Towards dynamic pharmacophore models through the use of coarse grained molecular dynamic simulations

Computer aided drug design (CADD) plays a crucial role in the drug discovery pipeline e.g. in virtual screening of chemical databases, de novo drug design, and lead optimization. Due to the increased numbers of protein structures elucidated, structure-based methods for developing pharmacophore models have started gaining in popularity and are becoming of particular importance. There have been a number of studies combining such methods with the use of molecular dynamics (MD) simulations to model protein exibility. In this project, the development and application of a new methodology, based on coarse grained (CG) MD, through the use of the MARTINI forcefield, and employed to explore protein ligand interactions, will be presented. An overview of the history of CADD is presented, along with current computational fragment based methods available for exploring protein-ligand interactions. An overview of the theory and methods behind MD simulations both all atom and CG is also provided. In the first results chapter, the parametrization of MARTINI beads as pharmacophoric probes, the analysis protocol and the application of this method to a data set of water soluble targets of pharmacological interest is described. The results suggest that the pharmacophoric probes have the ability to identify protein-ligand interactions on the targets of interest. The probes are also able to identify the residues involved in forming ligand binding interactions, showing a particular accuracy in identifying "hotspot" interactions. In the second results chapter, the extension of the initial data set to a range of GPCRs is described. The results suggest that the pharmacophoric probes have the ability to accurately explore both the orthosteric and allosteric binding sites of the GPCR targets and accurately identify the interactions and residues involved in ligand binding. This is done without the need to embed the protein in a lipid bilayer. In the final results chapter, the application of the dynamic pharmacophoric probes to identifying PIP2 and cholesterol binding sites, on membrane proteins, is presented. The results suggest that the probes can indeed identify these binding sites, along with identifying the residues that are involved in binding the PIP2 head groups. This was also done without embedding the protein in a lipid bilayer, which is the usual practice for identifying lipid binding interactions, reducing the computational resource requirements.</p

Towards dynamic pharmacophore models through the use of coarse grained molecular dynamic simulations

Computer aided drug design (CADD) plays a crucial role in the drug discovery pipeline e.g. in virtual screening of chemical databases, de novo drug design, and lead optimization. Due to the increased numbers of protein structures elucidated, structure-based methods for developing pharmacophore models have started gaining in popularity and are becoming of particular importance. There have been a number of studies combining such methods with the use of molecular dynamics (MD) simulations to model protein exibility. In this project, the development and application of a new methodology, based on coarse grained (CG) MD, through the use of the MARTINI forcefield, and employed to explore protein ligand interactions, will be presented. An overview of the history of CADD is presented, along with current computational fragment based methods available for exploring protein-ligand interactions. An overview of the theory and methods behind MD simulations both all atom and CG is also provided. In the first results chapter, the parametrization of MARTINI beads as pharmacophoric probes, the analysis protocol and the application of this method to a data set of water soluble targets of pharmacological interest is described. The results suggest that the pharmacophoric probes have the ability to identify protein-ligand interactions on the targets of interest. The probes are also able to identify the residues involved in forming ligand binding interactions, showing a particular accuracy in identifying "hotspot" interactions. In the second results chapter, the extension of the initial data set to a range of GPCRs is described. The results suggest that the pharmacophoric probes have the ability to accurately explore both the orthosteric and allosteric binding sites of the GPCR targets and accurately identify the interactions and residues involved in ligand binding. This is done without the need to embed the protein in a lipid bilayer. In the final results chapter, the application of the dynamic pharmacophoric probes to identifying PIP2 and cholesterol binding sites, on membrane proteins, is presented. The results suggest that the probes can indeed identify these binding sites, along with identifying the residues that are involved in binding the PIP2 head groups. This was also done without embedding the protein in a lipid bilayer, which is the usual practice for identifying lipid binding interactions, reducing the computational resource requirements.</p

Mechanical forces control the valency of the malaria adhesin VAR2CSA by exposing cryptic glycan binding sites.

Plasmodium falciparum (Pf) is responsible for the most lethal form of malaria. VAR2CSA is an adhesin protein expressed by this parasite at the membrane of infected erythrocytes for attachment to the placenta, leading to pregnancy-associated malaria. VAR2CSA is a large 355 kDa multidomain protein composed of nine extracellular domains, a transmembrane helix, and an intracellular domain. VAR2CSA binds to Chondroitin Sulphate A (CSA) of the proteoglycan matrix of the placenta. Shear flow, as the one occurring in blood, has been shown to enhance the (VAR2CSA-mediated) adhesion of Pf-infected erythrocytes on the CSA-matrix. However, the underlying molecular mechanism governing this enhancement has remained elusive. Here, we address this question by using equilibrium, force-probe, and docking-based molecular dynamics simulations. We subjected the VAR2CSA protein-CSA sugar complex to a force mimicking the tensile force exerted on this system due to the shear of the flowing blood. We show that upon this force exertion, VAR2CSA undergoes a large opening conformational transition before the CSA sugar chain dissociates from its main binding site. This preferential order of events is caused by the orientation of the molecule during elongation, as well as the strong electrostatic attraction of the sugar to the main protein binding site. Upon opening, two additional cryptic CSA binding sites get exposed and a functional dodecameric CSA molecule can be stably accommodated at these force-exposed positions. Thus, our results suggest that mechanical forces increase the avidity of VAR2CSA by turning it from a monovalent to a multivalent state. We propose this to be the molecular cause of the observed shear-enhanced adherence. Mechanical control of the valency of VAR2CSA is an intriguing hypothesis that can be tested experimentally and which is of relevance for the understanding of the malaria infection and for the development of anti placental-malaria vaccines targeting VAR2CSA