Remdesivir Augmented Reality Video

Tom Goddard
June 29, 2020

Augmented reality video explaining how remdesivir works on SARS-CoV-2 virus. I use ChimeraX virtual reality together with RealSense depth sensing camera to make an augmented reality video showing the action of remdesivir.

Preliminary video (9 minutes):

First take video was 20 minutes. and used hiding of hand cones which should be used in final version.

Storyboard

What does the drug remdesivir do to SARS coronavirus 2?

This is remdesivir, it is flexible.	When the virus copies its 30000 nucleotide RNA genome remdesivir can be inserted in the copy and jam the copying machinery.	Here is the virus RNA copying machine. Its structure was determined by electron microscopy.
The black specks in this electron microscopy image are the virus RNA copy macchine. There are about 1000 in this image.	From 130000 specks in 3000 images a 3D map of the copy machine was made.	From the map an atomic model was constructed.
The copy machine has the RNA polymerase in gray and two other virus proteins called non-structural protein 7 and 8 needed to load the RNA for copying.	The polymerase adds one nucleotide at a time to the red RNA copy using the blue template viral RNA. Here it adds remdesivir in yellow then three more nucleotides in green.	Remdesivir mimics an A (adenine) nucleotide. An A nucleotide comes from ATP shown at the right.
In the human body half the rendesivir atoms are removed and two phosphates (orange) are added to make the active remdesivir triphosphate that looks like ATP.	The modified remdesivir has a carbon and nitrogen that ATP does not have. They stick out and jam the copying machine.	The copy machine jams when three nucleotides are added after the remdesivir. The extra carbon and nitrogen in remdesivir collides with a bump on the polymerase shown in red.

Remdesivir gives a modest improvement in patients. 500 patients on remdesivir spent 11 days in the hospital versus 15 days for 500 patients who did not take remdesivir. Remdesivir does not completely stop the virus possibly because it does not get to all the infected cells.

ChimeraX session

All the data is included in ChimeraX session file remdesivir8.cxs that can be opened in ChimeraX from July 1, 2020 (daily build) or newer. Besides the session some extra files are needed to run molecular dynamics on remdesivir and to hide and show nucleotides added to the RNA.

Molecular dynamics

Running interactive molecular dynamics on remdesivir and remdesivir triphosphate with the ChimeraX tug mouse mode requires OpenMM parameter files and a Python script to use those paramters.

• rdv.xml - Remdesivier parameters
• rtp.xml - Remdesivier triphosphate parameters
• rtp.xml - ATP parameters
• gaff2.xml - Amber GAFF2 parameters
• tug_remdesivir.py - ChimeraX Python script to add above parameters to tug mouse mode.

These Amber simulation parameters were calculated with Antechamber.

Adding nucleotides

To show the RNA moving through the polymerase I made several states with the remdesivir at different positions. The electron microscopy structure only has the remdesivir at one position in the polymerase active site. How the other states were made is described here.

The states are included in the session file. But each state has the same nucleotides (including the ones yet to be added). ChimeraX morphs cannot add or remove atoms. So the script elongate.py shows and hides nucleotides as the morph is played.

Recording augmented reality

The steps and equipment for recording an augmented reality video are the same as described in for earlier coronavirus cell entry and opiods videos.

Data files

• rdv.pdb - remdesivir, RDV, from CCD with hydrogens readded in ChimeraX for OpenMM.
• atp.pdb - ATP, from CCD with hydrogens readded in ChimeraX for OpenMM.
• rtp.pdb - remdesivir triphosphate, RTP, built in ChimeraX from RDV.
• cov2_rna_twist.pdb - SARS-CoV-2 RNA model, made using ChimeraX rna command with secondary structure from this article.
• PDB 7bv2 - RNA polymerase assembly atomic model
• 7bv2_particles.tif - EM micrograph of polymerase particles, from article supplementary info.
• EMDB 30210 - Polymerase electron microscopy map.
• Elongating RNA atomic models.

Warning: Opening the 30,000 nucleotide (600,000 atom) RNA model needs the ChimeraX "autoStyle false" to avoid nucleotide slab display style which is extremely slow (command "open cov2_rna_twist.pdb autoStyle false"). This PDB should instead be an mmCIF file. Since PDB format is limited to 100,000 atoms it is using hexadecimal atom numbers which most software won't handle.

Some tricky parts

• Need to load RDV and RTP openmm parameters to run MD. Open scripts/tug_remdesivir.py.
• Need Python code to auto show/hide nucleotides as elongating. Open scripts/elongate.py.
• Elongation would cause molecular surface recalculation which is too slow. Could use surface option "update false", but easier to hide / show surfaces as separate model.
• Assign VR buttons in advance including button to toggle cone display.

Original outline

• RDV - remdesivir drug, adenine mimic.
• ATP - normal source of adenine when copying RNA.
• RTP - triphosphate form of remdesivir create in human body.
• Show cyano group attached to sugar that is the key difference from ATP.
• Tug atoms to show cyano group moves rigidly with sugar ring.
• Full RNA model, for sense of size
• RNA polymerase model 7bv2, for sense of size
• EM micrograph of polymerase particles, emdb 30210, from article supplementary info. About 3000 micrographs of 1000 particles each. Used 130,000 particles for reconstruction.
• Polymerase map, EMDB 30210
• 7bv2 atoms built from map
• Proteins as surface, RNA as cartoon with nucleotides, remdesivir at active site. NSP 7,8 proteins needed for polymerase to bind RNA.
• Hide proteins to show RNA clearly, elongate with play coords mouse mode.
• Show surfaces and clash elongating from 3 nucleotides to 4 after remdesivir.