Unfortunately with COVID-19 taking over and closing school, most of the research work we had done could not be completed. This semester I got the chance to work with Professor Deng on finding drug candidates to screen against the HIV virus. We started the year using molecular dynamics and programs such as “Amber Tutorials” to assist us. Throughout the semester, research did not go as planned and I ended up reading articles and research papers on my topic to better understand how previous researchers analyzed data and targeted the virus.
Drug discovery is very important in today’s society as new healthcare issues arise new drugs are needed. Structure based drug design is one of the very few techniques that uses 3D structures to target receptor proteins. Structure based drug design was introduced in the late 1970s, scientists did not have many resources or computational methods at that time and had to stick to combining chemical synthetic methods and factorial screening. Nowadays, computer based drug design is used along with comparative models and being able to derive complex protein structures with the help of prior knowledge. Knowing the structure of the protein model lets scientist make changes to build a more effective drug. Protein binding can be reversed whether it involves hydrogen bonds, ionic bonds, or van der Waals forces. For example, a specific protein can have water molecules bounded and if the drug was redesigned to have electrostatic interactions we can change the way it binds in that specific area.There are four stages to drug discovery which include; discovery phase where the target gene is cloned, developmental phase where you synthesize, optimize, and test for affinity as well as determine the 3D structure, and clinical trials which need to be passed before the structure can move onto the registry phase. MD stimulation play a huge role in designing drugs because they can track system behaviors with accuracy, provide flexibility, visuals of molecular processes as well as estimating binding energies.