Want to help? Please reply here if you are looking to find the best way you can help besides submitting designs at https://covid.postera.ai/covid or commenting on those designs in the Covid_submissions category https://discuss.postera.ai/c/covid/covid-submissions/6
If you are an virologist whose lab is still open or you are a drug discovery expert who wants to help with planning or just a concerned person, reply here and I am sure we can find a way for you to help!
Hi I am Rajat. I am very much interested in contributing to the COVID-19 research towards finding an effective drug. I read some online articles about “off-label” use of Lopinavir, Ritonavir as well as anti-malarial drugs to treat COVID-19 patients in severe cases. I just got my PhD in Computer-Aided drug design and after these news on “off-label” use of these drugs, I got really interested in looking into the structure of COVID-19 main Protease (Mpro) and did some docking calculations for studying interactions of Lopinavir, Ritonavir at the binding site. I am thinking of running free energy calculations and also running other docking simulations with the submitted compounds here at Postera, building the structures from SMILES. I know many groups are currently working on this problem and I am very interested to contribute to this research with my acquired knowledge and also by learning new things from fellow scientists. Please let me know if there are any opportunities available so that I can collaborate and work in groups, accessing resources to contribute to this noble cause.
Thanks Rajat! Really appreciate your interest in helping, and I’m sure we can find a group that is coordinating docking or free-energy calculations that could use your help. Let me reach out to some of them and get back to you soon. We should also be able to coordinate getting people computation time. Is there a good way to do this @JohnChodera ?
I am already working on this from a natural products approach - looking for compounds that are readily available to many people, are already safely used, and that might help, even if only a little. I will use the library of compounds to inform my work. I am a computational chemist and I will use simulations as a first screen of interesting compounds.
Will you be interested in these sorts of compounds? They will not be novel compounds and, as natural products, probably cannot be patented.
Thanks for all of the great efforts from everyone on this forum and project.
We have put together a page detailing a couple of ways we believe MiTeGen might be able help the broader efforts:
Enabling Research on SARS-CoV-2 and COVID-19 Webpage
But a quick summary might be easier here:
MiTeGen wants to do everything and anything we can to enable researchers to get immediate access to the tools, equipment, and information they need for work on SARS-CoV-2, and to help accelerate efforts to develop vaccines, treatments, etc.
We sit in a unique position in the structural biology research community. We have connections with nearly every crystallography beamline and cryo-EM user facility, as well as a customer base of thousands of researchers worldwide. We want to use this position to help in every way possible to benefit our community.
The main two ways we believe we can help are:
Sharing information, resources, and initiatives within our network (e.g. social, emails, etc.).
Prioritizing supplies of crystallography and cryo-EM materials and equipment for labs focused on related research, as well as sharing costs where needed. We are remaining open (with minimal on-site staff) to process requests for materials and equipment.
There are more details in the link above, but please don’t hesitate to contact us to share information, add resources, request materials, or to send us your ideas on how a supplier such as ourselves might be able to further help.
Thanks,
Ben @ MiTeGen
https://www.linkedin.com/posts/biovia_covid19-coronavirus-biovia-activity-6648321487004672000-FH0D
Some information on an international company who are offering “modelling/computer simulation” resources. Kind regards.
https://www.gatesfoundation.org/Media-Center/Press-Releases/2020/03/Life-Science-Companies-Commit-to-the-Fight-Against-COVID-19-Pandemic-alongside-Gates-Foundation Further list of companies committed to cooperate on COVID-19 work.
We are very keen to offer our robotic expertise and synthetic chemistry expertise to the COVID-19 research effort.
We have a robotic automation system within our research lab in York, which is particularly effective at reaction optimisation and lead compound derivative synthesis. I have examined some of the more recent lead compound structures and I believe we can contribute positively to this effort. We have world-leading expertise in metal-catalysed cross-coupling chemistry (Suzuki-Miyuara, Hartwig-Buchwald, Alpha-Arylation, Heck couplings, Kumada, Negishi and Sonogashira cross-coupling chemistries, including mechanistic information that is critical to well-performing catalyst systems). We can also assist with thinking about issues that might arise on reaction scale-up. With such rapid developments being made on lead compound hits, it is essential from a Process Chemistry perspective that reaction sensitivities are understood up-front. Something that can be easily missed is a side-product produced in a reaction or synthetic sequence, which may actually be an active compound in its own right, or have undesired side-effects. We can help with promising lead compound candidates in this respect, while also being able to complement the analysis of data using machine learning and statistical analysis.
We have a current research grant (EPSRC, Government grant) to use the robotic system in improving reaction optimisation and data analysis. Thus, we have the resource to work on these research activities. I am very much looking forward to making connections through this consortium. Thank you. Ian Fairlamb (ian.fairlamb@york.ac.uk) https://www.york.ac.uk/chemistry/staff/academic/d-g/ifairlamb/
Many thanks for offering to help. I think our synthesis design tools can interface with your robotic chemistry setup, and we’d be keen to collaborate. Does your robot perform multi-step synthesis? Is it a flow-based or batch setup?
Hi there, We have a batch set-up. We can potentially do multi-step syntheses, although that will depend on the types of reaction work-ups and purifications needed. We are best set-up for reaction optimisation and understanding how side-products result in classical cross-coupling reactions, for example. I appreciate it is vitally important to get to a target compound quickly and efficiently, but I think one needs to also bear in mind reaction selectivity and the implication of carrying through trace quantities of side-products. Please let me know how we might be able to help further. All the best, Ian
Hello, my name is Ben McDonald, and while I do not have any expertise related to virology, or more generally biology or medicine, I am trained in the experimental method from my undergraduate Engineering Physics degree related work, and currently work as a software engineer in a .NET framework. My only current contribution is allocating spare FLOPs via folding@home through CureCoin. Due to a debt-induced reliance on my salary, it would be unlikely that I could feasibly relocate to a lab to work as a low level tech in a meaningful capacity, despite my ability to perform my day job remotely (though if 6 hours a day after the traditional work day was adequate value to provide, then I suppose I could do that).
I would like to help however I can. I am trainable to the degree that I might be able to learn the necessary components of virology within a year to make direct ideological contributions towards a solution, but my guess is that we would prefer a faster solution than that. Please let me know what avenues would best be explored for my being able to contribute.
I’ve included my Linked-In profile for additional information.