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OpenZika Researchers Continue Calculations and Prepare for Next Stage
By: The OpenZika research team
21 Mar 2017   

Summary
The OpenZika researchers are continuing to screen millions of chemical compounds as they look for potential treatments for the Zika virus. In this update, they report on the status of their calculations and their continuing work to spread the word about the project.

Project Background

While the Zika virus may not be getting the continuous press coverage that it received in 2015 and 2016, it is still a threat to the health of people across the globe. New infections continue to be reported in both South America and North America, and medical workers are just beginning to assess the effects of the virus on young children whose mothers were infected while pregnant.

The search for effective treatments is crucial to stemming the tide of the virus. In addition to the OpenZika project, several other labs are doing cell-based screens with drugs already approved by the US Food and Drug Administration (FDA) agency, but few to none of the “hit” compounds that have been identified thus far are both potent enough against Zika virus and also safe for pregnant women.

Also, there are a number of efforts underway to develop a vaccine against the Zika virus. However, vaccines do not help people who already have the infection. It will be several years before they are proven effective and safe, and before enough doses can be mass produced and distributed. And even after approved vaccines are available and distributed to the public, not all people will be vaccinated. Consequently, in the meantime and in the future, cures for Zika infections are needed.

Progress on choosing compounds for lab testing

ZIKV NS3 helicase bound to RNA with the predicted binding modes of five approved drugs (from our second set of candidates) selected by virtual screening. These candidates are shown as surfaces with different shades of green. The identification of these candidates and the video were made by Dr. Alexander L. Perryman.

We began the analysis phase of the project by focusing on the results against the apo NS3 helicase crystal structure (apo means that the protein was not bound to anything else, such as a cofactor, inhibitor, or nucleic acid) to select our first set of candidates, which are currently being assayed by our collaborator at University of California San Diego, Dr. Jair L. Siqueira-Neto, using cell-based assays. The NS3 helicase is a component of the Zika virus that is required for it to replicate itself.

In the second set of screening results that we recently examined, we used the new crystal structure of NS3 helicase bound to RNA as the target (see the images / animation above). Similar to the first set of candidates, we docked approximately 7,600 compounds in a composite library composed of the US Food and Drug Administration-approved drugs, the drugs approved in the European Union, and the US National Institutes of Health clinical collection library against the new RNA-bound structure of the helicase. Below are the results of this second screening:

  • 232 compounds passed the larger collection of different energetic and interaction-based docking filters, and their predicted binding modes were inspected and measured in detail.
  • Of the compounds that were inspected in detail, 19 unique compounds passed this visual inspection stage of their docked modes.
  • From the compounds that passed the visual inspection, 9 passed subsequent medicinal chemistry-based inspection and will be ordered soon.

Status of the calculations

In total, we have submitted 2.56 billion docking jobs, which involved the virtual screening of 6 million compounds versus 427 different target sites. We have already received approximately 1.9 billion of these results on our server. (There is some lag time between when the calculations are performed on your volunteered machines and when we get the results, since all of the results per “package” of approximately 10,000 different docking jobs need to be returned to World Community Grid, re-organized, and then compressed before sending them to our server.)

Except for a few stragglers, we have received all of the results for our experiments that involve docking 6 million compounds versus the proteins NS1, NS3 helicase (both the RNA binding site and the ATP site), and NS5 (both the RNA polymerase and the methyltransferase domains).  We are currently receiving the results from our most recent experiments against the NS2B / NS3 protease.

A new stage of the project

We just finished preparing and testing the docking input files that will be used for the second stage of this project. Instead of docking 6 million compounds, we will soon be able to start screening 30.2 million compounds against these targets. This new, massive library was originally obtained in a different type of format from the ZINC15 server. It represents almost all of “commercially available chemical space” (that is, almost all of the “small molecule” drug-like and hit-like compounds that can be purchased from reputable chemical vendors). 

The ZINC15 server provided these files as “multi-molecule mol2” files (that is, many different compounds were contained in each “mol2” formatted file). These files had to be re-formatted (we used the Raccoon program from Dr. Stefano Forli, who is part of the FightAIDS@Home team) by splitting them into individual mol2 files (1 compound per file) and then converting them into the “pdbqt” docking input format.

We then ran a quick quality control test to make sure that the software used for the project, called AutoDock Vina, could properly use each pdbqt file as an input. Many compounds had to be rejected, because they had types of atoms that cause Vina to crash (such as silicon or boron), and we obviously don’t want to waste the computer time that you donate by submitting calculations that will crash.

By splitting, reformatting, and testing hundreds of thousands of compounds per day, day after day, after approximately six months this massive new library of compounds is ready to be used in our OpenZika calculations. Without the tremendous resources that World Community Grid volunteers provide for this project, we would not even dream of trying to dock over 30 million compounds against many different targets from the Zika virus. Thank you all very much!!!

For more information about these experiments, please visit our website.

Publications and Collaborations

Our PLoS Neglected Tropical Diseases paper, "OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery," was published on October 20, and it has already been viewed over 4,000 times. Anyone can access and read this paper for free. Another research paper “Illustrating and homology modeling the proteins of the Zika virus” has been accepted by F1000Research and viewed > 3800 times. 

A group from Brazil, coordinated by Prof. Glaucius Oliva, has contacted us because of our PLoS Neglected Tropical Diseases paper to discuss a new collaboration to test the selected candidate compounds directly on enzymatic assays with the NS5 protein of Zika virus. They have solved two high-resolution crystal structures of ZIKV NS5, which have been recently released on the PDB (Protein Data Bank) (PDB ID: 5TIT and 5U04).

Our paper entitled “Molecular Dynamics simulations of Zika Virus NS3 helicase: Insights into RNA binding site activity” was just accepted for publication in a special issue on Flaviviruses for the journal Biochemical and Biophysical Research Communications. This study of the NS3 helicase system helped us learn more about this promising target for blocking Zika replication. The results will help guide how we analyze the virtual screens that we already performed against NS3 helicase, and the molecular dynamics simulations generated new conformations of this protein that we will use as input targets in new virtual screens that we perform as part of OpenZika.

These articles are helping to bring additional attention to the project and to encourage the formation of new collaborations. 

Additional News

We have applied and been accepted to present “OpenZika: Opening the Discovery of New Antiviral candidates against Zika Virus and Insights into Dynamic behavior of NS3 Helicase” to the 46th World Chemistry Congress. The conference will be held in Sao Paulo, Brazil, on July 7-14.

Dr. Sean Ekins has hired a postdoc and a master level scientist who will get involved with the OpenZika project. We have also started to collate literature inhibitors from Zika papers.

Also, Drs. Sean Ekins and Carolina Andrade have offered to buy some of the candidate compounds that we identified in the virtual screens from OpenZika, so that they can be assayed in the next round of tests.  

Fundraising

Dr. Alex Perryman models an OpenZika shirt. Profits from the sale of OpenZika merchandise go to purchasing compounds for lab testing. (Photo by Keith Bratcher, courtesy of Rutgers University)

Thank you to anyone who has visited our store on Zazzle to check out OpenZika merchandise such as T-shirts, polo shirts, mugs, buttons, mouse pads, and phone cases. All profits from the sale of this merchandise will go toward buying compounds for lab testing. Drs. Alex Perryman and Sean Ekins have bought OpenZika shirts for themselves. Alex likes the polo style version the best, and he recommends getting the white or gray shirts. But avoid the red shirts, since the OpenZika logo does not stand out as well, especially after it is washed (Alex learned this the hard way).

The OpenZika team is working on grants from the National Institutes of Health, CNPq (a Brazilian funding agency), and other organizations to try raise funds for purchasing and testing compounds. 

Outreach

We have been working hard to promote the project, and we continue to look for additional opportunities. Below is a list of our most recent outreach efforts.

  • Dr. Carolina Horta Andrade gave one invited lecture at the 27th annual Institute of Biology Week, at Federal University of Goias, Brazil, to biology and pharmacy students and to the general public regarding the “Design and discovery of new drug candidates for the Zika and Dengue Viruses and OpenZika” (November, 2016).
  • Dr. Carolina Horta Andrade has been elected as an Affiliated Member of the Brazilian Academy of Sciences. She also gave a talk at the Federal University of Minas Gerais, Brazil, to researchers from many different fields of science and to authorities, in which she discussed OpenZika (October 2016).
  • Dr. Melina Mottin, one of the OpenZika team members, presented a poster and gave an oral presentation, titled “OpenZika: an open science collaboration project to discover drug candidates against Zika virus,” at the 8th Brazilian Symposium on Medicinal Chemistry, held in Búzios, Rio de Janeiro, Brazil, from November 27-30, 2016.
  • Dr. Melina Mottin also gave an invited lecture at the Federal University of Rio Grande do Sul, Brazil, at the Post-Graduation Program in Chemistry, to chemistry and pharmacy Ph.D. students and to the general public regarding “Identification of Drug Candidates for Zika virus using Virtual Screening and Molecular Dynamics Simulations,” in which she discussed the OpenZika project (December 2016).
  • Dr. Sean Ekins attended the National Institutes of Health (NIH) “Rare disease day” (February 27, 2017) and also the Gordon Research Conference on Tropical Infectious Diseases (March 12-17 2017).

 

We are very grateful for all of the volunteers who are donating their unused computing time to this project!  Thank you very much!!