Synthetic and Computational Investigations into the Development of Antivirals and Viral Protein Dynamics
Creators: Oraby, Ahmed K.
Publisher: name: University of Alberta Library
Year: 2022

<p>Respiratory viruses are the most common cause of disease in humans, causing high death rates worldwide. Among these, respiratory syncytial virus (RSV) infection is the most significant cause of severe lower respiratory infections in children in North America and one of the leading causes of infant death worldwide. There is no vaccine, and limited drug treatment options, so there is a great need for effective drugs. The emergence of SARS-CoV-2, the pathogen responsible for the COVID-19 pandemic, has created an even more urgent need to develop new antiviral drugs. The creation of antiviral drugs begins with understanding how the virus infects humans and then designing a potent compound that can target any step of the virus life cycle, including viral attachment to the cell, replication process, and release. The viral polymerase represents an attractive therapeutic target for inhibition of virus infection because it makes the virus genetic material (RNA). If this process is halted or slowed, then virus infection is stopped. This has been a highly successful approach in the antiviral drugs developed for HIV and hepatitis C virus (HCV) infections. Therefore, broad-spectrum antiviral agents are desirable because they could protect against the emergence of new viruses, like pandemic SARS-CoV-2.<br>
In Chapter 2, we computationally evaluated the RSV polymerase complex for potential allosteric sites that can accommodate a new class of non-nucleoside polymerase inhibitors reported previously by our group. The lead bis(indole) compound, compound 1, was used as a reference for the molecular docking and molecular dynamics simulations to develop a reliable computational model. The in-silico studies shed light on the putative allosteric site and potential protein-ligand interactions allowing for the design of a new series of compounds with potentially better activity. The synthesis of the compound 1 analogues is discussed. Evaluation of several analogues against RSV is also reported and showed that a new compound, compound 6, displayed the most promising antiviral activity using RSV viral progeny assay and viral RNA production quantification using qPCR.<br>
In light of the recent pandemic caused by SARS-CoV-2, Chapter 3 discusses efforts to develop effective antivirals to combat the virus. This chapter describes a detailed computational strategy to identify allosteric binding pockets within the SARS-CoV-2 polymerase and their druggability and accessibility for small molecules. A library of new analogues was rationally designed where the indole fragment of the bis(indole) was substituted with a phenolic hydroxyl to establish a hydrogen bond interaction to the side chain of Thr 394. Several analogues were evaluated using cell-based and biochemical assays and yielded two compounds, 5 and 6, with substantial low micromolar activity. The activity of the new compounds was also assessed in combination with the FDA-approved drug remdesivir, and a synergistic effect was observed when infected cells were treated with this blend.<br>
In Chapter 4, we describe the discovery of a new way of how viruses can evade immune pressure and sterilizing conditions through a single amino acid mutation at residue 305 in the RSV fusion protein (F) that switches the profile from RSV type A to RSV type B. Molecular dynamics demonstrated that the switch from leucine at position 305 (RSV type A) to isoleucine (RSV type B) causes a shape-shift in the protein conformation, altering the conformation of the antigenic epitopes and hence changing the susceptibility profile for antibodies and patient serum neutralization. A detailed computational, viral evolution, and mutants response to antibodies is described.</p>