Computational Modeling in Virus Infections and Virtual Screening, Docking, and Molecular Dynamics in Drug Design

de Queiroz Simões, Rachel Siqueira; Ferreira, Mariana Simões; Dumas de Paula, Nathalia; Machado, Thamires Rocco; Pascutti, Pedro Geraldo

Computer modeling is an area of broad multidisciplinary knowledge that includes the study of various biological systems. This chapter will describe the molecular aspects of viral infections and molecular modeling techniques applied to drug discovery with examples of applications in protein activity inhibition in several pathologies. The first part will cover topics of computational chemistry methods, DNA technologies, structural modeling of virus proteins, molecular biology, viral vectors, virus-like particles, and pharmaceutical bioprocess with application in some specific viruses such as papillomavirus, hepatitis B virus, hepatitis C virus, Coronavirus, and Zika Virus. The second part will deal with methods in Virtual Screening for the drug design based on ligands and on the structure of target macromolecules. Molecular docking in drug design, its search algorithms, and scoring functions will be covered in the third part. Finally, a protocol of the Molecular Dynamics technique for studies of protein-ligand complexes and analysis of free energy of binding will be exposed in the last part.