BACKGROUND: The high transmission and pathogenicity of SARS-CoV-2 has led to a pandemic that has halted the world's economy and health. The newly evolved strains and scarcity of vaccines has worsened the situation. The main protease (Mpro) of SARS-CoV-2 can act as a potential target due to its role in viral replication and conservation level. METHODS: In this study, we have enlisted more than 1100 phytochemicals from Asian plants based on deep literature mining. The compounds library was screened against the Mpro of SARS-CoV-2. RESULTS: The selected three ligands, Flemichin, Delta-Oleanolic acid, and Emodin 1-O-beta-D-glucoside had a binding energy of -8.9, -8.9, -8.7 KJ/mol respectively. The compounds bind to the active groove of the main protease at; Cys145, Glu166, His41, Met49, Pro168, Met165, Gln189. The multiple descriptors from the simulation study; root mean square deviation, root mean square fluctuation, radius of gyration, hydrogen bond, solvent accessible surface area confirms the stable nature of the protein-ligand complexes. Furthermore, post-md analysis confirms the rigidness in the docked poses over the simulation trajectories. CONCLUSIONS: Our combinatorial drug design approaches may help researchers to identify suitable drug candidates against SARS-CoV-2.
BACKGROUND: The high transmission and pathogenicity of SARS-CoV-2 has led to a pandemic that has halted the world's economy and health. The newly evolved strains and scarcity of vaccines has worsened the situation. The main protease (Mpro) of SARS-CoV-2 can act as a potential target due to its role in viral replication and conservation level. METHODS: In this study, we have enlisted more than 1100 phytochemicals from Asian plants based on deep literature mining. The compounds library was screened against the Mpro of SARS-CoV-2. RESULTS: The selected three ligands, Flemichin, Delta-Oleanolic acid, and Emodin 1-O-beta-D-glucoside had a binding energy of -8.9, -8.9, -8.7 KJ/mol respectively. The compounds bind to the active groove of the main protease at; Cys145, Glu166, His41, Met49, Pro168, Met165, Gln189. The multiple descriptors from the simulation study; root mean square deviation, root mean square fluctuation, radius of gyration, hydrogen bond, solvent accessible surface area confirms the stable nature of the protein-ligand complexes. Furthermore, post-md analysis confirms the rigidness in the docked poses over the simulation trajectories. CONCLUSIONS: Our combinatorial drug design approaches may help researchers to identify suitable drug candidates against SARS-CoV-2.
Authors: Mohammed Anowar Hosen; Nasrin Sultana Munia; Mohammed Al-Ghorbani; Mohammed Baashen; Faisal A Almalki; Taibi Ben Hadda; Ferdausi Ali; Shafi Mahmud; Md Abu Saleh; Hamid Laaroussi; Sarkar M A Kawsar Journal: Bioorg Chem Date: 2022-05-04 Impact factor: 5.307
Authors: Md Abu Saleh; Shafi Mahmud; Sarah Albogami; Ahmed M El-Shehawi; Gobindo Kumar Paul; Shirmin Islam; Amit Kumar Dutta; Md Salah Uddin; Shahriar Zaman Journal: Front Bioeng Biotechnol Date: 2022-02-11
Authors: Gobindo Kumar Paul; Shafi Mahmud; Afaf A Aldahish; Mirola Afroze; Suvro Biswas; Swagota Briti Ray Gupta; Mahmudul Hasan Razu; Shahriar Zaman; Md Salah Uddin; Mohammed H Nahari; Mohammed Merae Alshahrani; Mohammed Abdul Rahman Alshahrani; Mala Khan; Md Abu Saleh Journal: Arab J Chem Date: 2021-12-01 Impact factor: 5.165