Design of Polyphosphate Inhibitors: A Molecular Dynamics Investigation on Polyethylene Glycol-Linked Cationic Binding Groups

INHIBITORS OF INORGANIC POLYPHOSPHATE AND NUCLEIC ACIDS ATTENUATE IN VITRO THROMBIN GENERATION IN PLASMA FROM TRAUMA PATIENTS

ABSTRACT

Background: Inorganic polyphosphate (polyP) is a procoagulant polyanion. We assessed the impact of polyP inhibition on thrombin generation after trauma using the novel polyP antagonists, macromolecular polyanion inhibitor 8 (MPI 8), and universal heparin reversal agent 8 (UHRA-8). Methods: Plasma thrombin generation (calibrated automated thrombogram, CAT), in 56 trauma patients and 39 controls +/- MPI 8 and UHRA-8 (50 μg/mL), was expressed as lag time (LT, minutes), peak height (PH, nM), and time to peak (ttPeak, minutes), with change in LT (ΔLT) and change in ttPeak (ΔttPeak) quantified. Results expressed in median and quartiles [Q1, Q3], Wilcoxon matched-pairs testing, P < 0.05 significant. Results: Trauma patients had greater baseline PH than controls (182.9 [121.0, 255.2]; 120.5 [62.1, 174.8], P < 0.001). MPI 8 treatment prolonged LT and ttPeak in trauma (7.20 [5.88, 8.75]; 6.46 [5.45, 8.93], P = 0.020; 11.28 [8.96, 13.14]; 11.00 [8.95, 12.94], P = 0.029) and controls (7.67 [6.67, 10.50]; 6.33 [5.33, 8.00], P < 0.001; 13.33 [11.67, 15.33]; 11.67 [10.33, 13.33], P < 0.001). UHRA-8 treatment prolonged LT and ttPeak and decreased PH in trauma (9.09 [7.45, 11.33]; 6.46 [5.45, 8.93]; 14.02 [11.78, 17.08]; 11.00 [8.95, 12.94]; 117.4 [74.5, 178.6]; 182.9 [121.0, 255.2]) and controls (9.83 [8.00, 12.33]; 6.33 [5.33, 8.00]; 16.67 [14.33, 20.00]; 11.67 [10.33, 13.33]; 55.3 [30.2, 95.9]; 120.5 [62.1, 174.8]), all P < 0.001. Inhibitor effects were greater for controls (greater ΔLT and ΔttPeak for both inhibitors, P < 0.001). Conclusion: PolyP inhibition attenuates thrombin generation, though to a lesser degree in trauma than in controls, suggesting that polyP contributes to accelerated thrombin generation after trauma.

Plasma Gel Made of Platelet-Poor Plasma: In Vitro Verification as a Carrier of Polyphosphate

Plasma gel (PG) is a blood-derived biomaterial that can be prepared by heating or chemical cross-linking without the aid of intrinsic coagulation activity and has gradually been applied in the field of esthetic surgery. To explore the applicability of PG in regenerative therapy or tissue engineering, in this study, we focused on the advantages of the heating method and verified the retention capacity of the resulting PG for polyphosphate (polyP), a polyanion that contributes to hemostasis and bone regeneration. Pooled platelet-poor plasma (PPP) was prepared from four healthy male adult donors, mixed with synthetic polyP, and heated at 75 °C for 10 or 30 min to prepare PG in microtubes. The PG was incubated in PBS at 37 °C, and polyP levels in the extra-matrix PBS were determined by the fluorometric method every 24 h. The microstructure of PG was examined using scanning electron microscopy. In the small PG matrices, almost all of the added polyP (~100%) was released within the initial 24 h. In contrast, in the large PG matrices, approximately 50% of the polyP was released within the initial 24 h and thereafter gradually released over time. Owing to its simple chemical structure, linear polyP cannot be theoretically retained in the gel matrices used in this study. However, these findings suggest that thermally prepared PG matrices can be applied as carriers of polyP in tissue engineering and regenerative medicine.

Polyphosphate as an antithrombotic target and hemostatic agent

Polyphosphate (PolyP) is a polymer comprised of linear phosphate units connected by phosphate anhydride bonds. PolyP exists in a diverse range of eukaryotes and prokaryotes with varied chain lengths ranging from six to thousands of phosphate units. Upon activation, human platelets and neutrophils release short-chain PolyP, along with other components, to initiate the coagulation pathway. Long-chain PolyP derived from cellular or bacterial organelles exhibits higher proinflammatory and procoagulant effects compared to short-chain PolyP. Notably, PolyP has been identified as a low-hemorrhagic antithrombotic target since neutralizing plasma PolyP suppresses the thrombotic process without impairing the hemostatic functions. As an inorganic polymer without uniform steric configuration, PolyP is typically targeted by cationic polymers or recombinant polyphosphatases rather than conventional antibodies, small-molecule compounds, or peptides. Additionally, because of its procoagulant property, PolyP has been incorporated in wound-dressing materials to facilitate blood hemostasis. This review summarizes current studies on PolyP as a low-hemorrhagic antithrombotic target and the development of hemostatic materials based on PolyP.

Molecular Dynamics Simulations of Rhodamine B Zwitterion Diffusion in Polyelectrolyte Solutions

Polyelectrolytes continue to find wide interest and application in science and engineering, including areas such as water purification, drug delivery, and multilayer thin films. We have been interested in the dynamics of small molecules in a variety of polyelectrolyte (PE) environments; in this paper, we report simulations and analysis of the small dye molecule rhodamine B (RB) in several very simple polyelectrolyte solutions. Translational diffusion of the RB zwitterion has been measured in fully atomistic, 2 μs long molecular dynamics simulations in four different polyelectrolyte solutions. Two solutions contain the common polyanion sodium poly(styrene sulfonate) (PSS), one with a 30-mer chain and the other with 10 trimers. The other two solutions contain the common polycation poly(allyldimethylammonium) chloride (PDDA), one with two 15-mers and the other with 10 trimers. RB diffusion was also simulated in several polymer-free solutions to verify its known experimental value for the translational diffusion coefficient, D_RB, of 4.7 × 10^-6 cm²/s at 300 K. RB diffusion was slowed in all four simulated PE solutions, but to varying degrees. D_RB values of 3.07 × 10^-6 and 3.22 × 10^-6 cm²/s were found in PSS 30-mer and PSS trimer solutions, respectively, whereas PDDA 15-mer and trimer solutions yielded values of 2.19 × 10^-6 and 3.34 × 10^-6 cm²/s. Significant associations between RB and the PEs were analyzed and interpreted via a two-state diffusion model (bound and free diffusion) that describes the data well. Crowder size effects and anomalous diffusion were also analyzed. Finally, RB translation along the polyelectrolytes during association was characterized.

Influence of Steric Shield on Biocompatibility and Antithrombotic Activity of Dendritic Polyphosphate Inhibitor

The polyanion, inorganic polyphosphate (polyP), is a procoagulant molecule which has become a promising therapeutic target in the development of antithrombotics. Neutralizing polyP's prothrombotic activity using polycationic inhibitors is one of the viable strategies to design new polyP inhibitors. However, in this approach, a fine balance between the electrostatic interaction of polyP and the inhibitor is needed. Any unprotected polycations are known to interact with negatively charged blood components, potentially resulting in platelet activation, cellular toxicity, and bleeding. Thus, designing potent polycationic polyP inhibitors with good biocompatibility is a major challenge. Building on our previous research on universal heparin reversal agent (UHRA), we report polyP inhibitors with a modified steric shield design. The molecular weight, number of cationic binding groups, and the length of the polyethylene glycol (PEG) chains were varied to arrive at the desired inhibitor. We studied two different PEG lengths (mPEG-750 versus mPEG-350) on the polyglycerol scaffold and investigated their influence on biocompatibility and polyP neutralization activity. The polyP inhibitor with mPEG-750 brush layer, mPEG₇₅₀ UHRA-10, showed superior biocompatibility compared to its mPEG-350 analogs by a number of measured parameters without losing its neutralization activity. An increase in cationic binding groups (25 groups in mPEG₇₅₀ UHRA-8 and 32 in mPEG₇₅₀ UHRA-10 [HC]) did not alter the neutralization activity, which suggested that the mPEG-750 shield layer provides significant protection of cationic binding groups and thus helps to minimize unwanted nonspecific interactions. Furthermore, these modified polyP inhibitors are highly biocompatible compared to conventional polycations that have been previously used as polyP inhibitors (e.g., PAMAM dendrimers and polyethylenimine). Through this study, we demonstrated the importance of the design of steric shield toward highly biocompatible polyP inhibitors. This approach can be exploited in the design of highly biocompatible macromolecular inhibitors.

The Martini Model in Materials Science

The Martini model, a coarse-grained force field initially developed with biomolecular simulations in mind, has found an increasing number of applications in the field of soft materials science. The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Here, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future developments in this field is given, particularly in light of recent developments such as the new version of the model, Martini 3.

Understanding the Interaction of Polyelectrolyte Architectures with Proteins and Biosystems

The counterions neutralizing the charges on polyelectrolytes such as DNA or heparin may dissociate in water and greatly influence the interaction of such polyelectrolytes with biomolecules, particularly proteins. In this Review we give an overview of studies on the interaction of proteins with polyelectrolytes and how this knowledge can be used for medical applications. Counterion release was identified as the main driving force for the binding of proteins to polyelectrolytes: Patches of positive charge become multivalent counterions of the polyelectrolyte and lead to the release of counterions from the polyelectrolyte and a concomitant increase in entropy. This is shown from investigations on the interaction of proteins with natural and synthetic polyelectrolytes. Special emphasis is paid to sulfated dendritic polyglycerols (dPGS). The Review demonstrates that we are moving to a better understanding of charge-charge interactions in systems of biological relevance. Research along these lines will aid and promote the design of synthetic polyelectrolytes for medical applications.

Inorganic Polyphosphates As Storage for and Generator of Metabolic Energy in the Extracellular Matrix

Inorganic polyphosphates (polyP) consist of linear chains of orthophosphate residues, linked by high-energy phosphoanhydride bonds. They are evolutionarily old biopolymers that are present from bacteria to man. No other molecule concentrates as much (bio)chemically usable energy as polyP. However, the function and metabolism of this long-neglected polymer are scarcely known, especially in higher eukaryotes. In recent years, interest in polyP experienced a renaissance, beginning with the discovery of polyP as phosphate source in bone mineralization. Later, two discoveries placed polyP into the focus of regenerative medicine applications. First, polyP shows morphogenetic activity, i.e., induces cell differentiation via gene induction, and, second, acts as an energy storage and donor in the extracellular space. Studies on acidocalcisomes and mitochondria provided first insights into the enzymatic basis of eukaryotic polyP formation. In addition, a concerted action of alkaline phosphatase and adenylate kinase proved crucial for ADP/ATP generation from polyP. PolyP added extracellularly to mammalian cells resulted in a 3-fold increase of ATP. The importance and mechanism of this phosphotransfer reaction for energy-consuming processes in the extracellular matrix are discussed. This review aims to give a critical overview about the formation and function of this unique polymer that is capable of storing (bio)chemically useful energy.

Molecular Dynamics Simulations on Nucleic Acid Binding Polymers Designed To Arrest Thrombosis

Cancer-associated thrombosis is managed by the administration of anticoagulants and antithrombotic agents that have a high risk of inducing hemorrhagic complications. To develop safer strategies for antithrombotic therapy, in vivo activators of the intrinsic pathway, namely, cell-free nucleic acids (DNA and RNA) have been targeted with cationic, polyamine-based polymers. The cytotoxicity of the highly cationic polymers is a major drawback for their practical use, and biocompatible alternatives are in high demand. In this study, we carried out all-atom molecular dynamics simulations to systematically examine the DNA binding of polyamine-poly(ethylene glycol) (PEG) diblock polymers designed from biocompatible building blocks to inhibit the procoagulant activity of DNA. The differences in cationic charge, PEG chain length, and initial conformations of the polymers resulted in marked differences in their binding to DNA. We found that having an exposed cationic polyamine group is essential to polymer-DNA binding and a certain level of electrostatic interactions is necessary to maintain the bound state. Intrachain associations between the polyamine groups and PEG chains in some cases have led to a collapsed state of the polymer that precludes binding to DNA. This self-association is mainly due to a strong hydrogen bond between polymer polyamine and PEG groups and partly due to a partially charged semibranched polyamine group architecture. As polymer "masking" of DNA is thought to arrest DNA's prothrombotic activity, our findings highlight the desired structural features of the polymers for stronger DNA binding and provide insights into the design of novel antithrombotic agents.