Protein Cyclophilin Research Articles

High‐Efficiency Trifluoromethyl‐Methionine Incorporation into Cyclophilin A by Cell‐Free Synthesis for 19F NMR Studies

AbstractFluorine‐19 NMR spectroscopy has emerged as a powerful tool for studying protein structure, dynamics, and interactions. Of particular interest is the exploitation of trifluoromethyl (tfm) groups, given their high sensitivity and superior transverse relaxation properties, compared to single fluorine atoms. However, biosynthetic incorporation of tfm‐bearing amino acids remains challenging due to cytotoxicity and incompatibility with natural tRNA synthetases. Here, we report on overcoming this challenge using cell‐free synthesis, incorporating trifluoromethyl‐methionine (tfmM) into the protein Cyclophilin A (CypA) with remarkably high efficiency, impossible via biosynthetic means. Importantly, we demonstrate that tfmM CypA binds a native substrate, the N‐terminal domain of HIV‐1 capsid protein (HIV‐1 CA‐NTD), and retains peptidyl prolyl cis/trans isomerase activity. It also binds the peptide inhibitor Cyclosporine A (CsA) with the same affinity as non‐labeled, wild‐type CypA. Furthermore, we show that 19F isotope shifts and 19F solvent paramagnetic relaxation enhancements (PREs) provide valuable structural information on surface exposure. Taken together, our study illustrates that tfmM can be readily incorporated into proteins at very high levels by cell‐free synthesis without disturbing protein structure and function, significantly expanding the scope of 19F NMR spectroscopy for studying protein structure and dynamics.

High-Efficiency Trifluoromethyl-Methionine Incorporation into Cyclophilin A by Cell-Free Synthesis for 19F NMR Studies.

Fluorine-19 NMR spectroscopy has emerged as a powerful tool for studying protein structure, dynamics, and interactions. Of particular interest is the exploitation of trifluoromethyl (tfm) groups, given their high sensitivity and superior transverse relaxation properties, compared to single fluorine atoms. However, biosynthetic incorporation of tfm-bearing amino acids remains challenging due to cytotoxicity and incompatibility with natural tRNA synthetases. Here, we report on overcoming this challenge using cell-free synthesis, incorporating trifluoromethyl-methionine (tfmM) into the protein Cyclophilin A (CypA) with remarkably high efficiency, impossible via biosynthetic means. Importantly, we demonstrate that tfmM CypA binds a native substrate, the N-terminal domain of HIV-1 capsid protein (HIV-1 CA-NTD), and retains peptidyl prolyl cis/trans isomerase activity. It also binds the peptide inhibitor Cyclosporine A (CsA) with the same affinity as non-labeled, wild-type CypA. Furthermore, we show that 19F isotope shifts and 19F solvent paramagnetic relaxation enhancements (PREs) provide valuable structural information on surface exposure. Taken together, our study illustrates that tfmM can be readily incorporated into proteins at very high levels by cell-free synthesis without disturbing protein structure and function, significantly expanding the scope of 19F NMR spectroscopy for studying protein structure and dynamics.

Cyclophilin D plays a critical role in the survival of senescent cells

Senescent cells play a causative role in many diseases, and their elimination is a promising therapeutic strategy. Here, through a genome-wide CRISPR/Cas9 screen, we identify the gene PPIF, encoding the mitochondrial protein cyclophilin D (CypD), as a novel senolytic target. Cyclophilin D promotes the transient opening of the mitochondrial permeability transition pore (mPTP), which serves as a failsafe mechanism for calcium efflux. We show that senescent cells exhibit a high frequency of transient CypD/mPTP opening events, known as 'flickering'. Inhibition of CypD using genetic or pharmacologic tools, including cyclosporin A, leads to the toxic accumulation of mitochondrial Ca2+ and the death of senescent cells. Genetic or pharmacological inhibition of NCLX, another mitochondrial calcium efflux channel, also leads to senolysis, while inhibition of the main Ca2+ influx channel, MCU, prevents senolysis induced by CypD inhibition. We conclude that senescent cells are highly vulnerable to elevated mitochondrial Ca2+ ions, and that transient CypD/mPTP opening is a critical adaptation mechanism for the survival of senescent cells.

Overexpression of the Panax ginseng CyP gene enhances abiotic and biotic stress tolerance in transgenic Arabidopsis

To explore the response of the cyclophilin (CyP) gene to abiotic and biotic stress, transgenic Arabidopsis was exposed to salt stress and inoculated with Phytophthora cactorum. The CyP gene enhanced salt tolerance by increasing proline content and slowing chlorophyll decline compared to wild-type plants. Under P. cactorum infection, the CyP protein interacted with spores and restricted spore germination to enhance resistance to P. cactorum. Thus, the CyP protein positively regulates gene expression in the abiotic and biotic stress tolerance networks. The CyP gene may be valuable for ginseng breeding programs aiming to develop new cultivars with enhanced stress tolerance.

Role of the mitochondrial protein cyclophilin D in skin wound healing and collagen secretion.

Central for wound healing is the formation of granulation tissue, which largely consists of collagen and whose importance stretches past wound healing, including being implicated in both fibrosis and skin aging. Cyclophilin D (CyD) is a mitochondrial protein that regulates the permeability transition pore, known for its role in apoptosis and ischemia-reperfusion. To date, the role of CyD in human wound healing and collagen generation has been largely unexplored. Here, we show that CyD was upregulated in normal wounds and venous ulcers, likely adaptive as CyD inhibition impaired reepithelialization, granulation tissue formation, and wound closure in both human and pig models. Overexpression of CyD increased keratinocyte migration and fibroblast proliferation, while its inhibition reduced migration. Independent of wound healing, CyD inhibition in fibroblasts reduced collagen secretion and caused endoplasmic reticulum collagen accumulation, while its overexpression increased collagen secretion. This was confirmed in a Ppif-KO mouse model, which showed a reduction in skin collagen. Overall, this study revealed previously unreported roles of CyD in skin, with implications for wound healing and beyond.

Abstract 3340: RMC-5127, a first-in-class, orally bioavailable mutant-selective RASG12V(ON) inhibitor is central nervous system (CNS)-penetrant and demonstrates anti-tumor activity in a preclinical intracranial xenograft model

Abstract Patients with advanced cancers harboring activating mutations in RAS, particularly those with non-small cell lung cancer, often develop brain metastases leading to increased morbidity and mortality. KRASG12V is the second most frequent RAS mutation in RAS-addicted cancers, including pancreatic cancer (34 %), colorectal cancer (21 %), and non-small cell lung cancer (19%). RMC-5127 is an orally bioavailable, mutant-selective tri-complex inhibitor of the GTP-bound (ON) form of RASG12V. RMC-5127 non-covalently binds to an abundant intracellular chaperone protein cyclophilin A (CypA), resulting in a binary complex that engages RASG12V(ON) to form a high-affinity tri-complex that sterically inhibits RAS binding to effectors. RMC-5127 drove deep suppression of RAS pathway activity, inhibited cell proliferation, and induced apoptosis in a panel of KRASG12V mutant human cancer cells in vitro but only caused submaximal inhibition in the panel of K/N/HRAS wildtype cancer cells, indicative of selectivity for KRASG12V over K/N/HRAS wildtype. Repeated oral dosing of RMC-5127 resulted in profound and durable anti-tumor activity in subcutaneous CDX and PDX models of KRASG12V mutant NSCLC, PDAC, and CRC in vivo. Dose-dependent exposure of RMC-5127 was observed in the whole brain of naïve mice, indicating the compound is brain penetrant. An intracranial xenograft model of KRASG12V tumors was established in immunodeficient mice to assess the CNS anti-tumor activity of RMC-5127. The intracranial tumor exposure of RMC-5127 was comparable with that observed in the whole brains of naïve mice and was sufficient to drive robust pharmacodynamic responses in the brain tumor. Moreover, RMC-5127 exhibited profound and durable anti-tumor activity in the intracranial model, with tumor regressions at well-tolerated doses. The anti-tumor activity of RMC-5127 in intracranial tumors was consistent with that in subcutaneous tumors at equivalent tumor exposures. In conclusion, these preclinical data demonstrate that RMC-5127 is a CNS-penetrant RASG12V(ON) inhibitor and support further study to determine the potential to benefit patients with advanced RASG12V-mutated cancers, including those that have developed or are at risk of developing brain metastases. Citation Format: Zhe Chen, Andre Eriksson, Bianca Lee, Jay Dinglasan, Nilufar Montazer, Jim Cregg, Anne Edwards, Kate Sanders, Jacqueline A. Smith, David Wildes, Mallika Singh, Zhican Wang, Jingjing Jiang. RMC-5127, a first-in-class, orally bioavailable mutant-selective RASG12V(ON) inhibitor is central nervous system (CNS)-penetrant and demonstrates anti-tumor activity in a preclinical intracranial xenograft model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3340.

Elevations in the Mitochondrial Matrix Protein Cyclophilin D Correlate With Reduced Parvalbumin Expression in the Prefrontal Cortex of Patients With Schizophrenia.

Cognitive deficits in schizophrenia are linked to dysfunctions of the dorsolateral prefrontal cortex (DLPFC), including alterations in parvalbumin (PV)-expressing interneurons (PVIs). Redox dysregulation and oxidative stress may represent convergence points in the pathology of schizophrenia, causing dysfunction of GABAergic interneurons and loss of PV. Here, we show that the mitochondrial matrix protein cyclophilin D (CypD), a critical initiator of the mitochondrial permeability transition pore (mPTP) and modulator of the intracellular redox state, is altered in PVIs in schizophrenia. Western blotting was used to measure CypD protein levels in postmortem DLPFC specimens of schizophrenic patients (n = 27) and matched comparison subjects with no known history of psychiatric or neurological disorders (n = 26). In a subset of this cohort, multilabel immunofluorescent confocal microscopy with unbiased stereological sampling methods were used to quantify (1) numbers of PVI across the cortical mantle (20 unaffected comparison, 14 schizophrenia) and (2) PV and CypD protein levels from PVIs in the cortical layers 2-4 (23 unaffected comparison, 18 schizophrenia). In schizophrenic patients, the overall number of PVIs in the DLPFC was not significantly altered, but in individual PVIs of layers 2-4 PV protein levels decreased along a superficial-to-deep gradient when compared to unaffected comparison subjects. These laminar-specific PVI alterations were reciprocally linked to significant CypD elevations both in PVIs and total DLPFC gray matter. Our findings support previously reported PVI anomalies in schizophrenia and suggest that CypD-mediated mPTP formation could be a potential contributor to PVI dysfunction in schizophrenia.

Abstract B084: Overcoming drug resistance of ‘tri-complex’ pan-RAS inhibitors: Inhibition of mTOR signaling

Abstract Background: RAS mutations occur in ~20% of all cancers that drive tumor progression, and therapy targeting most predominant RAS mutations remains unavailable. Mutant-selective RAS inhibitors (RASi), such as FDA-approved KRAS G12C inhibitors, have demonstrated initial clinical responses but drug resistance frequently emerges that minimize the drug efficacy, mechanistically mediated by RAS signaling reactivation. Methods and Results: To address this challenge, we characterized a class of novel pan-RASi that universally inhibit all RAS mutations, which forms a ‘tri-complex’ with the chaperone protein (cyclophilin A) that specifically binds to RAS, including wild-type RAS (KRAS, NRAS, HRAS). Mutant-selective RASi induced RAS signaling rebound intensively, whereas pan-RASi enabling to inhibit wild-type RAS minimized this rebound, which was surmountable in a concentration-dependent manner. Importantly, pan-RASi abrogated cell viability in patient-derived KRAS-mutant cancer organoids rather than in normal patient-derived wild-type RAS organoids, implicating drug selectivity and manageable toxicity. Interestingly, intrinsic resistance to pan-RASi was rare in RAS-mutant cancer cell screening but was observed only in a handful of pancreatic and lung cancer cell lines. Our time-resolved signaling analyses of pan-RASi treatment showed the re-activation of mTOR signaling and a contrast correlation that mTOR signaling decreased in sensitive lines but remained in resistant lines, underscoring the critical contribution of mTOR pathways to RASi resistance. Mechanistically, we further identified mTOR signaling that drives intrinsic resistance to pan-RASi, and combined pan-RASi with mTOR inhibitors (mTORi) suppressed mTOR signaling in resistant lines, thereby improving efficacy. Conclusion: Pan-RASi hold promise in treating RAS-mutant cancer clinically and a combination of pan-RASi with mTORi can improve drug efficacy. Citation Format: Qingxiang (Nick) Lin. Overcoming drug resistance of ‘tri-complex’ pan-RAS inhibitors: Inhibition of mTOR signaling [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B084.

Stuttering associated with a pathogenic variant in the chaperone protein cyclophilin 40.

Stuttering is a common speech disorder that interrupts speech fluency and tends to cluster in families. Typically, stuttering is characterized by speech sounds, words or syllables which may be repeated or prolonged and speech that may be further interrupted by hesitations or 'blocks'. Rare variants in a small number of genes encoding lysosomal pathway proteins have been linked to stuttering. We studied a large four-generation family in which persistent stuttering was inherited in an autosomal dominant manner with disruption of the cortico-basal-ganglia-thalamo-cortical network found on imaging. Exome sequencing of three affected family members revealed the PPID c.808C>T (p.Pro270Ser) variant that segregated with stuttering in the family. We generated a Ppid p.Pro270Ser knock-in mouse model and performed ex vivo imaging to assess for brain changes. Diffusion-weighted MRI in the mouse revealed significant microstructural changes in the left corticospinal tract, as previously implicated in stuttering. Quantitative susceptibility mapping also detected changes in cortico-striatal-thalamo-cortical loop tissue composition, consistent with findings in affected family members. This is the first report to implicate a chaperone protein in the pathogenesis of stuttering. The humanized Ppid murine model recapitulates network findings observed in affected family members.

PPIH gene regulation system and its prognostic significance in hepatocellular carcinoma: a comprehensive analysis.

Peptidyl-prolyl isomerase H (PPIH) is a member of the cyclophilin protein family, which functions as a molecular chaperone and is involved in the splicing of pre-mRNA. According to reports, the malignant progression of HCC related to hepatitis B virus (HBV) is tightly associated with RNA-binding proteins. Nevertheless, there is no research on PPIH expression or its function in the occurrence and progression of HCC. We are the first to reveal that the mRNA and protein levels of Ppih are substantially overexpressed in HCC, as the outcomes show. A significant correlation existed between enriched expression of Ppih within HCC and more advanced, poorly differentiated, and TP53-mutated tumors. These findings, which suggest that Ppih may serve as a predictive biomarker for people with HCC, serve as a starting point for further investigation into the function of Ppih in the progression of carcinogenesis. Accordingly, we utilized clinical samples and bioinformatics analysis to assess Ppih's mRNA, protein expression, and gene regulatory system in HCC. Additionally, Wilcoxon signed-rank testing and logistic regression were utilized to inspect the association between clinicopathological factors and Ppih. Clinical pathological traits linked to overall survival (OS) among HCC patients were examined via TCGA data via Cox regression and the Kaplan-Meier approach. Additionally, via TCGA data collection, gene set enrichment assessment was also conducted.

The involvement of NETs in ANCA-associated vasculitis.

Anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis (AAV) is a serious autoimmune disease that is characterized by vascular necrosis. The pathogenesis of AAV includes ANCA-mediated neutrophil activation, subsequent release of inflammatory cytokines and reactive oxygen species (ROS), and formation of neutrophil extracellular traps (NETs). Excessive NETs could participate not only in ANCA-mediated vascular injury but also in the production of ANCAs per se as autoantigens. Thus, a vicious cycle of NET formation and ANCA production is critical for AAV pathogenesis. Elucidating the molecular signaling pathways in aberrant neutrophil activation and NETs clearance systems will allow specific therapeutics to regulate these pathways. Currently, standard therapy with high doses of glucocorticoids and immunosuppressants has improved outcomes in patients with AAV. However, AAV frequently develops in elderly people, and adverse effects such as severe infections in the standard regimens might contribute to the mortality. Mechanistically, cytokines or complement factors activate and prime neutrophils for ANCA-binding; thus, C5a receptor blocker has garnered attention as potential replacement for glucocorticoids in clinical settings. Recent studies have demonstrated that receptor-interacting protein kinases (RIPK3) and cyclophilin D (CypD), which regulate cell necrosis, may be involved in ANCA-induced NETs formation. Meanwhile, targeting NETs clearance, including the addition of deoxyribonuclease I (DNase I) and macrophage engulfment, may improve vasculitis. In this review, we focus on the pathogenesis of NETs and discuss potential targeted therapies for AAV based on recent experimental evidence.

Peptidyl-prolyl isomerase Cyclophilin71 promotes SERRATE phase separation and miRNA processing in Arabidopsis

MicroRNAs (miRNAs) play an important role in gene regulation. In Arabidopsis, mature miRNAs are processed from primary miRNA transcripts by the Dicing complex that contains Dicer-like 1 (DCL1), SERRATE (SE), and Hyponastic Leaves 1 (HYL1). The Dicing complex can form nuclear dicing bodies (D-bodies) through SE phase separation. Here, we report that Cyclophilin71 (CYP71), a peptidyl-prolyl isomerase (PPIase), positively regulates miRNA processing. We show that CYP71 directly interacts with SE and enhances its phase separation, thereby promoting the formation of D-body and increasing the activity of the Dicing complex. We further show that the PPIase activity is important for the function of CYP71 in miRNA production. Our findings reveal orchestration of miRNA processing by a cyclophilin protein and suggest the involvement of peptidyl-prolyl cis-trans isomerization, a structural mechanism, in SE phase separation and miRNA processing.

Abstract P3181: A Cyclophilin D-mitochondria-redox Differentiation Pathway Regulates Neonatal Heart Bioenergetics And Function

Background: During birth, demands on the heart increase when exposed to high oxidative stress. Cardiac myocyte differentiation is dependent on changes in mitochondrial function that regulate cell stress pathways to enhance differentiation. We have shown these changes are dependent on closure of the mitochondrial permeability transition pore (mPTP) controlled by the protein cyclophilin D (CypD). These studies aim to determine the effects of independently manipulating CypD, mitochondrial membrane potential, and reactive oxygen species (ROS) production on mitochondrial function, myocyte differentiation, and cardiac function in the neonate. Methods: Neonatal C57Bl6 mice were intraperitoneally injected on postnatal day (P) 1-6 of with mitoparaquat (0.025-0.05 mg/kg), Tempol (0.7 mg/kg), mitoTempo (0.7 mg/kg), 2,4-dinitrophenol (2 mg/kg), or vehicle. Hearts were harvested at P7 and mitochondrial respiration, enzymatic activity of the electron transport chain (ETC) complex (Cx) I and 2, and assembly of mitochondrial supercomplexes were measured by native gel electrophoresis. Results: Treatment with mitoparaquat to increase mitochondrial ROS caused a dose-dependent decrease of Cx I activity measured by oxygen consumption and enzyme assays. This corresponded to decrease in assembly of Cx-I containing supercomplexes. Decreasing mitochondrial ROS using mitoTempo had no effect on Cx I activity but increased assembly of Cx-III containing supercomplexes. Decreasing ROS in the cell with Tempol decreased Cx-I activity but had no effect on supercomplex assembly. Uncoupling at the mitochondrial membrane using 2,4-dinitrophenol increased electron flux from Cx I to Cx III but may decrease supercomplex assembly. Treatment of isolated mitochondria with cyclosporin A to inhibit CypD had no effects on these measures. Conclusions: Changes in ROS and mitochondrial membrane potential have selective effects on ETC assembly, activity in the neonatal period, and are not inhibited by closure of the mPTP. This data suggests a pathway where CypD regulates the mPTP to regulate the ETC, membrane potential, and ROS production to regulate myocyte differentiation; such a pathway could be targeted to increase cardiac maturation in infants with poor cardiac function.

Abstract P1153: ANT-Dependent MPTP Contributes To Necrotic Myofiber Death In Muscular Dystrophy

The Mitochondrial Permeability Transition Pore (MPTP) is a critical cell death mechanism that contributes to ischemia reperfusion injury in the heart and several degenerative diseases, including Muscular Dystrophy (MD). MD is a family of genetic disorders characterized by progressive muscle wasting, loss of muscle function, and premature death. We have recently demonstrated that the MPTP has two defined genetic components: one consisting of adenosine nucleotide translocase (ANT) family of proteins and a second, unidentified pore that requires the protein cyclophilin D (CypD) to activate. In this study we used MD as a model to test whether this new MPTP model could be applied to a physiological context of necrotic cell death in vivo . We observed that genetic deletion of ANT1 or CypD substantially reduced MD pathology in skeletal muscle, with reduced measures of muscle necrotic cell death, and improved muscle function compared to MD control animals. However, both ANT1KO and CypDKO MD mice still displayed elevated rates of cell death and MD pathology compared to healthy wildtype animals. MD mice lacking both ANT1 and CypD (ANT1KO-CypDKO) virtually eliminated features of skeletal muscle pathology in MD. We observed a near complete loss of MD histopathology, undetectable levels of tissue necrosis, and muscle function that was improved to non-MD levels in ANT1KO-CypDKO MD mice. This study demonstrates that inhibiting both the ANT-dependent and CypD-dependent components of MPTP together can prevent necrotic cell death in an in vivo model. This study also suggests that a therapy that inhibits both MPTP-components can effectively treat MD and may potentially reduce cardiac ischemia reperfusion injury.

Selection and Validation of Reference Genes in Virus-Infected Sweet Potato Plants.

Quantitative real-time PCR (qRT-PCR) in sweet potatoes requires accurate data normalization; however, there are insufficient studies on appropriate reference genes for gene expression analysis. We examined variations in the expression of eight candidate reference genes in the leaf and root tissues of sweet potatoes (eight nonvirus-infected or eight virus-infected samples). Parallel analyses with geNorm, NormFinder, and Best-Keeper show that different viral infections and origin tissues affect the expression levels of these genes. Based on the results of the evaluation of the three software, the adenosine diphosphate-ribosylation factor is suitable for nonvirus or virus-infected sweet potato leaves. Cyclophilin and ubiquitin extension proteins are suitable for nonvirus-infected sweet potato leaves. Phospholipase D1 alpha is suitable for virus-infected sweet potato leaves. Actin is suitable for roots of nonvirus-infected sweet potatoes. Glyceraldehyde-3-phosphate dehydrogenase is suitable for virus-infected sweet potato roots. The research provides appropriate reference genes for further analysis in leaf and root samples of viruses in sweet potatoes.

CC-4066 therapy delivered to kidneys during cold storage and assessed with normothermic reperfusion is feasible and safe.

Currently there is an urgent need to translate interventions that may be beneficial to marginal donor kidneys prior to transplant, to improve their quality from bench to bedside. This project investigated the effects of CC-4066, a potent dual inhibitor of cyclophilin proteins A and D, treatment during static cold storage (SCS) in a porcine model of renal ischemia-reperfusion injury (IRI) using Normothermic Reperfusion (NR). Porcine kidneys and autologous blood were retrieved in pairs from a local abattoir (n = 7). One kidney from each pair was randomly allocated to treatment and one allocated to control and flushed with preservation solution containing CC-4066 or vehicle. After 7 h of SCS kidneys underwent 3 h Normothermic Reperfusion (NR) with autologous whole blood while perfusion characteristics and samples were collected. Perfusion and metabolic parameters showed similar trends and no statistical differences were observed between the groups. IL-6 showed a significant increase over time but no significant difference between groups (p-value 0.009 and 0.14 respectively, two-way ANOVA). Oxygen consumption and lactate levels were similar between groups but there was increased vacuolation on histology in the control group. The addition of CC-4066 during SCS of kidneys is safe and feasible and has no adverse or detrimental effects on perfusion during assessment on NR. There was no difference in cytokine levels although there was a trend towards less vacuolation on histology in the treatment group.

Abstract 1598: RM-046, a first-in-class, mutant-selective, and oral KRASQ61H(ON) inhibitor that drives tumor regression in preclinical models and validates KRASQ61H as a therapeutic target

Abstract KRASQ61H mutant cancers represent a significant unmet medical need and include common solid tumor histotypes such as non-small cell lung cancer (NSCLC), pancreatic ductal adenocarcinoma (PDAC), and colorectal cancer (CRC). Currently, there are no targeted inhibitors of KRASQ61H in clinical development. Mutant RAS proteins exist predominantly in the GTP-bound active RAS(ON) state, leading to excessive downstream signaling via interaction with effectors such as RAF kinases. The properties of the intrinsic GTPase cycle of KRASQ61H should lead to accumulation of the active ON state. RM-046 is a potent, selective, and oral tri-complex inhibitor of KRASQ61H(ON). RM-046 binds to the abundant intracellular chaperone protein cyclophilin A (CypA) with high affinity to form a binary complex that then non-covalently and selectively engages the active ON state of KRASQ61H. The resulting tri-complex sterically blocks KRASQ61H binding to its effectors, thereby inhibiting its downstream signaling. RM-046 potently suppressed ERK phosphorylation and proliferation in KRASQ61H mutant cancer cells with sub-nanomolar EC50 and IC50 values while displaying selectivity over cancer cells with wildtype KRAS. RM-046 showed no evidence of off-target interactions based on in vitro GTPase, kinome, and safety panels. As a single agent, RM-046 induced dose-dependent, deep, and durable suppression of RAS pathway signaling in preclinical xenograft models in vivo. Daily oral administration of RM-046 demonstrated dose-dependent anti-tumor activity and drove deep tumor regressions across several preclinical xenograft models of human KRASQ61H tumors, including NSCLC and PDAC. All treatment regimens tested with RM-046 were tolerated in vivo. As far as we are aware, RM-046 is the first oral and mutant-selective inhibitor of KRASQ61H(ON). It also represents an example of a non-covalent, mutant-selective tri-complex inhibitor of a KRAS oncogenic driver mutation. Citation Format: Yu C. Yang, Severin Thompson, David Montgomery, Antonio J. Quiñones, Xing Wei, Benjamin Madej, Aidan Tomlinson, Nataliya T. Shifrin, Alexander McNamara, Ethan Ahler, Laura L. McDowell, Michael Flagella, John Setser, Stephanie Chang, Zhican Wang, Zhengping Wang, Jun Huang, Steve Ballmer, Shaong li, Andreas Buckl, Elena Koltun, Adrian Gill, Jingjing Jiang, Mallika Singh, Jacqueline A. Smith. RM-046, a first-in-class, mutant-selective, and oral KRASQ61H(ON) inhibitor that drives tumor regression in preclinical models and validates KRASQ61H as a therapeutic target [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 1598.

Structural Basis and Mechanism of Cyclophilin A‐Tau Interaction in Alzheimer’s Disease and Neuroinflammation

AbstractBackgroundTau protein that comprises neurofibrillary tangles in Alzheimer’s Disease (AD) interact with the abundant immunophilin protein Cyclophilin A (CypA) due to its peptidyl‐prolyl cis‐trans isomerase activity.MethodUsing surface plasmon resonance (SPR), nuclear magnetic resonance (NMR) and cell culture, structural details of CypA/tau interaction and its functional consequences are characterized.ResultUsing SPR, we observed a binding equilibrium constant (KD) of full‐length tau at ∼10 µM and identified the tau binding pocket on CypA using NMR. CypA and tau uptake by microglia was measured by immunofluorescence microscopy and flow cytometry. CypA‐tau interactions within microglia cell lines affect neuroinflammation by altering proinflammatory and anti‐inflammatory cytokine secretion responses.ConclusionCypA binds to tau with high affinity and specificity, which has functional significance in tau conformation, interaction, aggregation, and in neuroinflammation.

Requirement of Peptidyl-Prolyl Cis/Trans isomerases and chaperones for cellular uptake of bacterial AB-type toxins.

Bacterial AB-type toxins are proteins released by the producing bacteria and are the causative agents for several severe diseases including cholera, whooping cough, diphtheria or enteric diseases. Their unique AB-type structure enables their uptake into mammalian cells via sophisticated mechanisms exploiting cellular uptake and transport pathways. The binding/translocation B-subunit facilitates binding of the toxin to a specific receptor on the cell surface. This is followed by receptor-mediated endocytosis. Then the enzymatically active A-subunit either escapes from endosomes in a pH-dependent manner or the toxin is further transported through the Golgi to the endoplasmic reticulum from where the A-subunit translocates into the cytosol. In the cytosol, the A-subunits enzymatically modify a specific substrate which leads to cellular reactions resulting in clinical symptoms that can be life-threatening. Both intracellular uptake routes require the A-subunit to unfold to either fit through a pore formed by the B-subunit into the endosomal membrane or to be recognized by the ER-associated degradation pathway. This led to the hypothesis that folding helper enzymes such as chaperones and peptidyl-prolyl cis/trans isomerases are required to assist the translocation of the A-subunit into the cytosol and/or facilitate their refolding into an enzymatically active conformation. This review article gives an overview about the role of heat shock proteins Hsp90 and Hsp70 as well as of peptidyl-prolyl cis/trans isomerases of the cyclophilin and FK506 binding protein families during uptake of bacterial AB-type toxins with a focus on clostridial binary toxins Clostridium botulinum C2 toxin, Clostridium perfringens iota toxin, Clostridioides difficile CDT toxin, as well as diphtheria toxin, pertussis toxin and cholera toxin.

The Bursaphelenchus xylophilus effector BxML1 targets the cyclophilin protein (CyP) to promote parasitism and virulence in pine

BackgroundBursaphelenchus xylophilus is the causal agent of pine wilt disease (PWD) that has caused enormous ecological and economic losses in China. The mechanism in the interaction between nematodes and pine remains unclear. Plant parasitic nematodes (PPNs) secrete effectors into host plant tissues. However, it is poorly studied that role of effector in the infection of pine wood nematode (PWN).ResultsWe cloned, characterized and functionally validated the B. xylophilus effector BxML1, containing an MD-2-related lipid-recognition (ML) domain. This protein inhibits immune responses triggered by the molecular pattern BxCDP1 of B. xylophilus. An insitu hybridization assay demonstrated that BxML1 was expressed mainly in the dorsal glands and intestine of B. xylophilus. Subcellular localization analysis showed the presence of BxML1 in the cytoplasm and nucleus. Furthermore, number of B. xylophilus and morbidity of pine were significantly reduced in Pinus thunbergii infected with B. xylophilus when BxML was silenced. Using yeast two-hybrid (Y2H) and coimmunoprecipitation (CoIP) assays, we found that the BxML1 interacts with cyclophilin protein PtCyP1 in P. thunbergii.ConclusionsThis study illustrated that BxML1 plays a critical role in the B. xylophilus–plant interaction and virulence of B. xylophilus.