Prediction of Molecular Interaction between Platelet Glycoprotein Ibα and von Willebrand Factor using Molecular Dynamics Simulations

Investigation of von Willebrand factor multimer abnormalities before and after aortic valve replacement using the Hydragel-5 assay

BACKGROUND

Severe aortic stenosis (sAS) is associated with acquired von Willebrand syndrome (AVWS) by loss of high-molecular-weight multimers (HMWM) of von Willebrand factor (VWF), potentially resulting in perioperative bleeding. Analysis of VWF multimers remains challenging. Recently, the new, rapid Hydragel 5 assay has been developed, using electrophoretic protein separation for dividing VWF-multimers into low (LMWM), intermediate (IMWM), and HMWM, the hemostatically active part of VWF. Here, we evaluated its impact on predicting blood loss in presence of AVWS after surgical aortic valve replacement (SAVR).

METHODS

We prospectively examined 52 patients (age: 68 ± 7 years; 54 % male) admitted to SAVR. They were divided in two groups (A: normal VWF, n = 28; B: abnormal VWF, n = 24, defined as VWF-activity/antigen (VWF:Ac/Ag)-ratio < 0.7 and/or HMWM loss). Blood samples and echocardiographic data were collected before, seven days and three months after SAVR. Blood loss and transfusions were recorded.

RESULTS

Baseline characteristics and clinical data were similar in both groups. HMWM loss was present in 38.5 % of all patients. HMWM, the VWF:Ac/Ag- and HMWM/(IMWM+LMWM)-ratios were significantly decreased preoperatively in group B but normalized after SAVR. Bleeding, re-thoracotomy and transfusion rates were comparable. HMWM loss was inversely correlated with the peak aortic gradient (Pmax) and positively with the aortic valve area (AVA), while HMWM/(IMWM+LMWM)-ratio negatively correlated with the mean aortic gradient (Pmean).

CONCLUSION

HMWM and HMWM/(IMWM+LMWM)-ratio inversely correlate with severity of AS and normalize after SAVR. The Hydragel-5 assay's might be valuable for routine diagnostics to assess bleeding risk and postoperative normalization of AS and VWF abnormalities in SAVR patients.

Platelet Biorheology and Mechanobiology in Thrombosis and Hemostasis: Perspectives from Multiscale Computation

Thrombosis is the pathological clot formation under abnormal hemodynamic conditions, which can result in vascular obstruction, causing ischemic strokes and myocardial infarction. Thrombus growth under moderate to low shear (<1000 s-1) relies on platelet activation and coagulation. Thrombosis at elevated high shear rates (>10,000 s-1) is predominantly driven by unactivated platelet binding and aggregating mediated by von Willebrand factor (VWF), while platelet activation and coagulation are secondary in supporting and reinforcing the thrombus. Given the molecular and cellular level information it can access, multiscale computational modeling informed by biology can provide new pathophysiological mechanisms that are otherwise not accessible experimentally, holding promise for novel first-principle-based therapeutics. In this review, we summarize the key aspects of platelet biorheology and mechanobiology, focusing on the molecular and cellular scale events and how they build up to thrombosis through platelet adhesion and aggregation in the presence or absence of platelet activation. In particular, we highlight recent advancements in multiscale modeling of platelet biorheology and mechanobiology and how they can lead to the better prediction and quantification of thrombus formation, exemplifying the exciting paradigm of digital medicine.

Development of the Integrated Computer Simulation Model of the Intracellular, Transmembrane, and Extracellular Domain of Platelet Integrin α IIb β 3 (Platelet Membrane Glycoprotein: GPIIb-IIIa)

Background  The structure and functions of the extracellular domain of platelet integrin α IIb β 3 (platelet membrane glycoprotein: GPIIb-IIIa) change substantially upon platelet activation. However, the stability of the integrated model of extracellular/transmembrane/intracellular domains of integrin α IIb β 3 with the inactive state of the extracellular domain has not been clarified. Methods  The integrated model of integrin α IIb β 3 was developed by combining the extracellular domain adopted from the crystal structure and the transmembrane and intracellular domain obtained by Nuclear Magnetic Resonace (NMR). The transmembrane domain was settled into the phosphatidylcholine (2-oleoyl-1-palmitoyl-sn-glycerol-3-phosphocholine (POPC)) lipid bilayer model. The position coordinates and velocity vectors of all atoms and water molecules around them were calculated by molecular dynamic (MD) simulation with the use of Chemistry at Harvard Macromolecular Mechanics force field in every 2 × 10 -15 seconds. Results  The root-mean-square deviations (RMSDs) of atoms constructing the integrated α IIb β 3 model apparently stabilized at approximately 23 Å after 200 ns of calculation. However, minor fluctuation persisted during the entire calculation period of 650 ns. The RMSDs of both α IIb and β 3 showed similar trends before 200 ns. The RMSD of β 3 apparently stabilized approximately at 15 Å at 400 ns with persisting minor fluctuation afterward, while the structural fluctuation in α IIb persisted throughout the 650 ns calculation period. Conclusion  In conclusion, the integrated model of the intracellular, transmembrane, and extracellular domain of integrin α IIb β 3 suggested persisting fluctuation even after convergence of MD calculation.

Physical Characteristics of von Willebrand Factor Binding with Platelet Glycoprotein Ibɑ Mutants at Residue 233 Causing Various Biological Functions

Glycoprotein (GP: HIS ¹ -PRO ²⁶⁵ ) Ibɑ is a receptor protein expressed on the surface of the platelet. Its N-terminus domain binds with the A1 domain (ASP ¹²⁶⁹ -PRO ¹⁴⁷² ) of its ligand protein von Willebrand factor (VWF) and plays a unique role in platelet adhesion under blood flow conditions. Single amino acid substitutions at residue 233 from glycine (G) to alanine (A), aspartic acid (D), or valine (V) are known to cause biochemically distinct functional alterations known as equal, loss, and gain of function, respectively. However, the underlying physical characteristics of VWF binding with GPIbɑ in wild-type and the three mutants exerting different biological functions are unclear. Here, we aimed to test the hypothesis: biological characteristics of macromolecules are influenced by small changes in physical parameters. The position coordinates and velocity vectors of all atoms and water molecules constructing the wild-type and the three mutants of GPIbɑ (G233A, G233D, and G233V) bound with VWF were calculated every 2 × 10 ^-15 seconds using the CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field for 9 × 10 ^-10 seconds. Six salt bridges were detected for longer than 50% of the calculation period for the wild-type model generating noncovalent binding energy of -1096 ± 137.6 kcal/mol. In contrast, only four pairs of salt bridges were observed in G233D mutant with noncovalent binding energy of -865 ± 139 kcal/mol. For G233A and G233V, there were six and five pairs of salt bridges generating -929.8 ± 88.5 and -989.9 ± 94.0 kcal/mol of noncovalent binding energy, respectively. Our molecular dynamic simulation showing a lower probability of salt bridge formation with less noncovalent binding energy in VWF binding with the biologically loss of function G233D mutant of GPIbɑ as compared with wild-type, equal function, and gain of function mutant suggests that biological functions of macromolecules such as GPIbɑ are influenced by their small changes in physical characteristics.

Targeting shear gradient activated von Willebrand factor by the novel single-chain antibody A1 reduces occlusive thrombus formation in vitro

Intraluminal thrombus formation precipitates conditions such as acute myocardial infarction and disturbs local blood flow resulting in areas of rapidly changing blood flow velocities and steep gradients of blood shear rate. Shear rate gradients are known to be pro-thrombotic with an important role for the shear-sensitive plasma protein von Willebrand factor (VWF). Here, we developed a single-chain antibody (scFv) that targets a shear gradient specific conformation of VWF to specifically inhibit platelet adhesion at sites of SRGs but not in areas of constant shear. Microfluidic flow channels with stenotic segments were used to create shear rate gradients during blood perfusion. VWF-GPIbα interactions were increased at sites of shear rate gradients compared to constant shear rate of matched magnitude. The scFv-A1 specifically reduced VWF-GPIbα binding and thrombus formation at sites of SRGs but did not block platelet deposition and aggregation under constant shear rate in upstream sections of the channels. Significantly, the scFv A1 attenuated platelet aggregation only in the later stages of thrombus formation. In the absence of shear, direct binding of scFv-A1 to VWF could not be detected and scFV-A1 did not inhibit ristocetin induced platelet agglutination. We have exploited the pro-aggregatory effects of SRGs on VWF dependent platelet aggregation and developed the shear-gradient sensitive scFv-A1 antibody that inhibits platelet aggregation exclusively at sites of shear rate gradients. The lack of VWF inhibition in non-stenosed vessel segments places scFV-A1 in an entirely new class of anti-platelet therapy for selective blockade of pathological thrombus formation while maintaining normal haemostasis.

The Future Role of High-Performance Computing in Cardiovascular Medicine and Science -Impact of Multi-Dimensional Data Analysis

Advances in High-performance computing (HPC) technology have reached the capacity to inform cardiovascular (CV) science in the realm of both inductive and constructive approaches. Clinical trials allow for the comparison of the effect of an intervention without the need to understand the mechanism. This is a typical example of an inductive approach. In the HPC field, training an artificial intelligence (AI) model, constructed by neural networks, to predict future CV events with the use of large scale multi-dimensional datasets is the counterpart that may rely on as well as inform understanding of mechanistic underpinnings for optimization. However, in contrast to clinical trials, AI can calculate event risk at the individual level and has the potential to inform and refine the application of personalized medicine.

Despite this clear strength, results from AI analyses may identify otherwise unidentified/unexpected (i.e. non-intuitive) relationships between multi-dimensional data and clinical outcomes that may further unravel potential mechanistic pathways and identify potential therapeutic targets, therebycontributing to the parsing of observational associations from causal links. The constructive approach will remain critical to overcome limitations of existing knowledge and anchored biases to actualize a more sophisticated understanding of the complex pathobiology of CV diseases.

HPC technology has the potential to underpin this constructive approach in CV basic and clinical science. In general, even complex biological phenomena can be reduced to combinations of simple biological/chemical/physical laws. In the deductive approach, the focus/intent is to explain complex CV diseases by combinations of simple principles.

A multiscale model for multiple platelet aggregation in shear flow

We developed a multiscale model for simulating aggregation of multiple, free-flowing platelets in low-intermediate shear viscous flow, in which aggregation is mediated by the interaction of αIIbβ3 receptors on the platelet membrane and fibrinogen (Fg). This multiscale model uses coarse grained molecular dynamics (CGMD) for platelets at the microscales and dissipative particle dynamics (DPD) for the shear flow at the macroscales, employing our hybrid aggregation force field for modeling molecular level receptor ligand bonds. We define an aggregation tensor and use it to quantify the molecular level contact characteristics between platelets in an aggregate. We perform numerical studies under different flow conditions for platelet doublets and triplets and evaluate the contact area, detaching force and minimum distance between different pairs of platelets in an aggregate. We also present the dynamics of applied stress and velocity magnitude distributions on the platelet membrane during aggregation and quantify the increase in stress in the contact region under different flow conditions. Integrating the knowledge from our previously validated models, together with new aggregation scenarios, our model can dynamically quantify aggregation characteristics and map stress and velocity distribution on the platelet membrane which are difficult to measure in vitro, thus providing an insight into mechanotransduction bond formation response of platelets to flow-induced shear stresses. This modeling framework, together with the tensor method for quantifying inter-platelet contact, can be extended to simulate and analyze larger aggregates and their adhesive properties.

Platelet-type von Willebrand disease: Local disorder of the platelet GPIbα β-switch drives high-affinity binding to von Willebrand factor

BACKGROUND

Mutations in the β-switch of GPIbα cause gain-of-function in the platelet-type von Willebrand disease. Structures of free and A1-bound GPIbα suggest that the β-switch undergoes a conformational change from a coil to a β-hairpin.

OBJECTIVES

Platelet-type von Willebrand disease (VWD) mutations have been proposed to stabilize the β-switch by shifting the equilibrium in favor of the β-hairpin, a hypothesis predicated on the assumption that the complex crystal structure between A1 and GPIbα is the high-affinity state.

METHODS

Hydrogen-deuterium exchange mass spectrometry is employed to test this hypothesis using G233V, M239V, G233V/M239V, W230L, and D235Y disease variants of GPIbα. If true, the expectation is a decrease in hydrogen-deuterium exchange within the β-switch as a result of newly formed hydrogen bonds between the β-strands of the β-hairpin.

RESULTS

Hydrogen-exchange is enhanced, indicating that the β-switch favors the disordered loop conformation. Hydrogen-exchange is corroborated by differential scanning calorimetry, which confirms that these mutations destabilize GPIbα by allowing the β-switch to dissociate from the leucine-rich-repeat (LRR) domain. The stability of GPIbα and its A1 binding affinity, determined by surface plasmon resonance, are correlated to the extent of hydrogen exchange in the β-switch.

CONCLUSION

These studies demonstrate that GPIbα with a disordered loop is binding-competent and support a mechanism in which local disorder in the β-switch exposes the LRR-domain of GPIbα enabling high-affinity interactions with the A1 domain.

Prediction of binding characteristics between von Willebrand factor and platelet glycoprotein Ibα with various mutations by molecular dynamic simulation

INTRODUCTION

Binding of platelet glycoprotein (GP)Ibα with von-Willebrand factor (VWF) exclusively mediates the initial platelet adhesion to injured vessel wall. To understand the mechanism of biomedical functions, we calculated the dynamic fluctuating three-dimensional (3D) structures and dissociation energy for GPIbα with various single amino-acid substitution at G233, which location is known to cause significant changes in platelet adhesive characteristics.

MATERIAL AND METHODS

Molecular dynamics (MD) simulation was utilized to calculate 3D structures and Potential of Mean Force (PMF) for wild-type VWF bound with wild-type, G233A (equal function), G233V (gain of function), and G233D (loss of function) GPIbα. Simulation was done on water-soluble condition with time-step of 2 × 10^-15 s using NAnoscale Molecular Dynamics (NAMD) with Chemistry at HARvard Molecular Mechanics (CHARMM) force field. Initial structure for each mutant was obtained by inducing single amino-acid substitution to the stable water-soluble binding structure of wild-type.

RESULTS

The most stable structures of wild-type VWF bound to GPIbα in wild-type or any mutant did not differ. However, bond dissociation energy defined as difference of PMF between most stable structure and the structure at 65 Å mass center distances in G233D was 4.32 kcal/mol (19.5%) lower than that of wild-type. Approximately, 2.07 kcal/mol energy was required to dissociate VWF from GPIbα with G233V at mass center distance from 48 to 52 Å, which may explain the apparent "gain of function" in G233V.

CONCLUSION

The mechanism of substantially different biochemical characteristics of GPIbα with mutations in G233 location was predicted from physical movement of atoms constructing these proteins.

A Multiscale Model for Recruitment Aggregation of Platelets by Correlating with In Vitro Results

Introduction

We developed a multiscale model to simulate the dynamics of platelet aggregation by recruitment of unactivated platelets flowing in viscous shear flows by an activated platelet deposited onto a blood vessel wall. This model uses coarse grained molecular dynamics (CGMD) for platelets at the microscale and dissipative particle dynamics (DPD) for the shear flow at the macroscale. Under conditions of relatively low shear, aggregation is mediated by fibrinogen via αIIbβ3 receptors.

Methods

The binding of αIIbβ3 and fibrinogen is modeled by a molecular-level hybrid force field consisting of Morse potential and Hooke law for the nonbonded and bonded interactions, respectively. The force field, parametrized in two different interaction scales, is calculated by correlating with the platelet contact area measured in vitro and the detaching force between αIIbβ3 and fibrinogen.

Results

Using our model, we derived, the relationship between recruitment force and distance between the centers of mass of two platelets, by integrating the molecular-scale inter-platelet interactions during recruitment aggregation in shear flows. Our model indicates that assuming a rigid-platelet model, underestimates the contact area by 89% and the detaching force by 93% as compared to a model that takes into account the platelet deformability leading to a prediction of a significantly lower attachment during recruitment.

Conclusions

The molecular-level predictive capability of our model sheds a light on differences observed between transient and permanent platelet aggregation patterns. The model and simulation framework can be further adapted to simulate initial thrombus formation involving multiple flowing platelets as well as deposition and adhesion onto blood vessels.

Thrombus Formation and Propagation in the Onset of Cardiovascular Events

Ischemic cardiovascular disease is a major cause of morbidity and mortality worldwide and thrombus formation on disrupted atherosclerotic plaques is considered to trigger its onset. Although the activation of platelets and coagulation pathways has been investigated intensively, the mechanisms of thrombus formation on disrupted plaques have not been understood in detail. Platelets are thought to play a central role in the formation of arterial thrombus because of rapid flow conditions; however, thrombus that develops on disrupted plaques consistently includes large amounts of fibrin in addition to aggregated platelets. While, thrombus does not always become large enough to completely occlude the vascular lumen, indicating that the propagation of thrombus is also critical for the onset of cardiovascular events. Various factors, such as vascular wall thrombogenicity, altered blood flow and imbalanced blood hemostasis, modulate thrombus formation and propagation on disrupted plaques. Pathological findings derived from humans and experimental animal models of atherothrombosis have identified important factors that affect thrombus formation and propagation, namely platelets, extrinsic and intrinsic coagulation factors, proinflammatory factors, plaque hypoxia and blood flow alteration. These findings might provide insight into the mechanisms of thrombus formation and propagation on disrupted plaques that lead to the onset of cardiovascular events.

Platelet receptors as therapeutic targets: Past, present and future

Anti-platelet drugs reduce arterial thrombosis after plaque rupture and erosion, prevent stent thrombosis and are used to prevent and treat myocardial infarction and ischaemic stroke. Some of them may also be helpful in treating less frequent diseases such as thrombotic thrombocytopenic purpura. The present concise review aims to cover current and future developments of anti-platelet drugs interfering with the interaction of von Willebrand factor (VWF) with glycoprotein (GP) Ibα, and directed against GPVI, GPIIb/IIIa (integrin αIIbβ3), the thrombin receptor PAR-1, and the ADP receptor P2Y12. The high expectations of having novel antiplatelet drugs which selectively inhibit arterial thrombosis without interfering with normal haemostasis could possibly be met in the near future.

Systems Analysis of Thrombus Formation

The systems analysis of thrombosis seeks to quantitatively predict blood function in a given vascular wall and hemodynamic context. Relevant to both venous and arterial thrombosis, a Blood Systems Biology approach should provide metrics for rate and molecular mechanisms of clot growth, thrombotic risk, pharmacological response, and utility of new therapeutic targets. As a rapidly created multicellular aggregate with a polymerized fibrin matrix, blood clots result from hundreds of unique reactions within and around platelets propagating in space and time under hemodynamic conditions. Coronary artery thrombosis is dominated by atherosclerotic plaque rupture, complex pulsatile flows through stenotic regions producing high wall shear stresses, and plaque-derived tissue factor driving thrombin production. In contrast, venous thrombosis is dominated by stasis or depressed flows, endothelial inflammation, white blood cell-derived tissue factor, and ample red blood cell incorporation. By imaging vessels, patient-specific assessment using computational fluid dynamics provides an estimate of local hemodynamics and fractional flow reserve. High-dimensional ex vivo phenotyping of platelet and coagulation can now power multiscale computer simulations at the subcellular to cellular to whole vessel scale of heart attacks or strokes. In addition, an integrated systems biology approach can rank safety and efficacy metrics of various pharmacological interventions or clinical trial designs.

Rapid Restoration of Thrombus Formation and High-Molecular-Weight von Willebrand Factor Multimers in Patients with Severe Aortic Stenosis After Valve Replacement

AIM

Patients with severe aortic stenosis (AS) may have bleeding episodes due to the loss of high-molecular-weight (HMW) von Willebrand factor multimers (VWFMs). The absence of HMW-VWFMs and bleeding tendency are usually corrected after aortic valve replacement (AVR). To investigate the process of VWFM recovery and symptoms in patients with severe AS, we analyzed changes in VWF antigen (VWF:Ag), ADAMTS13 activity (ADAMTS13:AC), and platelet thrombus formation under high shear stress conditions.

METHODS

Nine patients with severe AS undergoing AVR were analyzed.

RESULTS

Evident deficiency of HMW-VWFMs was observed in six patients before surgery, which was rapidly restored within 8 days after AVR. Median levels of VWF:Ag before surgery, on postoperative days (PODs) 1, 8, 15, and 22, and one year after AVR were 78.1%, 130%, 224%, 155%, 134%, and 142%, respectively. In contrast, ADAMTS13:AC was 50.5%, 35.5%, 25.5%, 25.1%, 30.3%, and 84.6%, respectively. Preoperative thrombus formation but not surface coverage was significantly lower than that on POD 22, which was considered as normal level in each patient. Compared with preoperative levels, thrombus volume was significantly lower on POD 1, but rapidly increased by POD 8.

CONCLUSION

Bleeding tendency and loss of HMW-VWFMs observed in patients with severe AS before surgery was rapidly corrected after AVR. Instead, patients were in a VWF-predominant state between POD 8 and 22.