From Computers to Clinics: Advances in Designing Polyphosphate Inhibitors as Novel Anti-thrombotics

LilyTakeuchiBy Lily Takeuchi, Graduate Student, Kizhakkedathu Lab

Thrombosis, the formation of a potentially deadly blood clot, remains one of the leading causes of death and disability worldwide. Once formed, clots can slow or obstruct normal blood flow, leading to damage to surrounding tissue. In deep vein thrombosis, a blood clot forms in the veins deep inside the body between large muscle groups, most commonly in the leg or pelvis. When a clot in the deep vein breaks free, it can travel through the heart and cause a potentially fatal blockage in arteries to the lung known as a pulmonary embolism. While there are several antithrombotic drugs available on the market, many suffer from undesirable side effects, particularly bleeding. Currently, Dr. Jayachandran Kizhakkedathu’s research group is pursuing a number of avenues towards the development of novel anti-thrombotics without the limitations associated with current medications.

Recently, a new drug target to inhibit thrombosis, with potential for reduced bleeding side effects, has been identified called polyphosphate (polyP).1 Although most cells contain polyP, platelets are an abundant source. These cells play a central role in blood clotting. While the mechanisms by which polyP participates in blood clotting have yet to be fully understood, researchers are investigating the possibility of neutralizing the effects of polyP to prevent thrombosis. Unlike the current anti-thrombotic approaches, this strategy could minimize the bleeding risk, as these agents do not target key coagulation enzymes. However, nonspecific binding of these inhibitors to normal cells has been a hurdle in their clinical utility.

To mitigate these issues, the approach designed by the Kizhakkedathu lab uses positively charged groups known as cationic binding groups (CBGs), bound to a dendritic, or branched, polymer core. These CBGs are attracted to the highly negatively charged polyP, as well as other normal cellular components. To mitigate the issue of binding to normal cells, the design also uses a brush of polyethylene glycol (PEG) chains bound around the polymer core that act as a “shield”, limiting the amount of nonspecific binding to normal cells. In this collaborative study recently published in Biomacromolecules, Mafi et al. use computer simulation to study the binding mechanism and sensitivity of different CBGs to PEG in order to optimize their drug designs.2 While computer simulation has been used increasingly in the field of drug discovery, studying interactions on large molecules has proven challenging due to the fast interactions between molecules that occur on the order of nano- or micro-seconds. Here, the authors use an algorithm called Metadynamics and report that, as predicted, increasing the positive charge density of CBGs had more of an effect on binding to polyP than did increasing the PEG shield length. Further, the authors determined that the PEG-CBGs aggregate first and then make a sandwich with polyP, forming a complex in solution. By simulating these interactions, researchers are able to better understand the mechanisms of polyP inhibition and make predictive design decisions. Finally, in addition to targeting polyP, other negatively charged mediators of thrombosis have also been identified, including cell-free DNA, RNA and neutrophil extracellular traps. The Kizhakkedathu group is currently working towards applying similar design strategies to prevent the onset of thrombosis by these negatively charged mediators.

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  1. Müller, F., Mutch, N.J., Schenk, W.A., Smith, S.A., Esterl, L., Spronk, H.M., Schmidbauer, S., Gahl, W.A., Morrissey, J.H., Renné, T. Platelet Polyphosphates Are Proinflammatory and Procoagulant Mediators In Vivo. Cell Press. 2009 139 (6), 1143 – 1156.
  2. Mafi, A., Abbina, S., Kalathottukaren, M.T., Morrissey, J.H., Haynes,C., Kizhakkedathu, J.N., Pfaendtner, J., Chou, K.C. Design of Polyphosphate Inhibitors: A Molecular Dynamics Investigation on Polyethylene Glycol-Linked Cationic Binding Groups. Biomacromolecules. 2018 19 (4), 1358-1367.