Publications

2024
E Neumann, S.S., Yang , O., Karmi , M., Darash Yahana , A.E., Cardenas , E., Pikarsky , R., Elber , A., Friedler , R., Mittler , and R., Nechushtai . 12/26/2024. “Targeting Primary And Metastatic Ovarian Cancer With A Peptide Derived From The Human Naf-1/Cisd2 Protein”. Biorxiv. https://doi.org/10.1101/12/26/2024. 12.26.630413 . Publisher's Version Abstract
Ovarian cancer is the most fatal cancer of female reproductive organs. Ovarian cancer is typically diagnosed at a late stage, after metastasis occurred, leading to a 5-years relative survival rate of only ∼5%. Here, we demonstrate the anti-ovarian cancer properties of a peptide derived from the human protein CISD2/NAF-1 (3D-NAF-144-67-6K). This peptide selectively permeates the plasma membrane of ovarian cancer SKOV-3 cells without affecting healthy cells. 3D-NAF-144-67-6K targets and destroys the cancer cells’ mitochondria which leads to cancer cell death. In vivo studies of mice carrying xenograft tumours of SKOV-3 showed that the peptide significantly decreased the overall size and growth rate of both primary and metastatic ovarian cancer tumours. We further show that 3D-NAF-144-67-6K has a broad-spectrum anticancer activity targeting leukaemia, brain, and pancreas cancer cells. Our study suggests that 3D-NAF-144-67-6K could be used, alone or in drug combinations, to treat ovarian cancer and improve patient survival.
Pedrola J.A., Dekker, F.A. , T., Garfagnini , G., Mayer , M.B., Koopman , M., Bergmeijer , F., Forster , Hoozemans, J.J.M. , H., Jensen , A., Friedler , and S.G.D., Rüdiger . 12/21/2024. “Fibrilpaint To Determine The Length Of Tau Amyloids In Fluids”. Biorxiv. Abstract
Tau aggregation into amyloid fibrils is linked to the development of neurodegenerative diseases, including Alzheimer Disease. The molecular processes underlying aggregation in disease are poorly understood. Here, we introduce FibrilPaint1 as a tool to measure the size of Tau amyloid fibrils in fluids, from early aggregation stages to mature fibrils. FibrilPaint1 is a 22mer peptide with many exciting properties, which makes it a tool for diagnostics and an attractive start point for developing a class of effective fibril targeting degraders: (i) FibrilPaint1 binds fibrils with nanomolar affinity; (ii) it does also bind to oligomeric precursors, down to a size of only 4 layers; (iii) it does not bind to monomers (KD > 100 microM); (iv) it is fluorescently labelled, which allows monitoring and localising interactions. (v) FibrilPaint1 recognises various Tau fibrils, including patient derived fibrils from Alzheimer, Corticobasal degeneration and Frontotemporal dementia; (vi) FibrilPaint1 is selective for the amyloid state and does not have background binding to amorphous aggregates, blood serum or cell lysate. In combination with Flow Induced Dispersion Analysis (FIDA), a microfluidics technology, we determined the molecular size of amyloid fibrils with sub-microliter sample volumes. This set-up acts as a molecular ruler at layer resolution - we determined Tau fibril length from 4 to 1100 layers in solution. This is an interesting parameter that can be used for diagnostic applications and biochemical research in dementia.
Bressler S., D., Grunhaus , A., Aviram , G., Rüdiger S. , M., Hurevich , and A., Friedler . 12/15/2024. “ The Role Of Specific Phosphorylation Patterns In The Oligomerization Of Tau-R4 ”. Biorxiv. Abstract
Specific phosphorylation patterns control the activity of multiphosphorylated proteins. In case of the Tau protein, multiphosphorylation leads to the formation of different disease-related condensates and aggregates. Studying the role of these specific patterns at the protein level is crucial for understanding the molecular mechanisms of Tauopathies such as Alzheimers Disease. However, due to the extreme difficulty in obtaining recombinant proteins with specific phosphorylation patterns using kinase-based methods, it is practically impossible to study the connection between specific phosphorylation patterns and aggregation events at the protein level. Here we addressed this problem by reducing the system to the peptide level and studying the effect of specific phosphorylation patterns on the condensation and aggregation of a specific domain of Tau, R4 (residues 336-358). To achieve this aim, we have applied advanced methods to synthesize a library of multiphosphorylated peptides derived from R4. We showed that specific phosphorylation patterns stringently control the formation of Tau aggregates and condensates. Phosphorylation of Ser341 promoted aggregation of R4 while phosphorylation of Ser352 promoted its condensation. Interestingly, Ser356 phosphorylation inhibited both processes, which can be overridden by double-phosphorylation at Ser341/Ser352. Differences between the microenvironments of the phosphorylated residues lead to their different effects on R4 aggregation upon phosphorylation. Our results show that working at the domain level using advanced peptide synthesis methods is a highly useful and practical way to provide valuable information about the effects of post translational modifications on protein activity.
Neurodegenerative diseases are characterised by the formation and accumulation
of protein fibrils. The mechanism underlaying this aggregation process remains
poorly understood. Fibril fragmentation, resulting in seed generation, plays a role in
toxicity. Here we provide a quantitative picture of the impact of ultrasound on
patient-derived and recombinant fibrils from various diseases. Fragmentation of
recombinant Tau fibrils and patient-derived fibrils from Alzheimer’s Disease,
Corticobasal Degeneration and Frontotemporal Dementia generates amyloid and
non-amyloid species. Interestingly, patient-derived fibrils are more susceptible to
ultrasound than artificial fibrils. Understanding fibril fragmentation and the
generation and nature of seeds may provide insights to the molecular mechanism
of the disease progression, contributing to the development therapeutic
approaches.
Garfagnini T., L., Ferrari , MB., Koopman , G., Mayer , S., Bressler , and A., Friedler . 7/7/2024. “A Peptide Strategy For Inhibiting Different Protein Aggregation Pathways”. Chemistry—A European Journal, 24, Pp. 30. https://doi.org/10.1002/chem.202400080. Publisher's Version Abstract
Protein aggregation correlates with many human diseases. Protein aggregates differ in structure and shape. Strategies to develop effective aggregation inhibitors that reach the clinic failed so far. Here, we developed a family of peptides targeting early aggregation stages for both amorphous and fibrillar aggregates of proteins unrelated in sequence and structure. They act on dynamic precursors before mechanistic differentiation takes place. Using peptide arrays, we first identified peptides inhibiting the amorphous aggregation of a molten globular, aggregation-prone mutant of the Axin tumor suppressor. Optimization revealed that the peptides activity did not depend on their sequences but rather on their molecular determinants: a composition of 20–30 % flexible, 30–40 % aliphatic and 20–30 % aromatic residues, a hydrophobicity/hydrophilicity ratio close to 1, and an even distribution of residues of different nature throughout the sequence. The peptides also suppressed fibrillation of Tau, a disordered protein that forms amyloids in Alzheimer's disease, and slowed down that of Huntingtin Exon1, an amyloidogenic protein in Huntington's disease, both entirely unrelated to Axin. Our compounds thus target early stages of different aggregation mechanisms, inhibiting both amorphous and amyloid aggregation. Such cross-mechanistic, multi-targeting aggregation inhibitors may be lead compounds for developing drug candidates against various protein aggregation diseases.
2023
Garfagnini T., F., Bemporad , D., Harries , F., Chiti , and A., Friedler . 11/15/2023. “Amyloid Aggregation Is Potently Slowed Down By Osmolytes Due To Compaction Of Partially Folded State”. Journal Of Molecular Biology, 435, 22. . Link Abstract
Amyloid aggregation is a key process in amyloidoses and neurodegenerative diseases. Hydrophobicity is one of the major driving forces for this type of aggregation, as an increase in hydrophobicity generally correlates with aggregation susceptibility and rate. However, most experimental systems in vitro and prediction tools in silico neglect the contribution of protective osmolytes present in the cellular environment. Here, we assessed the role of hydrophobic mutations in amyloid aggregation in the presence of osmolytes. To achieve this goal, we used the model protein human muscle acylphosphatase (mAcP) and mutations to leucine that increased its hydrophobicity without affecting its thermodynamic stability. Osmolytes significantly slowed down the aggregation kinetics of the hydrophobic mutants, with an effect larger than that observed on the wild-type protein. The effect increased as the mutation site was closer to the middle of the protein sequence. We propose that the preferential exclusion of osmolytes from mutation-introduced hydrophobic side-chains quenches the aggregation potential of the ensemble of partially unfolded states of the protein by inducing its compaction and inhibiting its self-assembly with other proteins. Our results suggest that including the effect of the cellular environment in experimental setups and predictive softwares, for both mechanistic studies and drug design, is essential in order to obtain a more complete combination of the driving forces of amyloid aggregation.
Shamir M., F., Martin , D., Woolfson , and A., Friedler . 9/27/2023. “Molecular Mechanism Of Stil Coiled-Coil Domain Oligomerization”. International Journal Of Molecular Sciences, 24, 19. . Link Abstract
Coiled-coil domains (CCDs) play key roles in regulating both healthy cellular processes and the pathogenesis of various diseases by controlling protein self-association and protein–protein interactions. Here, we probe the mechanism of oligomerization of a peptide representing the CCD of the STIL protein, a tetrameric multi-domain protein that is over-expressed in several cancers and associated with metastatic spread. STIL tetramerization is mediated both by an intrinsically disordered domain (STIL400–700) and a structured CCD (STIL CCD718–749). Disrupting STIL oligomerization via the CCD inhibits its activity in vivo. We describe a comprehensive biophysical and structural characterization of the concentration-dependent oligomerization of STIL CCD peptide. We combine analytical ultracentrifugation, fluorescence and circular dichroism spectroscopy to probe the STIL CCD peptide assembly in solution and determine dissociation constants of both the dimerization, (KD = 8 ± 2 µM) and tetramerization (KD = 68 ± 2 µM) of the WT STIL CCD peptide. The higher-order oligomers result in increased thermal stability and cooperativity of association. We suggest that this complex oligomerization mechanism regulates the activated levels of STIL in the cell and during centriole duplication. In addition, we present X-ray crystal structures for the CCD containing destabilising (L736E) and stabilising (Q729L) mutations, which reveal dimeric and tetrameric antiparallel coiled-coil structures, respectively. Overall, this study offers a basis for understanding the structural molecular biology of the STIL protein, and how it might be targeted to discover anti-cancer reagents.
Rowland L., B., Marjault H. , O., Karmi , D., Grant , L.J., Webb , A., Friedler , R., Nechushtai , R., Elber , and R., Mittler . 8/31/2023. “A Combination Of A Cell Penetrating Peptide And A Protein Translation Inhibitor Kills Metastatic Breast Cancer Cells”. Cell Death Discovery, 9. . Link Abstract
Cell Penetrating Peptides (CPPs) are promising anticancer and antimicrobial drugs. We recently reported that a peptide derived from the human mitochondrial/ER membrane-anchored NEET protein, Nutrient Autophagy Factor 1 (NAF-1; NAF-144-67), selectively permeates and kills human metastatic epithelial breast cancer cells (MDA-MB-231), but not control epithelial cells. As cancer cells alter their phenotype during growth and metastasis, we tested whether NAF-144–67 would also be efficient in killing other human epithelial breast cancer cells that may have a different phenotype. Here we report that NAF-144–67 is efficient in killing BT-549, Hs 578T, MDA-MB-436, and MDA-MB-453 breast cancer cells, but that MDA-MB-157 cells are resistant to it. Upon closer examination, we found that MDA-MB-157 cells display a high content of intracellular vesicles and cellular protrusions, compared to MDA-MB-231 cells, that could protect them from NAF-144–67. Inhibiting the formation of intracellular vesicles and dynamics of cellular protrusions of MDA-MB-157 cells, using a protein translation inhibitor (the antibiotic Cycloheximide), rendered these cells highly susceptible to NAF-144–67, suggesting that under certain conditions, the killing effect of CPPs could be augmented when they are applied in combination with an antibiotic or chemotherapy agent. These findings could prove important for the treatment of metastatic cancers with CPPs and/or treatment combinations that include CPPs.
Nueman E., Y., Sung Sohn, S., Povilaitis , A., Cardenas , R., Mittler , A., Friedler , L., Webb , R., Nechushtai , and R., Elber . 7/7/2023. “Visualization Of Molecular Permeation Into A Multi-Compartment Phospholipid Vesicle”. The Journal Of Physical Chemistry Letters, 14, 28, Pp. 6328-6512. . Link Abstract

Passive permeation of small molecules into vesicles with multiple compartments is a critical event in many chemical and biological processes. We consider the translocation of the peptide NAF-144–67 labeled with a fluorescent fluorescein dye across membranes of rhodamine-labeled 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) into liposomes with internal vesicles. Time-resolved microscopy revealed a sequential absorbance of the peptide in both the outer and inner micrometer vesicles that developed over a time period of minutes to hours, illustrating the spatial and temporal progress of the permeation. There is minimal perturbation of the membrane structure and no evidence for pore formation. On the basis of molecular dynamics simulations of NAF-144–67, we extended a local defect model to migration processes that include multiple compartments. The model captures the long residence time of the peptide within the membrane and the rate of permeation through the liposome and its internal compartments. Imaging experiments confirm the semi-quantitative description of the permeation of the model by activated diffusion and open the way for studies of more complex systems.

Bressler S., A., Mitrany , A., Wenger , I., Näthke , and A., Friedler . 3/30/2023. “The Oligomerization Domains Of The Apc Protein Mediate Liquid-Liquid Phase Separation That Is Phosphorylation Controlled”. International Journal Of Molecular Sciences, 24, 7. . Link Abstract
One of the most important properties of intrinsically disordered proteins is their ability to undergo liquid-liquid phase separation and form droplets. The Adenomatous Polyposis Coli (APC) protein is an IDP that plays a key role in Wnt signaling and mutations in Apc initiate cancer. APC forms droplets via its 20R domains and self-association domain (ASAD) and in the context of Axin. However, the mechanism involved is unknown. Here, we used peptides to study the molecular mechanism and regulation of APC droplet formation. We found that a peptide derived from the ASAD of APC-formed droplets. Peptide array screening showed that the ASAD bound other APC peptides corresponding to the 20R3 and 20R5 domains. We discovered that the 20R3/5 peptides also formed droplets by themselves and mapped specific residues within 20R3/5 that are necessary for droplet formation. When incubated together, the ASAD and 20R3/5 did not form droplets. Thus, the interaction of the ASAD with 20R3 and 20R5 may regulate the droplet formation as a means of regulating different cellular functions. Phosphorylation of 20R3 or 20R5 at specific residues prevented droplet formation of 20R3/5. Our results reveal that phosphorylation and the ability to undergo liquid-liquid phase separation, which are both important properties of intrinsically disordered proteins, are related to each other in APC. Phosphorylation inhibited the liquid-liquid phase separation of APC, acting as an ‘on-off’ switch for droplet formation. Phosphorylation may thus be a common mechanism regulating LLPS in intrinsically disordered proteins.
2022
Solomon O., Z., Shpilt , H., Sapir , S., Marom , S., Bibas , Y., Chen , S., Yitzchaik , and A, Friedler . 10/25/2022. “Peptide Based Inhibitors That Target The Docking Site Of Erk2”. Israel Journal Of Chemistry. . Link Abstract
Abnormal kinase activity is highly associated with disease, especially cancer. Thus, kinases are important targets for developing anti-cancer drugs. The common approach for kinase inhibition is using small molecules that compete with ATP for binding the ATP-binding site of the kinase. However, since the ATP-binding site is in many cases common to numerous kinases, it is difficult to achieve selectivity when targeting this site. Here we present an alternative approach of targeting the protein-protein interactions of kinases as means for achieving selectivity in their inhibition. We demonstrate this approach by using peptides for inhibiting the docking D-recruitment site (DRS) of the kinase ERK2. We designed a library of peptides, derived from DRS binding sequences of ERK2-binding proteins. We synthesized the peptides and quantified their interactions with ERK2. Three peptides, derived from the proteins ELK1, SAP1 and SAP2, bound ERK2 in the low micromolar range. These peptides also inhibited the interaction of ERK2 with a surface-bound ELK1 derived peptide. The peptides penetrated HT29 colon cancer cells and induced a moderate decrease in cell viability. Our approach can be further utilized for developing selective peptide-based kinase inhibitors.
Garfagnini T., L., Ferrari , M., Koopman , S., Halters , E., Van Kappel , G., Mayer , M., Maurice M. , G., Rüdiger S. , and A, Friedler . 10/23/2022. “A Peptide Strategy For Inhibiting Different Protein Aggregation Pathways In Disease”. Biorxiv. https://www.biorxiv.org/content/10.1101/10/23/2022. 10.22.513060v1.full. Link Abstract
Protein aggregation correlates with many human diseases. Protein aggregates differ in shape, ranging from amorphous aggregates to amyloid fibrils. Possibly for such heterogeneity, strategies to develop effective aggregation inhibitors that reach the clinic failed so far. Here, we present a new strategy by which we developed a family of peptides targeting early aggregation stages for both amorphous and fibrillar aggregates of proteins unrelated in sequence and structure. Thus, they act on dynamic precursors before a mechanistic differentiation takes place. Using a peptide array approach, we first identified peptides inhibiting the predominantly amorphous aggregation of a molten globular, aggregation-prone protein, a thermolabile mutant of the Axin tumor suppressor. A series of optimization steps revealed that the peptides activity did not depend on their sequences but rather on their molecular determinants. The key properties that made a peptide active were a composition of 20-30% flexible, 30-40% aliphatic and 20-30% aromatic residues, a hydrophobicity/hydrophilicity ratio close to 1 and an even distribution of residues of different nature throughout the sequence. Remarkably, the optimized peptides also suppressed fibrillation of Tau, a disordered protein that forms amyloids in Alzheimer’s disease, and entirely unrelated to Axin. Our compounds thus target early aggregation stages, independent of the aggregation mechanism, inhibiting both amorphous and amyloid aggregation. Such cross-mechanistic, multi-targeting aggregation inhibitors may be attractive lead compounds against multiple protein aggregation diseases.
Solomon O., I., Alshanski , A., Shitrit , Y., Chen , A., Friedler , and S., Yitzchaik . 10/14/2022. “Using A Single Peptide To Electrochemically Sense Multiple Kinases”. Biochemistry. . Full Text Abstract
Kinases are responsible for regulating cellular and physiological processes, and abnormal kinase activity is associated with various diseases. Therefore, kinases are being used as biomarkers for disease and developing methods for their sensing is highly important. Usually more than one kinase is involved in phosphorylating a target protein. However, kinase detection methods usually detect the activity of only one specific kinase. Here we describe an electrochemical kinase sensing tool for the selective detection of two kinases using the same target peptide. We demonstrate the sensing of kinases ERK2 and PKCδ. This is based on a single sensing element, a peptide that contains two distinct phosphorylation sites of these two kinases. Reversibility experiments with alkaline phosphatase and reaction with the electrochemically active ferrocene-labeled ATP showed that the mechanism of sensing is by detecting the enzymatic phosphorylation. Our approach can be further utilized to develop devices for the detection of multiple kinases and can be expanded to other types of enzymes involved in disease.
Grunhaus D., E., Molina R. , R., Cohen , T., Stein , A., Friedler , and M., Hurevich . 2022. “Accelerated Multiphosphorylated Peptide Synthesis”. Organic Process Research & Development. . Link Abstract
Preparing phosphorylated peptides with multiple adjacent phosphorylations is synthetically difficult, leads to β-elimination, results in low yields, and is extremely slow. We combined synthetic chemical methodologies with computational studies and engineering approaches to develop a strategy that takes advantage of fast stirring, high temperature, and a very low concentration of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) to produce multiphosphorylated peptides at an extremely rapid time and high purity.
Joshi P. N., E., Mervinetsky , O., Solomon , Y.-J., Chen , S., Yitzchaik , and A., Friedler . 2022. “Electrochemical Biosensors Based On Peptide-Kinase Interactions At The Kinase Docking Site”. Biosens. Bioelectron. . Link Abstract

Kinases are important cancer biomarkers and are conventionally detected based on their catalytic activity. Kinases regulate cellular activities by phosphorylation of motif-specific multiple substrate proteins, resulting in a lack of selectivity of activity-based kinase biosensors. We present an alternative approach of sensing kinases based on the interactions of their allosteric docking sites with a specific partner protein. The new approach was demonstrated for the ERK2 kinase and its substrate ELK-1. A peptide derived from ELK-1 was bound to a gold electrode and ERK2 sensing was performed by electrochemical impedance spectroscopy. We performed a detailed analysis of the interaction between the ELK-1 peptide and the kinase on gold surfaces. Atomic force microscopy, variable angle spectroscopic ellipsometry, X-ray Photoelectron Spectroscopy, and polarization modulation IR reflection-absorption spectroscopy analysis of the gold surface revealed the adsorbed layer of the ERK2 on the peptide monolayer. The sensors showed a high level of target selectivity for ERK2 compared to the p38γ kinase and BSA. ERK2 was detected in its cellular concentration range, 0.5–2.0 μM, and the limit of detection was calculated to be 0.35 μM. Using the flexibility of peptide design, our method is generic for developing sensitive and substrate-specific biosensors and other disease-related enzymes based on their interactions.

Solomon O., H., Sapir , E., Mervinetsky , Y.-J., Chen , A., Friedler , and S., Yitzchaik . 2022. “Kinase Sensing Based On Protein Interactions At The Catalytic Site”. Chem. Eur. J. . Link Abstract

The role kinases play in regulating cellular processes makes them potential biomarkers for detecting the onset and prognosis of various diseases, including many types of cancer. Current kinase biosensors, including electrochemical and radiometric methods, rely on sensing the ATP-dependant enzymatic phosphorylation reaction. Here we introduce a new type of interaction-based electrochemical kinase biosensor that does not require any chemical labelling or modification. The basis for sensing is the interactions between the catalytic site of the kinase and the phosphorylation site of its substrate rather than the phosphorylation reaction. We demonstrated this concept with the ERK2 kinase and its substrate protein HDGF, which is involved in lung cancer. A peptide monolayer derived from the HDGF phosphorylation site was adsorbed onto a gold electrode and was used to sense ERK2 without ATP. The sensitivity of the assay was down to 10 nM of ERK2, corresponding with the range of its cellular concentrations. Surface chemistry analysis confirmed that ERK2 was bound to the HDGF peptide monolayer. This increased the permeability of redox-active species through the monolayer and resulted in ERK2 electrochemical sensing. Since our detection approach is based on protein-protein interactions and not on the enzymatic reaction, it can be further utilized for more selective detection of different types of enzymes. See our cover profile.

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Iosub-Amir A., S., Sohn Y. , A.E., Cardenas , O., Karmi , M., Darash Yahana , T., Gruman , L., Rowland , B., Marjault H. , L.J., Webb , R., Mittler , R., Elber , A., Friedler , and R., Nechushtai . 2022. “A Peptide-Derived Strategy For Specifically Targeting The Mitochondria And Er Of Cancer Cells: A New Approach In Fighting Cancer”. Chemical Sci. . Link Abstract
An effective anti-cancer therapy should exclusively target cancer cells and trigger in them a broad spectrum of cell death pathways that will prevent avoidance. Here, we present a new approach in cancer therapy that specifically targets the mitochondria and ER of cancer cells. We developed a peptide derived from the flexible and transmembrane domains of the human protein NAF-1/CISD2. This peptide (NAF-144-67) specifically permeates through the plasma membranes of human epithelial breast cancer cells, abolishes their mitochondria and ER, and triggers cell death with characteristics of apoptosis, ferroptosis and necroptosis. In vivo analysis revealed that the peptide significantly decreases tumor growth in mice carrying xenograft human tumors. Computational simulations of cancer vs. normal cell membranes reveal that the specificity of the peptide to cancer cells is due to its selective recognition of their membrane composition. NAF-144-67 represents a promising anti-cancer lead compound that acts via a unique mechanism.
Mayer G., Z., Shpilt , H., Kowalski , E.Y., Tshuva , and A., Friedler . 2022. “Targeting Protein Interaction Hotspots Using Structured And Disordered Chimeric Peptide Inhibitors”. Acs Chemical Biology. . Link Abstract

The main challenge in inhibiting protein–protein interactions (PPI) for therapeutic purposes is designing molecules that bind specifically to the interaction hotspots. Adding to the complexity, such hotspots can be within both structured and disordered interaction interfaces. To address this, we present a strategy for inhibiting the structured and disordered hotspots of interactions using chimeric peptides that contain both structured and disordered parts. The chimeric peptides we developed are comprised of a cyclic structured part and a disordered part, which target both disordered and structured hotspots. We demonstrate our approach by developing peptide inhibitors for the interactions of the antiapoptotic iASPP protein. First, we developed a structured, α-helical stapled peptide inhibitor, derived from the N-terminal domain of MDM2. The peptide bound two hotspots on iASPP at the low micromolar range and had a cytotoxic effect on A2780 cancer cells with a half-maximal inhibitory concentration (IC50) value of 10 ± 1 μM. We then developed chimeric peptides comprising the structured stapled helical peptide and the disordered p53-derived LinkTer peptide that we previously showed to inhibit iASPP by targeting its disordered RT loop. The chimeric peptide targeted both structured and disordered domains in iASPP with higher affinity compared to the individual structured and disordered peptides and caused cancer cell death. Our strategy overcomes the inherent difficulty in inhibiting the interactions of proteins that possess structured and disordered regions. It does so by using chimeric peptides derived from different interaction partners that together target a much wider interface covering both the structured and disordered domains. This paves the way for developing such inhibitors for therapeutic purposes.

2021
Grunhaus D., A., Friedler , and M, Hurevich . 2021. “Automated Synthesis Of Heavily Phosphorylated Peptides”. Eur. J. Org. Chem. . Link Abstract

Multi phosphorylated peptides are key tools in understanding the biological roles of protein phosphorylation patterns. In this work, we focused on multi phosphorylated peptides with over four, clustered, phosphorylation sites that are termed herein heavily phosphorylated peptides (HPPs). The synthesis of heavily phosphorylated peptides is extremely difficult and requires the use of a wide temperature range. Standard peptide synthesizers are incapable of both cooling and heating, which impedes the automated synthesis of those peptides. Herein, we used the oligosaccharide synthesizer Glyconeer 2.1 to develop a protocol for the automated synthesis of heavily phosphorylated peptides. The Glyconeer 2.1 is able to both cool and heat, which enabled the development of highly controlled coupling and deprotection conditions that were used for the automated synthesis of four different heavily phosphorylated peptides with five or more, clustered, phosphorylation sites. Our approach paves the way for an easy automated synthesis of a variety of heavily phosphorylated peptides.

Reyes A. J. F., B., Kitata R. , dela C, Rosa M. A. , Y.-T., Wang , P.-Y., Lin , P.-C., Yang , A., Friedler , S., Yitzchaik , and Y.-J., Chen . 2021. “Integrating Site-Specific Peptide Reporters And Targeted Mass Spectrometry Enables Rapid Substrate-Specific Kinase Assay At The Nanogram Cell Level”. Anal. Chim. Acta. . Link Abstract

Dysregulation of phosphorylation-mediated signaling drives the initiation and progression of many diseases. A substrate-specific kinase assay capable of quantifying the altered site-specific phosphorylation of its phenotype-dependent substrates provides better specificity to monitor a disease state. We report a sensitive and rapid substrate-specific kinase assay by integrating site-specific peptide reporter and multiple reaction monitoring (MRM)-MS platform for relative and absolute quantification of substrate-specific kinase activity at the sensitivity of nanomolar kinase and nanogram cell lysate. Using non-small cell lung cancer as a proof-of-concept, three substrate peptides selected from constitutive phosphorylation in tumors (HDGF-S165, RALY-S135, and NRD1-S94) were designed to demonstrate the feasibility. The assay showed good accuracy (<15% nominal deviation) and reproducibility (<15% CV). In PC9 cells, the measured activity for HDGF-S165 was 3.2 ± 0.2 fmol μg−1 min−1, while RALY-S135 and NRD1-S94 showed 4- and 20-fold higher activity at the sensitivity of 25 ng and 5 ng lysate, respectively, suggesting different endogenous kinases for each substrate peptide. Without the conventional shotgun phosphoproteomics workflow, the overall pipeline from cell lysate to MS data acquisition only takes 3 h. The multiplexed analysis revealed differences in the phenotype-dependent substrate phosphorylation profiles across six NSCLC cell lines and suggested a potential association of HDGF-S165 and NRD1-S94 with TKI resistance. With the ease of design, sensitivity, accuracy, and reproducibility, this approach may offer rapid and sensitive assays for targeted quantification of the multiplexed substrate-specific kinase activity of small amounts of sample.