Farewell and Hello to OpenZika Team Members
|By: The OpenZika research team|
|1 Aug 2018|
The data analysis continues while the OpenZika team bids farewell to one of the project co-investigators and brings on new team members.
The Zika virus has “evolved” from a global health emergency to a long-term threat. Scientists throughout the world continue to study the virus and search for ways to stem its spread, including potential vaccines and means of controlling the mosquito population, as well as looking for treatments. As of this update, there is still no vaccine for the Zika virus, and no cure.
We remain convinced that 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 U.S. Food and Drug Administration (FDA). Still, few to none of the compounds that have been identified thus far are both potent enough against Zika virus and also safe for pregnant women.
A change in roles
Dr. Alexander Perryman will be leaving the OpenZika team. In mid-August, Dr. Perryman will become a Senior Scientist II at Repare Therapeutics, a start-up pharmaceutical company in Montreal, Quebec, Canada, that focuses on drug discovery for cancer. According to their website, Repare Therapeutics is developing new, precision oncology drugs for patients that target specific vulnerabilities of tumor cells. Its approach integrates insights from several fields of cell biology including DNA repair and synthetic lethality. Repare’s platform combines a proprietary, high throughput, CRISPR‐enabled gene editing target discovery method with high‐resolution protein crystallography, computational biology and clinical informatics. They use CRISPR-based biological screens to discover new targets that have “synthetic lethality” with the lesions (mutations) that are common in different types of cancer cells. Synthetic lethality means that the target protein is normally not essential to cell survival; however, if a particular cancer lesion is present in that cell, only then does that target protein become essential. The combination of a defective mutation elsewhere makes that target become essential in that cancer cell. Since these targets are not required for healthy cells to survive, this strategy should have the potential to reduce the toxic side effects that can accompany chemotherapy for cancer.
A fond farewell from Dr. Perryman
“I have been working with the IBM team on different World Community Grid projects for almost a decade. Starting with FightAIDS@Home, followed by GO Fight Against Malaria, and for the last two years with OpenZika, it has been a pleasure and a profound privilege to work with the IBM team, the project scientists, and the volunteers who donate their computer power to advance these projects that combat infectious diseases. Although I will be switching from academia to industry, and from infectious diseases to cancer, I will keep focusing on advancing the discovery of drugs that can make a significant impact by reducing suffering and improving human health. The OpenZika team will keep on fighting this good fight without me, and I am confident that progress against the Zika virus will continue to be made. I wish them well, and I thank all of you for your tremendous support during this last decade.”
“We would like to sincerely acknowledge Alex’s dedication, contributions and hard work to the OpenZika project and we all wish him well with his new job. We all will miss him a lot! Our goal will be to transition and build on this firm foundation,” adds Dr. Carolina Andrade.
How job creation and data analysis will be handled going forward
Dr. Melina Mottin, a research associate on the OpenZika team, has been trained by Dr. Perryman, and she will be in charge of the data analysis. She is also going to handle the file preparation to “feed the beast” (that is, to keep creating the docking jobs that you all crunch for us).
In addition, we are going to have the help of other OpenZika researchers, including Dr. Roosevelt Alves da Silva (Federal University of Goias), and Dr. Joao H. Martins Sena (Oswaldo Cruz Foundation, FIOCRUZ) to handle the massive amount of data we have been generating. Moreover, we hired a new student at Federal University of Goias, Bruna Souza, who is being trained by Dr. Melina to help analyze the data.
Plans for Melina to visit Sean’s lab
Dr. Melina Mottin is going to spend one month as a visiting researcher at Dr. Sean Ekins’ lab in North Carolina. She is going to work on Bayesian and Random Forest models for Zika, dengue, and Ebola using publicly available data. The main goal of this work is to develop and implement these models to help increase the efficiency of the final selection of the compounds to test against the viruses. For example, we would like to build a machine learning model for Zika and related flaviviruses that could help predict which compounds are more likely to have whole-cell activity, which will complement our target-based docking in OpenZika.
New candidate inhibitors were recently discovered
We finished analyzing a virtual screen from OpenZika against the ZIKV NS2B/NS3 protease, a key viral enzyme that is required for the virus to mature and form infectious viral particles. 6 million compounds were docked against the ZIKV protease, followed by interaction-based docking filters to find compounds that were predicted to dock well to the allosteric site. We then used machine learning models as filters (our suite of Bayesian models that predict mouse liver microsomal stability, lack of cytotoxicity, and solubility). We ultimately visually inspected the binding modes of the top 318 compounds, and we narrowed it down to 27 candidates. These candidates will be purchased and then assayed by our collaborators, to discern their potency at inhibiting the protease, as well as their efficacy in ZIKV in cell-based assays.
In the figure above (created by Dr. Perryman), H-bond signifies hydrogen bonds (a key type of interaction that drives both the strength of binding and the specificity of binding to only the target that you want it to hit). In the image on the bottom right-hand corner, the spheres depict the results of AutoLigand calculations, which detect binding sites and characterize the “hot spots” that give the tightest binding. Green spheres represent hydrophobic interactions in the allosteric site, red spheres depict hydrogen bond acceptors, and blue spheres signify hydrogen bond donors.
For more information about these experiments, please visit our website.
We recently had two new review papers on the Zika virus accepted for publication. One is a keynote review paper, “The A-Z of Zika drug discovery”, to be published in the journal Drug Discovery Today. The online version of this paper is now available here. This is a comprehensive review of the recent advances in ZIKV drug discovery efforts, highlighting drug repositioning and computationally guided compounds, including recently discovered viral and host cell inhibitors. Promising ZIKV molecular targets are also described and discussed, as well as targets belonging to the host cell, as new opportunities for ZIKV drug discovery. All this knowledge is not only crucial to advancing the fight against the Zika virus and other flaviviruses, but it will also help the scientific community prepare for the next emerging virus outbreak to which we will have to respond.
The other paper, “Computational drug discovery for the Zika virus”, will be published soon in a special issue of the Brazilian Journal of Pharmaceutical Sciences. In this paper, we summarize current computational drug discovery efforts and their applicability to the discovery of anti-ZIKV drugs. We also present successful examples of the use of computational approaches to ZIKV drug discovery, including our OpenZika project.
In addition, Dr. Perryman, Dr. Ekins, and Dr. Joel Freundlich recently published the paper “Naïve Bayesian Models for Vero Cell Cytotoxicity” in the journal Pharmaceutical Research. (Read the paper here.) This paper describes our creation and validation of new machine learning models that can predict toxicity to mammalian cells. (The Vero cells discussed in the paper are African Green Monkey kidney cells, which are one of the model systems that are frequently used to initially assay the toxicity of drug-like compounds). These models can help us advance aspects of the OpenZika research, and since we are freely releasing these training and test sets for our models to the community, this research can also help other labs pursue their own drug discovery projects.
Moreover, the OpenZika project results will be presented at the 256th ACS National Meeting, on August 19-23, 2018, in Boston, MA, USA. Dr. Melina Mottin will be giving an oral presentation and presenting a poster titled “OpenZika: Discovery of new antiviral candidates against Zika virus”, in the session Chemoinformatics Approaches to Enhance Drug Discovery Based on Natural Products.
Past publications and outreach
Dr. Ekins presented a poster at Cell Symposia: Emerging and Re-emerging Viruses, on October 1-3, 2017, in Arlington, VA, USA, titled “OpenZika: Opening up the discovery of new antiviral candidates against zika virus”.
Our PLoS Neglected Tropical Diseases paper, “OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery,” was published on October 20 2016, and it has already been viewed more than 5,200 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 formally accepted by F1000Research and viewed more than 4,200 times.
We have also published another research paper entitled “Molecular Dynamics simulations of Zika Virus NS3 helicase: Insights into RNA binding site activity” 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 performed against NS3 helicase, and the Molecular Dynamics simulations generated new conformations of this system that we have been using as targets in new virtual screens that we performed as part of OpenZika.
These articles and presentations are helping to bring additional attention to the project and to encourage the formation of new collaborations.
We started a very important collaboration with Center for Innovation in Biodiversity and Drug Discovery (CIBFar), coordinated by Professor Glaucius Oliva, hosted at University of Sao Paulo (USP), Brazil, São Carlos Institute of Physics (IFSC). The main goal of this collaboration is to test our compounds directly on enzymatic assays with Zika virus proteins. Our selected compounds are being tested to see if they can bind to the NS3 helicase, using the differential scanning fluorescence (DSF) technique and/or if they can inhibit the ATPase activity of this protein.
Another collaboration has been started with a Brazilian group working on semi-synthetic and natural products, led by Professor Luis Octavio Regasini, from the Department of Chemistry and Environmental Sciences, São Paulo State University (UNESP), and Professor Ana Carolina Gomes Jardim, from the Institute of Biomedical Sciences, Federal University of Uberlandia (UFU), a virologist expert in running phenotypic assays (cell-based assays) with viruses. They are screening a library of natural and synthetic compounds which include flavonoids, alkaloids and diarylamines to assess their antiviral potential against ZIKV infection in vitro. For the discovered experimental hits, we are performing docking calculations using AutoDock Vina with ZIKV proteins, using the same protocols and models that we developed in the OpenZika project. The results of this collaboration are being written in a research paper, which will be submitted soon to a scientific journal for publication.
Dr. Ekins started a collaboration with Dr. Scott Laster and Frank Scholle at NC State to study flaviviruses. They have access to cell-based plaque assays for these viruses.
Dr. Andrade has hired a new graduate student, Bruna Souza, to work in the OpenZika project. She started working on Dr. Andrade’s lab in March 2018, and she is very enthusiastic about learning and collaborating with the project.
Status of the calculations
In total, we have submitted almost 5 billion docking jobs, which involved 427 different target sites. Our initial screens used an older library of 6 million commercially available compounds, and our current experiments use a newer library of 30.2 million compounds. We have already received approximately 4.6 billion of these results on our server. (As mentioned in our last update, there is some lag time between when the calculations are performed on your volunteer machines and when we get the results, since all of the results per “package” of approximately 10,000 – 50,000 different docking jobs need to be returned to World Community Grid, re-organized, and then compressed before sending them to our server).
Thus far, the more than 80,000 volunteers who have donated their spare computing power to OpenZika have given us more than 51,471 CPU years’ worth of docking calculations, at a current average of 64.5 CPU years per day! Thank you all very much for your help!
Except for a few stragglers, we have received all the results for our experiments that involve docking 6 million compounds versus NS1, NS3 helicase (both the RNA binding site and the ATP site), NS5 (both the RNA polymerase and the methyltransferase domains) and NS2B/NS3 protease.
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, tote bags, hats, ties, pillows, key rings, and phone cases that have the OpenZika logo! All profits that we receive from the sale of this merchandise will go toward buying compounds for lab testing.
We are very grateful for all the volunteers who are donating their unused computing time to this project! Thank you very much!