi as a regulator of progenitor cell identity in Drosophila, the human Musashi proteins were initially linked to control of maintenance of hematopoietic stem cells, then stem cell compartments for additional cell types. More recently, the Musashi proteins were found to be overexpressed and prognostic of outcome in numerous cancer types, including colorectal, lung, and pancreatic cancers; glioblastoma; and several leukemias. MSI1 and MSI2 bind and regulate the mRNA stability and translation of proteins operating in essential oncogenic signaling pathways, including NUMB/Notch, PTEN/mTOR, TGFβ/SMAD3, MYC, cMET, and others. On the basis of these activities, MSI proteins maintain cancer stem cell populations and regulate cancer invasion, metastasis, and development of more aggressive cancer phenotypes, including drug resistance. Although RBPs are viewed as difficult therapeutic targets, initial efforts to develop MSI-specific inhibitors are promising, and RNA interference-based approaches to inhibiting these proteins have had promising outcomes in preclinical studies. In the interim, understanding the function of these translational regulators may yield insight into the relationship between mRNA expression and protein expression in tumors, guiding tumor-profiling analysis. This review provides a current overview of Musashi as a cancer driver and novel therapeutic target. Clin Cancer Res; 23(9); 2143-53. ©2017 AACR.

When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode?

Traditional hit-to-lead optimization assumes that upon elaboration of chemical structure, the ligand retains its binding mode relative to the receptor. Here, we build a large-scale collection of related ligand pairs solved in complex with the same protein partner: we find that for 41 of 297 pairs (14%), the binding mode changes upon elaboration of the smaller ligand. While certain ligand physiochemical properties predispose changes in binding mode, particularly those properties that define fragments, simple structure-based modeling proves far more effective for identifying substitutions that alter the binding mode. Some ligand pairs change binding mode because the added substituent would irreconcilably conflict with the receptor in the original pose, whereas others change because the added substituent enables new, stronger interactions that are available only in a different pose. Scaffolds that can engage their target using alternate poses may enable productive structure-based optimization along multiple divergent pathways.

Full and Partial Agonism of a Designed Enzyme Switch

Chemical biology has long sought to build protein switches for use in molecular diagnostics, imaging, and synthetic biology. The overarching challenge for any type of engineered protein switch is the ability to respond in a selective and predictable manner that caters to the specific environments and time scales needed for the application at hand. We previously described a general method to design switchable proteins, called "chemical rescue of structure", that builds de novo allosteric control sites directly into a protein's functional domain. This approach entails first carving out a buried cavity in a protein via mutation, such that the protein's structure is disrupted and activity is lost. An exogenous ligand is subsequently added to substitute for the atoms that were removed by mutation, restoring the protein's structure and thus its activity. Here, we begin to ask what principles dictate such switches' response to different activating ligands. Using a redesigned β-glycosidase enzyme as our model system, we find that the designed effector site is quite malleable and can accommodate both larger and smaller ligands, but that optimal rescue comes only from a ligand that perfectly replaces the deleted atoms. Guided by these principles, we then altered the shape of this cavity by using different cavity-forming mutations, and predicted different ligands that would better complement these new cavities. These findings demonstrate how the protein switch's response can be tuned via small changes to the ligand with respect to the binding cavity, and ultimately enabled us to design an improved switch. We anticipate that these insights will help enable the design of future systems that tune other aspects of protein activity, whereby, like evolved protein receptors, remolding the effector site can also adjust additional outputs such as substrate selectivity and activation of downstream signaling pathways.

Chaperonin-Based Biolayer Interferometry To Assess the Kinetic Stability of Metastable, Aggregation-Prone Proteins

Stabilizing the folded state of metastable and/or aggregation-prone proteins through exogenous ligand binding is an appealing strategy for decreasing disease pathologies caused by protein folding defects or deleterious kinetic transitions. Current methods of examining binding of a ligand to these marginally stable native states are limited because protein aggregation typically interferes with analysis. Here, we describe a rapid method for assessing the kinetic stability of folded proteins and monitoring the effects of ligand stabilization for both intrinsically stable proteins (monomers, oligomers, and multidomain proteins) and metastable proteins (e.g., low Tm) that uses a new GroEL chaperonin-based biolayer interferometry (BLI) denaturant pulse platform. A kinetically controlled denaturation isotherm is generated by exposing a target protein, immobilized on a BLI biosensor, to increasing denaturant concentrations (urea or GuHCl) in a pulsatile manner to induce partial or complete unfolding of the attached protein population. Following the rapid removal of the denaturant, the extent of hydrophobic unfolded/partially folded species that remains is detected by an increased level of GroEL binding. Because this kinetic denaturant pulse is brief, the amplitude of binding of GroEL to the immobilized protein depends on the duration of the exposure to the denaturant, the concentration of the denaturant, wash times, and the underlying protein unfolding-refolding kinetics; fixing all other parameters and plotting the GroEL binding amplitude versus denaturant pulse concentration result in a kinetically controlled denaturation isotherm. When folding osmolytes or stabilizing ligands are added to the immobilized target proteins before and during the denaturant pulse, the diminished population of unfolded/partially folded protein manifests as a decreased level of GroEL binding and/or a marked shift in these kinetically controlled denaturation profiles to higher denaturant concentrations. This particular platform approach can be used to identify small molecules and/or solution conditions that can stabilize or destabilize thermally stable proteins, multidomain proteins, oligomeric proteins, and, most importantly, aggregation-prone metastable proteins.