Using supercomputer simulations to develop a base of aptamers binding with SARS-CoV-2 spike protein

Anti CoVID-19 medicine and pharma

Using supercomputer simulations to develop a base of aptamers binding with SARS-CoV-2 spike protein

Development of treatment and diagnostic tools to fight against COVID-19 coronavirus infection

1. Created a base of 256 oligonucleotides with randomized section of 4 nucleotides and a duplex component. The most promising candidate treatment (aptamer) binding with recipient-binding domain of the coronavirus spike protein has been selected from this library.
2. Oligonucleotide сandidate has been improved within the course of multiple rounds of sequential mutagenesis with mandatory verification of binding point and binding energy.
3. Vector Government Scientific Center of Virusology and Biotechnology has synthesized recombinant spike proteins for further research and experimental verification of properties of aptamers simulated on the supercomputer.
4. Demo version of ClarioStar spectral fluorophotometer with fluorescence polarization feature provided by Helicon enabled experimental proof of bonds between selected aptamers with coronavirus spike protein and its recipient-binding domain.
5. Synchrotron radiation treatment in Kurchatov Institute (Moscow, Russia) and National Synchrotron Radiation Research Center in Taiwan provided spectrums of small-angle X-ray scattering on aptamer molecules and molecular complexes in solution with protein. This helped the scientists to identify spatial structure of oligonucleotides and to confirm their binding in complex with the target protein.
6. The Good Hope Net project are going to develop treatment medications based on these oligonucleotides, analyze their physical, chemical and antivirus properties and perform detailed studies of their action. This research will include experimental work with proteins, cell cultures and animals as well as supercomputer simulation using more advanced computing methods.

299 PFLOPs/hours