Lagerstroemia, Euphorbia hirta, and Kleinhovia hospita as inhibitors of heptad repeat (HR) SARS-CoV-2 spike protein based on an in silico study

ABSTRACT

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease-19 (COVID-19), has become a global health issue. Spike proteins from the virus have a vital role in infection. Herbal medicines such as Lagerstroemia, Euphorbia hirta, and Kleinhovia hospita have several pharmacological functions such as anticancer, antiviral, and antioxidant because of their bioactive compound content. Based on an in silico study, this research was conducted on the possibility of phytochemicals from herbal Lagerstroemia, E. hirta, and K. hospita to inhibit spike protein SARS-CoV-2. A three-dimensional (3D) compound structure of each herbal medicine was docked with HR protein using AutoDock Vina software. The docking result, which has the best binding energy value, is continued with the analysis of molecular dynamics simulation. Lagerine, rutin, and nicotiflorin compounds might bind to proteins with lower binding energy. Protein was unstable when complexed with compounds compared with control, as seen from the root-mean-square deviation (RMSD) value. Therefore, this research is pre-experimental to inhibit SARS-CoV-2 spike proteins by herbal medicines.