An atomistic molecular dynamics simulations approach to the study of H-LDHA inhibition
Creators: name: Vyrkou, Antonia
name: Allison, Simon
name: Cooke, David
name: Philips, Roger
Publisher: name: F1000 Research Limited
Year: 2019

description: It has been known that cancer cells reprogram their metabolism in a way that allows them to produce the energy needed for their functions and growth through the conversion of pyruvate to lactate. This reaction is catalysed by the enzyme h-LDHA (human Lactate Dehydrogenase A) which is therefore considered a promising target in cancer pharmacology. Inhibition of this enzyme can deprive cancer cells from their energy supply with insignificant side effects to normal cells.<br>Ag8 (Ag(NHC)<sub>2</sub>AgBr<sub>2</sub>) is an organometallic complex, with increased stability and reduced toxicity, which could be used as an h-LDHA inhibitor. Its inhibitory function is being currently experimentally studied and is the focus of this atomistic molecular dynamics (MD) study.<br>Molecular dynamics can be proven an invaluable tool in the effort to design and develop novel anticancer pharmaceutical such as h-LDHA inhibitors. Computer simulations, are a relatively fast, inexpensive way to study complex systems under various conditions. Therefore, the results obtained can be an important addition to experimental studies.<br><br>In molecular dynamics, the dynamic evolution of the system is produced by allowing the atoms to interact with one another for a period of time under specific conditions. The atomic positions and energies are then obtained by solving Newton’s equations of motion, and the post processing of these data provides information about the structure, properties and behaviour of the system under study. For this study, all molecular dynamics simulations are performed using the open source software GROMACS 5.1.4.<br><br>In order to perform MD simulations with meaningful results, structural information and a reliable force field, that is a description of all the inter- and intramolecular interactions, are required. For h-LDHA, this process has been quite straightforward as it has been studied before. Therefore, the initial structure chosen was PDB 1i10, obtained from the protein data bank were h-LDHA is in the form of a tetramer. The force field parameters selected for the description of the bonded and non-bonded interactions were those provided by Amber ff99SB. The initial PDB structured contained oxamate, which for our study was replaced by pyruvate, and the results obtained over a simulation time of 30 ns in the NPT ensemble were in good agreement with the bibliography.<br><br>In the case of Ag8, this process is not as easy. First, the initial structure of the molecule had to be described in the form of a PDB file. This was achieved by using the online tool “SMILES Translator and Structure File Generator”. The biggest obstacle encountered, was to find a reliable set of force field parameters. To that end, the partial charges were calculated with the semi-empirical quantum mechanics program MOPAC2016 whereas the bond distances, angles and interaction parameters were approximated by comparison to similarly structured molecules. Short MD calculations in water were conducted in order to confirm structural stability.<br>Next, a simulation box was produced, by randomly combining an h-LDHA monomer and an Ag8 molecule. The system also contained water and ions in order to keep the total charge of the system neutral. Short cycles of energy minimization, NVT and NPT at a high temperature were performed before a longer (10ns) NPT atomistic simulation took place (at 310K). The results were encouraging, despite the system's limitations. The following step, that will provide more reliable results, will be to simulate a bigger system, containing the whole h-LDHA tetramer in the presence of Ag8