A drug repurposing study to target bacterial ribosome decoding center with molecular docking and molecular dynamics simulations

Abstract

Antibiotic resistance is a growing threat globally. As it becomes more widespread, antibiotics available on the market are expected to become insufficient for treatments soon. For instance, E. coli which causes many pathogenic diseases that can be treated today poses a serious threat as an antibiotic-resistant bacteria. To this end, drug repurposing can be a very effective approach to implementing new treatments using drugs already on the market for different types of diseases, especially in the fight against antibiotic-resistant bacteria. This thesis uses various computational methods to propose compounds that have the potential to inhibit protein synthesis by targeting the decoding center (DC) binding site in the small subunit (30S) of the E. coli ribosome. Hygromycin B bound 30S E. coli ribosome (PDB ID: 4v64) is used as a reference structure in all calculations. Hygromycin B is an aminoglycoside that binds to the decoding center and inhibit the translocation process by causing a conformational change locally. First, the binding affinities of FDA-approved, experimental, and investigational compound libraries are investigated by performing standard precision (SP-) and extra precision (XP-) docking studies against 30S ribosome structure using Glide program. This is followed by binding energy estimation with truncated ribosome structure using Prime MM-GBSA calculations of Glide program. A filtering procedure based on the docking scores, Prime MM-GBSA interaction energy estimation, and the extent of non-bonded interactions with the ribosome is followed. Additionally, non-antibiotics and especially non-aminoglycosides are preferred when making the selection of the hit compounds. The molecule size is another parameter taken into consideration. After the filtering; Chlorhexidine (-169.77 kcal/mol), DB04718 (-301.74 kcal/mol), DB08018 (-156.62 kcal/mol), Enviomycin (-191.59 kcal/mol), and Ciraparantag (-256.46 kcal/mol) are selected to assess the binding cavity using all atom molecular dynamics (MD) simulations in explicit water. DB04718 and Enviomycin are chosen for the MD simulations even though they are derivatives of the drug Paromomycin, a not FDA-approved aminoglycoside and Viomycin, a tuberactinomycin. The reason is to provide a positive control in addition to the validation with the reference ligand, Hygromycin B (-163.63 kcal/mol). Furthermore, Setmelanotide (-155.57 kcal/mol) and Icatibant (-248.00 kcal/mol) from the docking calculations by AutoDock Vina followed by estimation of the interaction energies using Prime MM-GBSA from another study are also added to the selected molecules. Then, the motions and interactions are observed performing two independent 100 ns MD simulations for each selected molecule-ribosome complex in Desmond. A total of 16 MD simulations are conducted in this thesis. The temperature, pressure and energy values throughout the simulations are observed to check the stability of the system. The movements and configurational changes of the molecules and the ribosome are examined by creating separate root mean squared displacement (RMSD) graphs for the structures. Normalized mean squared fluctuations (MSFs) are calculated to detect nucleotide-based movements. The number of hydrogen bonds during the simulation and their occupancies are also determined as a part of the MD analysis. Moreover, the interactions made in the last frame of the MD simulations are examined to monitor the non-bonded interactions. Finally, the binding free energy values of the docked compounds are estimated with MM-GBSA calculations based on the full atom MD simulations using thermal_mmgbsa.py script. OPLS-2005 force field is used in the energy minimization of the ribosome and the ligand libraries, Prime MM-GBSA calculations and MD simulations. As a result, five hit compounds get high docking and Prime MM-GBSA scores by making many interactions, stay in the cavity throughout the MD simulations, interact with nucleotides similar to the reference ligand and get high binding free energy values in the MM-GBSA calculations. Therefore, five potential hit molecules that are Chlorhexidine (R1: -39.24±6.88 kcal/mol and R2: -48.98±5.97 kcal/mol), Setmelanotide (R1: -83.25±7.49 kcal/mol and R2: -97.56±9.37 kcal/mol), Icatibant (R1: -77.62±9.69 kcal/mol and R2: -81.01±8.30 kcal/mol), DB08018 (R1: -61.38±3.90 kcal/mol and R2: -72.80±3.74 kcal/mol) and Ciraparantag (R1: -62.80±9.58 kcal/mol and R2: -78.97±6.24 kcal/mol) for the E. coli ribosome are proposed to be examined in further experimental studies.