Gerry A. F. Nicolaes

Cation–π interactions are widely considered key contributors to protein structure and molecular recognition, with quantum chemical studies often predicting substantial stabilization energies. However, their actual prevalence and strength in protein environments remain debated. Here, we combine high‐level quantum chemical calculations with large‐scale statistical analyses of high‐resolution protein structures to reassess the role of lysine–π interactions. While gas‐phase calculations confirm strong cation–π binding for idealized geometries, with corresponding energies of −19.0 kcal·mol ⁻¹ and −16.0 kcal·mol ⁻¹ for Lys‐Phe and Arg‐Phe pairs respectively, we demonstrate that even small geometric distortions and the inclusion of dielectric screening significantly reduce interaction energies to respective values of −5.9 kcal·mol ⁻¹ and −6.5 kcal·mol ⁻¹ at a dielectric constant of 6 and to −3.7 kcal·mol ⁻¹ and −4.7 kcal·mol ⁻¹ at a dielectric constant of 78. By leveraging the current size of the Protein Data Bank, we analyzed a much larger set of high‐resolution protein structures than previously feasible, enabling a more rigorous evaluation of the structural prevalence of lysine–π interactions. Our statistical analysis reveals a low occurrence of geometries consistent with optimal cation–π interactions. By bridging quantum chemical results with structural data, this work reconciles the discrepancy between strong intrinsic interaction energies and their limited manifestation in proteins. These findings highlight the importance of geometric and environmental effects and suggest that Lys–π interactions in proteins are context‐dependent and likely contribute less to protein structure than previously assumed.

Inflammation-driven injury, a significant source of morbidity and mortality worldwide, is largely mediated by the cytotoxic activities of neutrophils, which extend the initial lesion and jeopardize organ function. Intriguingly, inflammatory injury naturally declines at specific times of day, suggesting that circadian mechanisms exist that mitigate the destructive activity of neutrophils and protect the host. Here, we show that the periods of diurnal protection coincide with peaks in plasma CXCL12, a chemokine that inhibits the neutrophil-intrinsic circadian clock by signaling through CXCR4. Genetic deletion of this clock, or a hyperactive form of CXCR4, prevented the diurnal spikes of injury, and treatment with a synthetic CXCR4 agonist conferred protection from myocardial and vascular injury. In tissues, this protection was mediated by repositioning neutrophils in the wound core, which spared neighboring host cells from apoptotic death. Thus, a circadian neutrophil checkpoint protects from exuberant inflammation and can be activated to protect the host.

Immune-mediated thrombotic thrombocytopenic purpura (iTTP) is a rare life-threatening thrombotic disorder, which results from the development of autoantibodies targeting ADAMTS13. Most patients (>90%) with iTTP display antibodies against a shared epitope in the spacer domain of ADAMTS13. Nevertheless, a smaller population of patients (20%-40%) also has antibodies directed toward the CUB (complement C1r/C1s, Uegf, Bmp1) domains of ADAMTS13. Here, we explored whether anti-CUB antibodies have a shared epitope located on CUB domains of ADAMTS13 that overlaps with the spacer-CUB domain interface. Hydrogen-deuterium exchange mass spectrometry revealed that a panel of patient-derived human monoclonal anti–CUB domain antibodies specifically targeted peptides 1248-1253 and 1359-1377 in the CUB1 and CUB2 domains, respectively. A parallel alanine screen showed that residues W1250, K1252, and R1367 are crucially involved in binding of anti–CUB domain antibodies. A triple alanine variant containing W1250A/K1252A/R1367A ameliorated the binding of all patient-derived monoclonal antibodies. This triple-alanine variant also showed greatly reduced binding of anti-CUB antibodies upon analysis of plasma samples of a panel of 27 patients with iTTP. Functional analysis of the anti-CUB antibodies showed that all antibodies were able to induce an open conformation but did not inhibit activity toward either peptide substrates or von Willebrand factor multimers under flow conditions. Collectively, our findings show that anti-CUB antibodies target residues W1250/K1252 and R1367. Binding of pathogenic antibodies disrupt the spacer-CUB domain interface, thereby inducing an open conformation in ADAMTS13.

Purpose of review: Thromboembolic complications are a major contributor to global mortality. The relationship between inflammation and coagulation pathways has become an emerging research topic where the role of the innate immune response, and specifically neutrophils in “immunothrombosis” are receiving much attention. This review aims to dissect the intricate interplay between histones (from neutrophils or cellular damage) and the haemostatic pathway, and to explore mechanisms that may counteract the potentially procoagulant effects of those histones that have escaped their nuclear localization. Recent findings: Extracellular histones exert procoagulant effects via endothelial damage, platelet activation, and direct interaction with coagulation proteins. Neutralization of histone activities can be achieved by complexation with physiological molecules, through pharmacological compounds, or via proteolytic degradation. Details of neutralization of extracellular histones are still being studied. Summary: Leveraging the understanding of extracellular histone neutralization will pave the way for development of novel pharmacological interventions to treat and prevent complications, including thromboembolism, in patients in whom extracellular histones contribute to their overall clinical status.

Extracellular histones have been shown to act as DAMPs in a variety of inflammatory diseases. Moreover, they have the ability to induce cell death. In this study, we show that M6229, a low-anticoagulant fraction of unfractionated heparin (UFH), rescues rats that were challenged by continuous infusion of calf thymus histones at a rate of 25 mg histones/kg/h. Histone infusion by itself induced hepatic and homeostatic dysfunction characterized by elevated activity of hepatic enzymes (ASAT and ALAT) and serum lactate levels as well as by a renal dysfunction, which contributed to the significantly increased mortality rate. M6229 was able to restore normal levels of both hepatic and renal parameters at 3 and 9 mg M6229/kg/h and prevented mortality of the animals. We conclude that M6229 is a promising therapeutic agent to treat histone-mediated disease.

Extracellular histones are cytotoxic molecules involved in experimental acute kidney injury. In patients receiving a renal transplant from donors after circulatory death, who suffer from additional warm ischemia, worse graft outcome is associated with higher machine perfusate extracellular histone H3 concentrations. We now investigated temperature-dependent extracellular histone release in an ex vivo porcine renal perfusion model, and subsequently studied histone release in the absence and presence of non-anticoagulant heparin. Seven pairs of ischemically damaged porcine kidneys were machine perfused at 4°C (cold ischemia) or 28°C (warm ischemia). Perfusate histone H3 concentration was higher after warm as compared to cold ischemia (median (IQR) = 0.48 (0.20–0.83) μg/mL vs. 0.02 (0.00–0.06) μg/mL; p = .045, respectively). Employing immune-electron microscopy (EM), histone containing cytoplasmic protrusions of tubular and endothelial cells were found after warm ischemic injury. Furthermore, abundant histone localization was detected in debris surrounding severely damaged glomerular cells, in a “buck shot” pattern. In vitro, histones were cytotoxic to endothelial and kidney epithelial cells in a temperature-dependent manner. In a separate ex vivo experiment, addition of heparin did not change the total histone H3 levels observed in the perfusate but revealed a continuous increase in the level of a lower molecular weight histone H3 variant. Our findings show that ischemically damaged kidneys release more extracellular histones in warm ischemia, which by EM was due to histone release by renal cells. Blocking of histone-mediated damage during transplantation may be beneficial in prevention of renal injury.

Vascular calcification (VC) is an important contributor and prognostic factor in the pathogenesis of cardiovascular diseases. VC is an active process mediated by the release of extracellular vesicles by vascular smooth muscle cells (VSMCs), and the enzyme neutral sphingomyelinase 2 (nSMase2 or SMPD3) plays a key role. Upon activation, the enzyme catalyzes the hydrolysis of sphingomyelin, thereby generating ceramide and phosphocholine. This conversion mediates the release of exosomes, a type of extracellular vesicles (EVs), which ultimately forms the nidus for VC. nSMase2 therefore represents a drug target, the inhibition of which is thought to prevent or halt VC progression. In search of novel druglike small molecule inhibitors of nSMase2, we have used virtual ligand screening to identify potential ligands. From an in-silico collection of 48,6844 small druglike molecules, we selected 996 compounds after application of an in-house multi-step procedure combining different filtering and docking procedures. Selected compounds were functionally tested in vitro; from this, we identified 52 individual hit molecules that inhibited nSMase2 activity by more than 20% at a concentration of 150 µM. Further analysis showed that five compounds presented with IC₅₀s lower than 2 µM. Of these, compounds ID 5728450 and ID 4011505 decreased human primary VSMC EV release and calcification in vitro. The hit molecules identified here represent new classes of nSMase2 inhibitors that may be developed into lead molecules for the therapeutic or prophylactic treatment of VC.