Interaction of compounds derived from the Chinese medicinal formula Huangqi Guizhi Wuwu Tang with stroke-related numbness and weakness targets: An in-silico docking and molecular dynamics study

Huangqi Guizhi Wuwu Tang (HGWT) is a traditional Chinese herbal formula used for managing post-stroke symptoms. Existing research have supported the use of this formula particularly for stroke-related numbness and weakness (SRNW); however, their mechanisms of actions are not fully understood. This study aims to investigate the molecular mechanisms of components from HGWT targeting specific proteins related to numbness and weakness through computational docking and molecular dynamics (MD) simulations. A total of 786 compounds from HGWT were retrieved from a herbal compound database and docked against a candidate SRNW target protein, with the asernestioside B (HQ068)-mitogen-activated protein kinase 3 (MAPK3) complex predicted to exhibit the highest binding affinity (-10.4 kcal/mol) and number of ligand-receptor contacts. Subsequent molecular dynamics (MD) simulations were performed in triplicate on the apo-MAPK3 protein and asernestioside B -bound form in a solvated system for 200 ns per trajectory to ascertain the stability of the enzyme-ligand complex, and to determine the structural impact of ligand binding. The stability of the complex and overall tertiary structural changes were characterized using root-mean-square deviation (RMSD), radius of gyration (Rg), root-mean-square fluctuation (RMSF) calculations Differences in the RMSF of apo and ligand-bound MAPK3 were most prominent in three major regions: (a) activation loop Asp184:Pro213 (b) MAPK3 insertion site Gly262:Ala291 and (c) loop region at the C-terminus Tyr334:Pro356. Lower values of RMSF for the HQ068-bound protein at the activation loop suggest that HQ068 binding stabilizes MAPK3 in a different conformation in this region compared to the apo protein. Free energy calculations of the asernestioside B-MAPK3 complex revealed key residues contributing to the interaction, which include Pro264, Gln 266, Asp268 and Thr288. These key residues may play an integral role in the binding of selective modulators or substrates of extracellular signal-regulated kinase (ERK) within the MAPK cascade. Overall, this study provides a mechanistic overview of compounds from HGWT. Modelling predicted that asernestioside B may act with high potency against MAPK3, while exhibiting a favourable ADMET profile, and this compound should be explored as a potential agent to alleviate SRNW-related symptoms in future studies.