With hydroxychloroquine no longer a candidate for treating COVID-19, it was time to turn attention towards modeling the more likely helpful, yet more complex molecule, Remdesivir. This proved to be a daunting task. Rather than attempting to model Remdesivir entirely at once, the approach was taken to divide the molecule into four separate moieties. After modeling each of the four moeities indivdually, the plan would then be to combine the four moieties into the larger final molecule, Remdesivir.
More concretely, the steps taken for modeling were the following:
- Model the most complex of the four moieties, the fused ring structure containing a pyrrole azine fusion.
- Model the second most complex of the moieties, the structure containing the furan ring to which the pyrrole azine is attached.
- Model the phosphoryl group to which the furan is attached.
- Model the structure containing the ester linkage to which the phosphoryl group is attached.
- Once all four groups were properly modeled individually, model all three combinations of two adjacent groups connected to each other. That is: the pyrrole azine and furan ring group, the furan ring and phosophoryl group, and finally the phosphoryl group and the ester containing group.
- Once the three combinations of adjacent groups had been properly modeled, model the two combinations of three adjacent groups. That is: the pyrolle azine, furan ring, and phosphoryl group combination; and the furan ring, phosphoryl group, and ester containing group combination.
- Finally, model all four individual groups as attached to each other thus forming Remdesivir.
- When checking the locant numbering for a bicyclo fused ring, check if the ring is napthalene. If not, proceed to step 2.
- Check if the ring is aromatic. If so, proceed to step 3
- Determine the name of the components of the fused ring (each indvidual ring).
- Determine the main component (larger bridge length) and side component (smaller bridge length).
- Name the main and side components
- Generate the fusion numbering (following the format ([matching locant 1 of main component, matching locant 2 of main component - matching face of side component]) where the matching locants and faces are the two atoms that are found in both components
- Generate full fusion name of both components including fusion numbering
- The existing way. That is, clicking on the attachment and dragging it to a specific target atom on the molecule. By default, this will attach the atom numbered 1 of the new attachment.
- If the user instead clicks and HOLDS on the attachment for one second (a long press event), the attachment will then be expanded and the user will be able to click on which specific atom of the new skeletal attachment they want to attach to the target atom of the existing molecule. The user can then drag the skeletal attachment as usual to a target atom on the molecule.