Probing biased activation of mu-opioid receptor by the biased agonist PZM21 using all atom molecular dynamics simulation.

Morphine is a commonly used opioid drug to treat acute pain by binding to the mu-opioid receptor (MOR), but its effective analgesic efficacy via triggering of the heterotrimeric Gi protein pathway is accompanied by a series of adverse side effects via triggering of the ß-arrestin pathway. Recently, PZM21, a recently developed MOR biased agonist, shows preferentially activating the G protein pathway over ß-arrestin pathway. However, there is no high-resolution receptor structure in complex with PZM21 and its action mechanism remains elusive. In this study, PZM21 and Morphine were docked to the active human MOR-1 homology structure and then subjected to the molecular dynamics (MD) simulations in two different situations (i.e., one situation includes the crystal waters but another does not). Detailed comparisons between the two systems were made to characterize the differences in protein-ligand interactions, protein secondary and tertiary structures and dynamics networks. PZM21 could strongly interact with Y3287.43 of TM7, besides the residues (Asp1493.32 and Tyr1503.33) of TM3. The two systems' network paths to the intracellular end of TM6 were roughly similar but the paths to the end of TM7 were different. The PZM21-bound MOR's intracellular ends of TM5-7 bent outward more along with the distance changes of the three key molecular switches (ionic lock, transmission and Tyr toggle) and the distance increase of some conserved inter-helical residue pairs. The larger intracellular opening of the receptor could potentially facilitate G protein binding.

Binding Interactions of Ergotamine and Dihydroergotamine to 5-Hydroxytryptamine Receptor 1B (5-HT1b) Using Molecular Dynamics Simulations and Dynamic Network Analysis.

Ergotamine (ERG) and dihydroergotamine (DHE), common migraine drugs, have small structural differences but lead to clinically important distinctions in their pharmacological profiles. For example, DHE is less potent than ERG by about 10-fold at the 5-hydroxytrptamine receptor 1B (5-HT1B). Although the high-resolution crystal structures of the 5-HT1B receptor with both ligands have been solved, the high similarity between these two complex structures does not sufficiently explain their activity differences and the activation mechanism of the receptor. Hence, an examination of the dynamic motion of both drugs with the receptor is required. In this study, we ran a total of 6.0 µs molecular dynamics simulations on each system. Our simulation data show the subtle variations between the two systems in terms of the ligand-receptor interactions and receptor secondary structures. More importantly, the ligand and protein root-mean-square fluctuations (RMSFs) for the two systems were distinct, with ERG having a trend of lower RMSF values, indicating it to be bound tighter to 5-HT1B with less fluctuations. The molecular mechanism-general born surface area (MM-GBSA) binding energies illustrate this further, proving ERG has an overall stronger MM-GBSA binding energy. Analysis of several different microswitches has shown that the 5-HT1B-ERG complex is in a more active conformation state than 5-HT1B-DHE, which is further supported by the dynamic network model, with reference to mutagenesis data with the critical nodes and the first three low-energy modes from the normal mode analysis. We also identify Trp3276.48 and Phe3316.52 as key residues involved in the active state 5-HT1B for both ligands. Using the detailed dynamic information from our analysis, we made predictions for possible modifications to DHE and ERG that yielded five derivatives that might have more favorable binding energies and reduced structural fluctuations.

Analysis of vismodegib resistance in D473G and W535L mutants of SMO receptor and design of novel drug derivatives using molecular dynamics simulations.

AIMS: Vismodegib is an effective antagonist of smoothened receptors for treatment of locally advanced or metastatic basal cell carcinoma. However, it often suffers from drug resistance due to mutations. Two common mutants, D4736.55G and W5357.55L, were found to cause serious drug resistance. Although the reduction of drug binding affinity (~40-fold) was thought to be the major reasons, the detailed structural, energetic and dynamic mechanisms at the molecular level are still unknown. MAIN METHODS: Molecular dynamics simulations and molecular mechanics-generalized Born surface area (MM-GBSA) binding energy calculations were performed on three complex systems of wild-type (WT) and two mutants with vismodegib. Then, virtual screening was used to select three potential derivatives of vismodegib from the 77 new derivatives designed by modifying the substitutions on the phenylpyridine ring of vismodegib. KEY FINDINGS: The MM-GBSA binding energy data of the two mutants showed a significant reduction in binding affinity. The energy decomposition identified that the key contributing residues were in the binding site. The D4736.55G mutant affected the binding of the ligand by directly changing the conformations of the key residues in TM6, while the W5357.55L mutant mainly depended on long range allosteric effect. More importantly, the methylsulfonyl benzamide moiety was identified to be the pharmacophore of the ligand, and two of the three derivatives from the virtual screening showed much higher MM-GBSA binding affinity to the two mutants than vismodegib did. SIGNIFICANCE: These results might help to understand resistance mechanisms and the two derivatives can be good candidates for future experiments.