Discovering Dengue Drugs - Together

This project has the potential to yield novel antiviral drugs for infectious diseases that greatly impact global health. Specifically, our aim is to identify and develop antiviral drugs against dengue, hepatitis C, West Nile, and yellow fever viruses. In addition, this study will provide the foundation for a new and more efficient approach to drug development for other diseases that plague the world.
This project is distributed using the BOINC client, which is available for download on this site for computers with Windows, Macintosh, or Linux operating systems. For system requirements, click here.
The calculations done on World Community Grid will predict which small molecule compound, out of the millions contained in our library database, should be tested for their ability to inhibit the flavivirus protease. This is a major step towards our ultimate goal of discovering new drugs to stop flavivirus infections.

Phase 1 of this project will predict how each small molecule might bind to the active site of the viral protease. This phase also produces preliminary "energies" that coarsely rank the strength of the intermolecular interactions between the compound and viral protease.

Phase 2 will accurately predict free energies of binding between each compound and the viral protease. This calculation utilizes the binding orientations calculated in phase 1. Due to computation time required for each free energy of binding calculation, only compounds with "good" scores from phase1 will be selected for phase 2 calculations.

As analogy, phase 1 will tell us how two people might hold hands, whereas phase 2 will tell us whether or not they want to hold hands.
After completion of the project and internal analysis by our groups, all data will be made available on the Discovering Dengue Drugs-Together web site.
Phase 1 began in August, 2007 and finished in August, 2009. Phase 2 is expected to start in late 2009 and may finish by mid 2010.
Docking is the process of bringing together two objects. For example, a ship docks with a pier in a harbor. Molecular docking refers to a computer simulation in which two molecules are brought together. In our case, we dock a "small" molecule (i.e., a possible drug) to a target molecule (i.e., the viral NS3 protease). A docking program predicts the orientation or pose of the small molecule when bound to the target. This is accomplished by maximizing favorable interactions and minimizing unfavorable interactions between the two molecules. In addition, the program gives each pose a score based on these interactions and the conformation of the small molecule.

Virtual screening is the process of systematically screening a database of small molecules against a defined target molecule. The scores provided by the docking programs rank how well the small molecule docks to the target protein relative to other molecules in the database. Unfortunately, these rankings typically produce a large number of false positives. In this project, binding free energy calculations, combined with docking scores, will provide an accurate prediction of compounds that most strongly bind to the target protease.
Binding free energy is a thermodynamic measure of the difference in energy between a bound and an unbound state. In this project, it is the energy difference between a small molecule bound to the protease in solution, and a small molecule alone in solution. Large negative binding free energies correspond to molecules that tightly bind to the protein.
Viruses are composed of a protein coat and the genetic material (RNA or DNA) that encodes the proteins needed for replication. They are dependent on a host cell and the cellular machinery for translation of the genetic material into those proteins. Without a cell, the virus cannot replicate. Some scientists refer to viruses as "cellular parasites."
The viruses that belong to the family Flaviviridae include three genera: the flaviviruses, the hepaciviruses, and the pestiviruses. The two genera on which this project focuses include the flaviviruses and the hepaciviruses. The genus flavivirus includes (but is not limited to) the mosquito-borne dengue, West Nile virus, Japanese encephalitis, and yellow fever virus. It also includes the tick-borne encephalitis viruses. The genus hepacivirus includes hepatitis C virus.
Cryo-electron microscopy is one way to determine the structure of a virus. After isolating and concentrating virus particles, one can quickly freeze them on a microscope grid. The freezing allows the particles to be preserved "intact." Images of the particles on the grid are then obtained with an electron microscope. By reconstructing thousands of images, one can obtain a final three-dimensional structure with enough detail to observe the entire virus particle as well as the individual structural proteins that comprise the particle.

Another method of obtaining virus structure is X-ray crystallography. For this method, virus (or the viral protein of interest) is isolated, purified, concentrated, and crystallized. High-powered X-rays are beamed onto the crystal, and the diffraction pattern is analyzed computationally and ultimately reveals a structure of the molecule of interest.
While the flaviviruses and the hepaciviruses have some differences in their genome and coding strategies, the proteins they encode are very similar. They all encode the structural proteins that surround the nucleic acids. These include the envelope glycoproteins, the capsid protein, and the membrane protein. In addition, they encode non-structural proteins. These include a helicase, polymerase, methyl transferase, and the protease. It is the highly conserved protease that is the target of inhibition for this study.
A primary method for determining atomic resolution protein structures is X-ray crystallography. For this method, the protein of interest is isolated, purified, concentrated, and crystallized. High-powered X-ray is beamed onto the crystal, and the diffraction pattern is analyzed computationally and ultimately reveals the protein structure.
About half of the antiviral drugs that exist are targeted against HIV. These include protease inhibitors, reverse-transcriptase inhibitors, nucleotide and non-nucleotide analogs, and a fusion inhibitor. There are a few antiviral drugs that target herpes virus, including nucleotide analogs and drugs that disrupt virus uncoating. There are also a few drugs that target influenza virus, cytomegalovirus, and hepatitis B virus. Many of these drugs have very limited efficacy.
Finding drugs that can be used safely remains one of the major difficulties in producing new drugs. Millions of compounds may need to be screened to discover a handful of compounds with a desired activity. Unfortunately, many compounds that show activity are either toxic or poorly absorbed in the human body. Since it is difficult to accurately predict the behavior of drug leads in the human body, perhaps only 1% of drug leads eventually become drugs.