Browsing by Subject "docking"
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Exploring transient pockets in membrane bound pyrophosphatases using molecular dynamics simulations (2022)Malaria is a major cause of human mortality, morbidity, and economic loss. P. falciparum is one of six Plasmodium species that cause malaria and is widespread in sub-Saharan Africa. Many of the currently used drugs for malaria have become less effective, have adverse effects, and are highly expensive, so new ones are needed. mPPases are membrane integral pyrophosphatases that are found in the vacuolar membranes of protozoa but not in humans. These enzymes pump sodium ions and/or protons across the membrane and are crucial for parasite survival and proliferation. This makes them promising targets for new drug development. In this study we aimed to identify and characterize transient pockets in mPPases that could offer suitable ligand binding sites. P. falciparum was chosen because of its therapeutical interest, and T. maritima and V. radiata were chosen because they are test systems in compound discovery. The research was performed using molecular modelling techniques, mainly homology modelling, molecular dynamics, and docking. mPPases from three species were used to make five different systems: P. falciparum (apo closed conformation), T. maritima (apo open, open with ligand, and apo closed) and V. radiata (open with ligand). P. falciparum mPPase does not have a 3D structure available, so a homology model was built using the closest structure available from V. radiata mPPase as a template. Runs of 100 ns molecular dynamics simulations were conducted for these five systems: monomeric mPPase from P. falciparum and dimeric mPPases for the others. Two representative 3D structures for each of the five trajectories, the most dissimilar one to another, were selected for further analysis using clustering. The scrutinized 3D structures were first analyzed to identify possible binding pockets using two independent methods, SiteMap and blind docking (where no pre-determined cavity is set for docking). A second set of experiments using different scores (druggability, enclosure, exposure, …) and targeted docking were then run to characterize all the located pockets. As a result, only half of the catalytic pockets were identified. None of the transient pockets were identified in P. falciparum mPPase and all of them were located within the membrane. Docking was performed using compounds that have shown inhibiting behavior in previous studies but did not give good results in the tested structures. In the end none of the transient pockets were interesting for further study.
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(2019)Cancer is a worldwide health problem; in 2018 9.6 million people died of cancer, meaning that about 1 in 6 deaths was caused by it. The challenge with cancer drug therapy has been the development of cancer drugs that are effective against cancer but are not harmful to the healthy cells. One of the solutions to this has been antibody-drug conjugates (ADCs), where a cytotoxic drug is bound to an antibody. The antibody binds to specific antigen present on the surface of the cancer cell, thus working as a vessel to carry the drug specifically to the cancer cells. Monomethyl auristatin E (MMAE) and monomethyl auristatin F (MMAF) are mitosis preventing cancer drugs. The auristatins are pentapeptides that were developed from dolastatin 10. MMAE consist of monomethyl valine (MeVal), valine (Val), dolaisoleiune (Dil), dolaproine (Dap) and norephedrine (PPA). MMAF has otherwise similar structure, but norephedrine is replaced by phenylalanine (Phe). They prevent cell division and cancer cell proliferation by binding to microtubules and are thus able to kill any kind of cell. By attaching the auristatin to an antibody that targets cancer cells, they can effectively be used in the treatment of cancer. MMAE and MMAF exist as two conformers in solution, namely as cis- and trans-conformers. The trans-conformer resembles the biologically active conformer. It was recently noted that in solution 50-60 % of the MMAE and MMAF-molecules exist in the biologically inactive cis-conformer. The molecule changes from one conformer to the other by the rotation of an amide bond. However, this takes several hours in body temperature. As the amount of the cis-conformer is significant, the efficacy of the drug is decreased, and the possibility of side effects is increased. It is possible that the molecule leaves the cancer cell in its inactive form, migrates to healthy cells and tissue, and transforms to the active form there, damaging the healthy cell. The goal of this study was to modify the structure of the auristatins so that the cis/trans-equilibrium would change to favor the biologically active trans-conformer. The modifications were done virtually, and the relative energies were computed using high-level quantum chemical methods, at density functional theory (DFT), 2nd order perturbation theory (MP2) and coupled cluster levels. Intramolecular interactions were analyzed computationally, employing symmetry-adapted perturbation theory and the non-covalent interactions analysis. The results suggest that simple halogenation of the benzene ring para-position is able to significantly shift the cis/trans-equilibrium to favor the trans-conformer. This is due to changes in intramolecular interactions that favor the trans-conformer after halogenation. For example, the NCI analysis shows that the halogen atom invokes stabilizing intramolecular interactions with the Dil amino acid; there is no such interaction between the para-position hydrogen and Dil in the original molecules. We also performed docking studies that show that the halogenated molecules can bind to microtubules, thus confirming that the modified structures have potential to be developed into new, more efficient and safe cancer drugs. The most promising drug candidates are Cl-MMAF, F-MMAF, and F-MMAE where 94, 90, and 79 % of the molecule is predicted to exist in the biologically active trans-conformer, respectively.
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