Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics

• Published in: Scientific reports 2022-02, Vol.12 (1), p.3316-20, Article 3316
• Main Authors: Alencar, Wilson Luna Machado, da Silva Arouche, Tiago, Neto, Abel Ferreira Gomes, de Castro Ramalho, Teodorico, de Carvalho Júnior, Raul Nunes, de Jesus Chaves Neto, Antonio Maia
• Format: Article
• Language: English
• Subjects: 631/114/116; 631/114/2248; 631/114/2397; 631/114/2398; 631/114/2410; 631/114/663; 631/114/794; Air conditioning; Antagonists; Cobalt; Cobalt - chemistry; Contamination; Coordination Complexes - chemistry; Copper; Copper - chemistry; Coronaviruses; COVID-19; Free energy; Humanities and Social Sciences; Humans; Isoindoles - chemistry; Lethality; Macromolecules; Molecular Docking Simulation; Molecular Dynamics Simulation; Molecular modelling; multidisciplinary; Pandemics; SARS-CoV-2 - chemistry; Science; Science (multidisciplinary); Severe acute respiratory syndrome coronavirus 2; Spike glycoprotein; Viral envelope proteins; Viral Proteins - chemistry
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-022-07396-w

The new coronavirus, SARS-CoV-2, caused the COVID-19 pandemic, characterized by its high rate of contamination, propagation capacity, and lethality rate. In this work, we approach the use of phthalocyanines as an inhibitor of SARS-CoV-2, as they present several interactive properties of the phthalocyanines (Pc) of Cobalt (CoPc), Copper (CuPc) and without a metal group (NoPc) can interact with SARS-CoV-2, showing potential be used as filtering by adsorption on paints on walls, masks, clothes, and air conditioning filters. Molecular modeling techniques through Molecular Docking and Molecular Dynamics were used, where the target was the external structures of the virus, but specifically the envelope protein, main protease, and Spike glycoprotein proteases. Using the g_MM-GBSA module and with it, the molecular docking studies show that the ligands have interaction characteristics capable of adsorbing the structures. Molecular dynamics provided information on the root-mean-square deviation of the atomic positions provided values between 1 and 2.5. The generalized Born implicit solvation model, Gibbs free energy, and solvent accessible surface area approach were used. Among the results obtained through molecular dynamics, it was noticed that interactions occur since Pc could bind to residues of the active site of macromolecules, demonstrating good interactions; in particular with CoPc. Molecular couplings and free energy showed that S-gly active site residues interacted strongly with phthalocyanines with values ​​of − 182.443 kJ/mol (CoPc), 158.954 kJ/mol (CuPc), and − 129.963 kJ/mol (NoPc). The interactions of Pc's with SARS-CoV-2 may predict some promising candidates for antagonists to the virus, which if confirmed through experimental approaches, may contribute to resolving the global crisis of the COVID-19 pandemic.