Reversibly Reactive Affinity Selection-Mass Spectrometry Enables Identification of Covalent Peptide Binders.

Covalent peptide binders have found applications as activity-based probes and as irreversible therapeutic inhibitors. Currently, there is no rapid, label-free, and tunable affinity selection platform to enrich covalent reactive peptide binders from synthetic libraries. We address this challenge by developing a reversibly reactive affinity selection platform termed ReAct-ASMS enabled by tandem high-resolution mass spectrometry (MS/MS) to identify covalent peptide binders to native protein targets. It uses mixed disulfide-containing peptides to build reversible peptide-protein conjugates that can enrich for covalent variants, which can be sequenced by MS/MS after reduction. Using this platform, we identified covalent peptide binders against two oncoproteins, human papillomavirus 16 early protein 6 (HPV16 E6) and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 protein (Pin1). The resulting peptide binders efficiently and selectively cross-link Cys58 of E6 at 37 °C and Cys113 of Pin1 at room temperature, respectively. ReAct-ASMS enables the identification of highly selective covalent peptide binders for diverse molecular targets, introducing an applicable platform to assist preclinical therapeutic development pipelines.

Development of an α-Klotho Recognizing High-Affinity Peptide Probe from In-Solution Enrichment.

The kidney, parathyroid gland, and choroid plexus express the aging-related transmembrane protein α-Klotho, a coreceptor of the fibroblast growth factor 23 (FGF23) receptor complex. Reduced α-Klotho levels are correlated with chronic kidney disease and other age-related diseases, wherein they are released from membranes into circulation. Klotho's potential physiological action as a hormone is of current scientific interest. Part of the challenges associated with advancing these studies, however, has been the long-standing difficulty in detecting soluble α-Klotho in biofluids. Here, we describe the discovery of peptides that recognize α-Klotho with high affinity and selectivity by applying in-solution size-exclusion-based affinity selection-mass spectrometry (AS-MS). After two rounds of AS-MS and subsequent N-terminal modifications, the peptides improved their binding affinity to α-Klotho by approximately 2300-fold compared to the reported starting peptide Pep-10, previously designed based on the C-terminal region of FGF23. The lead peptide binders were shown to enrich α-Klotho from cell lysates and to label α-Klotho in kidney cells. Our results further support the utility of in-solution, label-free AS-MS protocols to discover peptide-based binders to target proteins of interest with high affinity and selectivity, resulting in functional probes for biological studies.

Structure of the p53 degradation complex from HPV16.

Human papillomavirus (HPV) is a significant contributor to the global cancer burden, and its carcinogenic activity is facilitated in part by the HPV early protein 6 (E6), which interacts with the E3-ligase E6AP, also known as UBE3A, to promote degradation of the tumor suppressor, p53. In this study, we present a single-particle cryoEM structure of the full-length E6AP protein in complex with HPV16 E6 (16E6) and p53, determined at a resolution of ~3.3 Å. Our structure reveals extensive protein-protein interactions between 16E6 and E6AP, explaining their picomolar binding affinity. These findings shed light on the molecular basis of the ternary complex, which has been pursued as a potential therapeutic target for HPV-driven cervical, anal, and oropharyngeal cancers over the last two decades. Understanding the structural and mechanistic underpinnings of this complex is crucial for developing effective therapies to combat HPV-induced cancers. Our findings may help to explain why previous attempts to disrupt this complex have failed to generate therapeutic modalities and suggest that current strategies should be reevaluated.

Electrophile Scanning Reveals Reactivity Hotspots for the Design of Covalent Peptide Binders.

Protein-protein interactions (PPIs) are intriguing targets in drug discovery and development. Peptides are well suited to target PPIs, which typically present with large surface areas lacking distinct features and deep binding pockets. To improve binding interactions with these topologies and advance the development of PPI-focused therapeutics, potential ligands can be equipped with electrophilic groups to enable binding through covalent mechanisms of action. We report a strategy termed electrophile scanning to identify reactivity hotspots in a known peptide ligand and demonstrate its application in a model PPI. Cysteine mutants of a known ligand are used to install protein-reactive modifiers via a palladium oxidative addition complex (Pd-OAC). Reactivity hotspots are revealed by cross-linking reactions with the target protein under physiological conditions. In a model PPI with the 9-mer peptide antigen VL9 and major histocompatibility complex (MHC) class I protein HLA-E, we identify two reactivity hotspots that afford up to 87% conversion to the protein-peptide conjugate within 4 h. The reactions are specific to the target protein in vitro and dependent on the peptide sequence. Moreover, the cross-linked peptide successfully inhibits molecular recognition of HLA-E by CD94-NKG2A possibly due to structural changes enacted at the PPI interface. The results illustrate the potential application of electrophile scanning as a tool for rapid discovery and development of covalent peptide binders.

Discovery of reactive peptide inhibitors of human papillomavirus oncoprotein E6.

Human papillomavirus (HPV) infections account for nearly all cervical cancer cases, which is the fourth most common cancer in women worldwide. High-risk variants, including HPV16, drive tumorigenesis in part by promoting the degradation of the tumor suppressor p53. This degradation is mediated by the HPV early protein 6 (E6), which recruits the E3 ubiquitin ligase E6AP and redirects its activity towards ubiquitinating p53. Targeting the protein interaction interface between HPV E6 and E6AP is a promising modality to mitigate HPV-mediated degradation of p53. In this study, we designed a covalent peptide inhibitor, termed reactide, that mimics the E6AP LXXLL binding motif by selectively targeting cysteine 58 in HPV16 E6 with quantitative conversion. This reactide provides a starting point in the development of covalent peptidomimetic inhibitors for intervention against HPV-driven cancers.

Cryo-EM structure of human PAPP-A2 and mechanism of substrate recognition.

Pregnancy-Associated Plasma Protein A isoforms, PAPP-A and PAPP-A2, are metalloproteases that cleave insulin-like growth factor binding proteins (IGFBPs) to modulate insulin-like growth factor signaling. The structures of homodimeric PAPP-A in complex with IGFBP5 anchor peptide, and inhibitor proteins STC2 and proMBP have been recently reported. Here, we present the single-particle cryo-EM structure of the monomeric, N-terminal LG, MP, and the M1 domains (with the exception of LNR1/2) of human PAPP-A2 to 3.13 Å resolution. Our structure together with functional studies provides insight into a previously reported patient mutation that inactivates PAPP-A2 in a distal region of the protein. Using a combinational approach, we suggest that PAPP-A2 recognizes IGFBP5 in a similar manner as PAPP-A and show that PAPP-A2 cleaves IGFBP5 less efficiently due to differences in the M2 domain. Overall, our studies characterize the cleavage mechanism of IGFBP5 by PAPP-A2 and shed light onto key differences with its paralog PAPP-A.

Percutaneous Coronary Intervention in Men, Women, and Minorities With a Previous Coronary Artery Bypass Graft Surgery (from the Pooled PLATINUM Diversity and PROMUS Element Plus Registries).

There is limited data on new-generation stent outcomes in patients with previous coronary artery bypass graft (CABG) and the associated risk of gender and race/ethnicity is unclear. We investigated 1-year outcomes after platinum chromium everolimus-eluting stent implantation in a diverse population of men, women, and minorities with previous CABG pooled from the PLATINUM Diversity (NCT02240810) and PROMUS Element Plus (NCT01589978) registries. Our primary outcome was major adverse cardiac events (MACE), a composite of all-cause death, myocardial infarction (MI), and target vessel revascularization (TVR) at 1-year post percutaneous coronary intervention (PCI). Secondary end points included all-cause death, MI, TVR, target vessel failure, and stent thrombosis. A total of 4,175 patients were included in the analysis, including 1,858 women (44.5%), 1,057 minorities (25.3%), and 662 (15.9%) with previous CABG. Patients with previous CABG were older, included more men and White patients, and had more co-morbidities compared with patients without previous CABG. At 1 year, patients with previous CABG had a higher risk of MACE (12.6% vs 7.5%, hazard ratio 1.70, 95% confidence interval 1.32 to 2.19, p <0.001) and end points, including death/MI, TVR, and target vessel failure. After multivariate adjustment, no differences were observed in MACE (adjusted hazard ratio 1.11, 95% confidence interval 0.82 to 1.49, p = 0.506) or any secondary end points. No interaction was observed between previous CABG and gender or minority status. In conclusion, in a contemporary PCI population, patients with previous CABG remain at high risk for PCI because of their elevated risk profile. Previous CABG status was however not independently associated with worse outcomes after adjustment, nor was any interaction observed with gender or race/ethnicity.

Recurrent Spontaneous Coronary Artery Dissection: A Case of Triple Trouble.

SCAD (Spontaneous Coronary Artery Dissection) is a rare disorder which rarely recurs. It is increasingly diagnosed as a cause for acute coronary syndrome (ACS) with limited insight into its pathophysiology and treatment. Lack of randomized trials and consensus guidelines make this a unique and challenging disease to manage. We describe a complex case of recurrent idiopathic SCAD with prior history of NSTE-ACS (Non-ST elevation Acute Coronary Syndrome) and discuss its management based on current clinical practices.

Branched Multimeric Peptides as Affinity Reagents for the Detection of α-Klotho Protein.

α-Klotho, an aging-related protein found in the kidney, parathyroid gland, and choroid plexus, acts as an essential co-receptor with the fibroblast growth factor 23 receptor complex to regulate serum phosphate and vitamin D levels. Decreased levels of α-Klotho are a hallmark of age-associated diseases. Detecting or labeling α-Klotho in biological milieu has long been a challenge, however, hampering the understanding of its role. Here, we developed branched peptides by single-shot parallel automated fast-flow synthesis that recognize α-Klotho with improved affinity relative to their monomeric versions. These peptides were further shown to selectively label Klotho for live imaging in kidney cells. Our results demonstrate that automated flow technology enables rapid synthesis of complex peptide architectures, showing promise for future detection of α-Klotho in physiological settings.

High-Throughput Proteome Profiling of Plasma and Native Plasma Complexes Using Native Chromatography.

We describe a high-throughput method for co-fractionation mass spectrometry (CF-MS) profiling for native plasma protein profiling. CF-MS allows the profiling of endogenous protein complexes between samples. Proteins often interact with other proteins and form macromolecular complexes that are different in disease states as well as cell states and cell types. This protocol describes an example for the sample preparation of 954 individual size exclusion chromatography (SEC) fractions, derived from 18 plasma samples that were separated into 53 fractions. Eighteen plasma samples were chosen based on the TMTpro multiplexing, but this methodology can be adapted for fewer or larger numbers of samples as appropriate. Our automated sample preparation method allows for high-throughput native plasma profiling, and we provide detailed methods for both a label-free and an isobaric labeling approach, discuss the merits of each approach, and detail the advantages of combining these strategies for comprehensive native plasma proteome profiling.

Pathological gaming: a longitudinal study from the perspectives of mental health problems and social stress model.

Debates about pathological gaming continues in the wake of the World Health Organization's (WHO) decision to establish a gaming disorder diagnosis. Questions persist whether gaming disorder is best conceived as a stand-alone psychiatric disorder, or whether it heralds or accompanies other, more established conditions, such as depression or ADHD. We tested these hypotheses in a sample of 3,034 youth from Singapore. Evidence suggests that pathological gaming is a somewhat unstable construct, often remitting spontaneously. Youth with preexisting ADHD or depression were more likely to develop later pathological gaming problems, while the inverse was not true, with neither early pathological gaming nor gaming time predictive of later mental health problems. Results suggest that, whenever there is any need to conduct robust evidence-based studies, more evidence should be collected before new disorders are recognized by means of "expert consensus".

Influence of Race/Ethnicity and Sex on Coronary Stent Outcomes in Diabetic Patients.

Background: How diabetes mellitus (DM), race/ethnicity, and sex impact ischemic events following coronary artery stent procedures is unknown. Methods: Using the PLATINUM Diversity and PROMUS Element Plus Post-Approval Pooled Study (N = 4184), we examined the impact of race/ethnicity, sex, and DM on coronary stent outcomes. Primary outcome was 1-year major adverse cardiac events (MACE) (MACE composite: death, myocardial infarction [MI], and target vessel revascularization). Results: The study sample included 1437 diabetic patients (501 White men, 470 White women, 246 minority men, 220 minority women) and 2641 patients without medically treated DM (561 minority, 1090 women). Mean age (years) ranged from 61 in minority men to 65 in White women. Diabetic patients had a higher prevalence of atherosclerotic risk factors and comorbidities. Diabetic minority women (DMW; 70% Black, 27% Hispanic) had similar atherosclerotic risk factors to other diabetics, but experienced higher 1-year MACE (14.4% vs 7.5%, P <.01) and MI (4.3% vs 1.6%, P <.01) rates compared with patients without medically treated DM. No other diabetic cohort (White men, White women, minority men) showed an increased risk of MACE vs patients without medically treated DM. The incremental risk of MACE in DMW was associated with insulin use and persisted after risk adjustment (adjusted odds ratio 1.6 vs patients without medically treated DM; 95% CI, 1.0-2.5). Independent predictors of 1-year MACE included insulin use, hyperlipidemia, renal disease, and prior MI. Conclusions: DMW face the highest risk of ischemic events following coronary stenting, driven, in part, by insulin use. Aggressive secondary prevention and strict glycemic control are imperative in this cohort, and further research is warranted to elucidate the biologic mechanisms underpinning these observations. Clinical Trial Registration: NCT02240810 (http://clinicaltrials.gov/).

Structure of the PAPP-ABP5 complex reveals mechanism of substrate recognition.

Insulin-like growth factor (IGF) signaling is highly conserved and tightly regulated by proteases including Pregnancy-Associated Plasma Protein A (PAPP-A). PAPP-A and its paralog PAPP-A2 are metalloproteases that mediate IGF bioavailability through cleavage of IGF binding proteins (IGFBPs). Here, we present single-particle cryo-EM structures of the catalytically inactive mutant PAPP-A (E483A) in complex with a peptide from its substrate IGFBP5 (PAPP-ABP5) and also in its substrate-free form, by leveraging the power of AlphaFold to generate a high quality predicted model as a starting template. We show that PAPP-A is a flexible trans-dimer that binds IGFBP5 via a 25-amino acid anchor peptide which extends into the metalloprotease active site. This unique IGFBP5 anchor peptide that mediates the specific PAPP-A-IGFBP5 interaction is not found in other PAPP-A substrates. Additionally, we illustrate the critical role of the PAPP-A central domain as it mediates both IGFBP5 recognition and trans-dimerization. We further demonstrate that PAPP-A trans-dimer formation and distal inter-domain interactions are both required for efficient proteolysis of IGFBP4, but dispensable for IGFBP5 cleavage. Together the structural and biochemical studies reveal the mechanism of PAPP-A substrate binding and selectivity.

Triple-threat quantitative multiplexed plasma proteomics analysis on immune complex disease MRL-lpr mice.

Systemic lupus erythematosus is a common autoimmune inflammatory disease which is associated with increases in autoantibodies and immune complexes that deposit in the kidney. The MRL-lpr mouse is a common mouse model used for the study of lupus and immune complex glomerulonephritis but very little is known about the plasma proteome changes in this model. We performed in-depth quantitative proteome profiling on MRL-lpr and control (strain MpJ) mice to investigate the changes in the proteome, immunoglobulins and their glycoproteome as well as protein and immune complexes. Methodologies used included immunohistochemistry, immunoglobulin isotyping, multiplexed proteome profiling, immunoglobulin immunoprecipitation with glycoproteome profiling, and size exclusion chromatography (SEC) profiling to enable a comprehensive proteome profiling of proteins and protein complexes. We also used a novel native multiplexed plasma proteome profiling (NativeMP3) method that relies on native enrichment of plasma proteins enabling ultra-deep single shot profiling where we identified 922 plasma proteins at 1% false discovery rate (FDR) in a single shot mass spectrometry run. We observed many large plasma protein differences between the MRL-lpr and control strain including differences in the immunoglobulins, immunoglobulins against specific antigens, chemokines, and proteases as well as changes in protein complexes such as the immunoproteasome.

Impact of left ventricular outflow tract calcium on valve geometry in self-expanding transcatheter aortic-valve replacement.

OBJECTIVES: Evaluate transcatheter heart valve (THV) geometry according to left ventricular outflow tract (LVOT) calcium degree and its impact on hemodynamics and outcomes in patients undergoing transcatheter aortic valve replacement (TAVR) with a contemporary self-expanding THV. BACKGROUND: LVOT calcium remains challenging for contemporary THVs. LVOT calcium location and degree may affect THV deployment and impact flow patterns and shear stress, accelerating THV degeneration. METHODS: EPROMPT (CoreValve Evolut Pro Prospective Registry; NCT03423459) is a prospective, investigator-initiated, multicenter registry of patients undergoing TAVR using CoreValve Evolut PRO/PRO + THVs. A total of 107 patients were enrolled in EPROMPT's computed tomography (CT) cohort between January 2018 and October 2021. These patients underwent follow-up CT scan 30 days post-TAVR. We analyzed THV geometry and its interaction with the aortic root following deployment using 30-day post-TAVR CT in patients with none/mild versus moderate/severe LVOT calcium. RESULTS: Thirty-day THV inflows were less eccentric in the short axis in patients with none/mild versus moderate/severe LVOT calcium (1.16 ± 0.09 vs. 1.21 ± 0.12; p = 0.007). THV became more circular and was similar between both cohorts at the THV waist (1.08 ± 0.06 vs. 1.09 ± 0.11; p = 0.551), leaflet tips (1.03 ± 0.04 vs. 1.05 ± 0.09; p = 0.299), and THV outflow (1.04 ± 2.2 vs. 1.03 ± 2.7; p = 0.143). Thirty-day > mild paravalvular leak was low in both cohorts (1.5% vs. 2.4%; p = 0.724); mean gradients were similar (7.7 ± 3.6 vs. 7.7 ± 3.4 mmHg; p = 0.955). CONCLUSIONS: Despite inflow deformities observed in patients with moderate/severe LVOT calcium, Evolut PRO/PRO + conforms to elliptical aortic annuli, maintaining circularity and proper function at the leaflets and outflow, even in patients with moderate/severe LVOT calcium.

Lifetime management of patients with symptomatic severe aortic stenosis: a computed tomography simulation study.

BACKGROUND: Given enough time, transcatheter heart valves (THVs) will degenerate and may require reintervention. Redo transcatheter aortic valve implantation (TAVI) is an attractive strategy but carries a risk of coronary obstruction. AIMS: We sought to predict how many TAVIs patients could undergo in their lifetime using computed tomography (CT) simulation. METHODS: We analysed paired CT scans (baseline and 30 days post-TAVI) from patients in the LRT trial and EPROMPT registry. We implanted virtual THVs on baseline CTs, comparing predicted valve-to-coronary (VTC) distances to 30-day CT VTC distances to evaluate the accuracy of CT simulation. We then simulated implantation of a second virtual THV within the first to estimate the risk of coronary obstruction due to sinus sequestration and the need for leaflet modification. RESULTS: We included 213 patients with evaluable paired CTs. There was good agreement between virtual (baseline) and actual (30 days) CT measurements. CT simulation of TAVI followed by redo TAVI predicted low coronary obstruction risk in 25.4% of patients and high risk, likely necessitating leaflet modification, in 27.7%, regardless of THV type. The remaining 46.9% could undergo redo TAVI so long as the first THV was balloon-expandable but would likely require leaflet modification if the first THV was self-expanding. CONCLUSIONS: Using cardiac CT simulation, it is possible to predict whether a patient can undergo multiple TAVI procedures in their lifetime. Those who cannot may prefer to undergo surgery first. CT simulation could provide a personalised lifetime management strategy for younger patients with symptomatic severe aortic stenosis and inform decision-making. CLINICALTRIALS: gov: NCT02628899; ClinicalTrials.gov: NCT03557242; ClinicalTrials.gov: NCT03423459.

Impact of Left Ventricular Outflow Tract Calcium on Hemodynamics and Outcomes in Patients After Transcatheter Aortic Valve Implantation With a Contemporary Self-Expanding Valve.

Left ventricular outflow tract (LVOT) calcium remains a challenge for transcatheter aortic valve implantation (TAVI) and is associated with an increased risk of debris embolization, permanent pacemaker requirement, and annular rupture. We report the results of the (EPROMPT) CoreValve Evolut PRO Prospective Registry, which sought to evaluate the real-world performance of the CoreValve Evolut PRO transcatheter heart valve (THV) according to computed tomography-defined extent of LVOT calcium. The prospective, investigator-initiated, multicenter registry includes patients who underwent TAVI using the CoreValve Evolut PRO/PRO+ THV system. Analyzed patients were dichotomized on the basis of the severity of their LVOT calcium at baseline (none/mild vs moderate/severe). Patients were followed with 30-day clinical assessment and echocardiography. Of the 277 patients included, 177 had computed tomography-defined none/mild LVOT calcium (63.9%), and 100 had moderate/severe LVOT calcium (36.1%). Device success was similar in both cohorts (97.7% vs 95.0%; p = 0.217). Stroke rates were numerically higher in the moderate/severe LVOT calcium cohort (in-hospital and 30 day: 1.7% vs 4.0%; p = 0.240). Patients with none/mild LVOT calcium had higher rates of permanent pacemaker implantation (in-hospital: 21.5% vs 9.0%; p = 0.008 and 30-day: 22.0% vs 12.0%; p = 0.027). At 30 days, there were numerically higher rates of >mild paravalvular leak in patients with moderate/severe LVOT calcium (1.7% vs 4.0%; p = 0.240). Thirty-day mean gradients were similar (7.5 vs 7.6 mm Hg; p = 0.782). In conclusion, patients in the EPROMPT registry receiving the contemporary self-expanding CoreValve Evolut PRO/PRO+ THV demonstrated similar short-term outcomes and hemodynamics across the entire spectrum of LVOT calcium.