A crystallography-based investigation of weak interactions for drug design against COVID-19.

Interactions between proteins and small molecules play important roles in the inhibition of protein function. However, a lack of proper knowledge about non-covalent interactions can act as a barrier towards gaining a complete understanding of the factors that control these associations. To find effective molecules for COVID-19 inhibition, we have quantitatively investigated 143 X-ray crystal structures of the SARS-CoV-2 Mpro protein of coronavirus with covalently or non-covalently bound small molecules (SMs). Our present study is able to explain ordinary and perceptive aspects relating to protein inhibition. The active site of the protein consists of 21 amino acid residues, but only nine are actively involved in the ligand binding process. The H41, M49, and C145 residues have highest priority with respect to interactions with small molecules through hydrogen bond, CH-π, and van der Waals interactions. At the active site, this ranking of amino acids is clear, based on different spatial orientations of ligands, and consistent with the electronic properties. SMs with aromatic moieties that bind to the active site of the protein play a distinct role in the determination of the following order of interaction frequency with the amino acids: CH-π > H-bonding > polar interactions. This present study revealed that the G143 and C145 residues play crucial roles in the recognition of the carbonyl functionality of SMs through hydrogen bonding. With this knowledge in mind, an effective inhibitor small-molecule for SARS-CoV-2 Mpro was designed: docking studies showed that the designed molecule has strong binding affinity towards the protein. The non-covalent interactions in the protein-ligand complex are in good agreement with the results obtained from X-ray crystallography. Moreover, the present study focused on weak forces and their influence on protein inhibition, henceforth shedding much light on the essential requirements for moieties that should be present in a good inhibitor and their orientations at the ligand binding site.

Effect of Transmembrane Electric Field on GM1 Containing DMPC-Cholesterol Monolayer: A Computational Study.

Transmembrane electric potentials and membrane curvature have always provided pathways to mediate different cellular processes. We present results of molecular dynamics (MD) simulations of lipid monolayer composed of 1, 2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and cholesterol (CHOL) under a transverse electric field to monitor the effect of electric field on membrane containing ganglioside monosialo 1 (GM1). Four systems were studied with membrane monolayer in the presence and absence of GM1 with and without applying electric field along the normal of the monolayer. The applied transmembrane electric field was 0.4 mV/Å which corresponds to the action potential of animal cell. Our results indicate that the electric field induces a considerable lateral stress on the monolayer in the presence of GM1, which is evident from the lateral pressure profiles. It was found that due to the application of electric field major perturbation was caused to the system containing GM1, manifested by the bending of the monolayer. We believe this study provides correlation between electric field and spontaneous membrane bending, specially based on the membrane composition. The consequences of these MD simulations provide considerable insights to different biological phenomenon and lipid membrane models.

Phase Behavior of GM1-Containing DMPC-Cholesterol Monolayer: Experimental and Theoretical Study.

Organization and distribution of lipids in cellular membranes play an important role in a diverse range of biological processes, such as membrane trafficking and signaling. Here, we present the combined experimental and simulated results to elucidate the phase behavioral features of ganglioside monosialo 1 (GM1)-containing mixed monolayer of the lipids 1,2-dimyristoyl- sn-glycero-3-phosphocholine (DMPC) and cholesterol (CHOL). Two monolayers having compositions DMPC-CHOL and GM1-DMPC-CHOL are investigated at air-water and air-solid interfaces using Langmuir-Blodgett experiments and scanning electron microscopy (SEM), respectively, to ascertain the phase behavior change of the monolayers. Surface pressure isotherms and SEM imaging of domain formation indicate that addition of GM1 to the monolayer at low surface pressure causes a fluidization of the system but once the system attains the surface pressure corresponding to its liquid-condensed phase, the monolayer becomes more ordered than the system devoid of GM1 and interacts among each other more cooperatively. Besides, the condensing effect of cholesterol on the DMPC monolayer was also verified by our experiments. Apart from these, the effects induced by GM1 on the phase behavior of the binary mixture of DMPC-CHOL were studied with and without applying liquid-expanded (LE)-liquid-condensed (LC) equilibrium surface pressure using molecular dynamics (MD) simulation. Our molecular dynamics (MD) simulation results give an atomistic-level explanation of our experimental findings and furnish a similar conclusion.

Interaction Between Luteinizing Hormone-Releasing Hormone and GM1-Doped Cholesterol/Sphingomyelin Vesicles: A Spectroscopic Study.

Understanding the role of neural membrane in translocation and action of neurohormone is of great importance. Luteinizing hormone-releasing hormone (LHRH) is a neuropeptide hormone and it acts as a final signaling molecule by stimulating the synthesis of LH and FSH to maintain reproduction in all vertebrates. The receptors of LHRH are found in breast tumors and pituitary gland in the brain. Moreover, neural plasma membrane is also found to contain specific binding site for LHRH. The mechanism by which LHRH binds to membrane before it binds to the receptors is a very critical step and can have a profound impact upon the translation of peptide across the membrane. A complex form of glycosphingolipids known as Ganglioside is an important component of plasma membrane of nerve cells and breast tumor tissues. They play an important role in various physiological membrane processes. Therefore, the interaction of ganglioside-containing membrane with LHRH might be crucial in aiding the LHRH to translate through the neural membrane and reach its receptor for binding and activation. Using CD, UV-Absorbance, and fluorescence spectroscopy, the effect of Ganglioside Monosialo 1(GM1)-induced conformational changes of LHRH in the presence of Cholesterol (CHOL)/Sphingomyelin (SM) and GM1/CHOL/SM vesicles was studied. The aforesaid spectroscopic studies show that LHRH is able to bind with both the vesicles, but GM1-containing vesicles interact more effectively than vesicles without GM1. CHOL/SM vesicles partially disturb the conformation of the peptide. Moreover, binding of LHRH to GM1/CHOL/SM vesicles induces loss of conformational rigidity and attainment of a random coil.

Temperature dependent aggregation mechanism and pathway of lysozyme: By all atom and coarse grained molecular dynamics simulation.

Aggregation of protein causes various diseases including Alzheimer's disease, Parkinson's disease, and type II diabetes. It was found that aggregation of protein depends on many factors like temperature, pH, salt type, salt concentration, ionic strength, protein concentration, co solutes. Here we have tried to capture the aggregation mechanism and pathway of hen egg white lysozyme using molecular dynamics simulations at two different temperatures; 300 K and 340 K. Along with the all atom simulations to get the atomistic details of aggregation mechanism, we have used coarse grained simulation with MARTINI force field to monitor the aggregation for longer duration. Our results suggest that due to the aggregation, changes in the conformation of lysozyme are more at 340 K than at 300 K. The change in the conformation of the lysozyme at 300 K is mainly due to aggregation where at 340 K change in conformation of lysozyme is due to both aggregation and temperature. Also, a more compact aggregated system is formed at 340 K.