Sandbox Reserved 1849: Difference between revisions

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These mini binders, <scene name='10/1075249/Ahb2_fullspikeprotein/1'>AHB2</scene> and <scene name='10/1075249/Lcb1_fullspike_rotating/1'>LCB1</scene>, were designed from “scratch” (de novo) with the intention to mimic the binding of ACE2 to spike protein <ref name="Longxing">PMID:32907861</ref>. Using Rotamer Interaction Field (RIF) docking, the proteins were able to make the most efficient bonding using the ACE2 spike protein binding interface <ref name="Longxing">PMID:32907861</ref>. Using Site Saturation Mutagenesis (SSM), every residue in the minibinder’s helix scaffold will be substituted with each of the 20 amino acids, one at a time <ref name="Valleti">PMID:24970191</ref>. Forming SSM libraries, each of the libraries converged on a small number of closely related sequences, and from these libraries, the design was selected for AHB2 and LCB1 to find the sequence that yields a protein with a high affinity for the spike proteins receptor binding domain <ref name="Longxing">PMID:32907861</ref>. AHB2 was designed using ACE2 helix scaffold, while LCB1 and LCB3 were designed full from scratch, attempting to make the best possible helix with the greatest affinity for the spike protein receptors <ref name="Longxing">PMID:32907861</ref>. Although LCB1 was designed before LCB3, LCB3 was less effective at neutralizing the viral response with a higher IC50 value <ref name="Longxing">PMID:32907861</ref>.

== Implications ==

Examining the IC50 values of the various mini binders gives quantitative data to the effectiveness of the proteins in preventing an immune response. The highest IC50 was AHB2 (15.5 nM) <ref name="Longxing">PMID:32907861</ref>. The higher IC50 indicates a larger amount of mini binder required to inhibit the biological process. Both LCB1 and LCB3 proved to be significantly more effective than AHB2, “LCB1 and LCB3 were within a factor of 3 of the most potent anti-Spike monoclonal antibodies described to date” <ref name="Longxing">PMID:32907861</ref>. The IC50 values of LCB1 and LCB3 are 23.54 pM and 48.1 pM, respectively<ref name="Longxing">PMID:32907861</ref>.

Given that LCB1 proved to be the most effective mini binder, an experiment examined the effectiveness of the mini binder in mice. LCB1 was administered to the mice via nasal delivery. As expected, compared to control mini protein, the LCB1 was significantly more effective at reducing the viral burden, diminishing the immune cell infiltration, and inflammation <ref name="Case">PMID:34192518</ref>. The virus was not detected in the lungs 4-7 days post-infection, and the spleen, heart, and brain had viral RNA at very low concentrations <ref name="Case">PMID:34192518</ref>.

The size of these mini binders is a large reason why they are so effective. The mini binders are “5% the molecular weight of a full antibody molecule with… 20-fold more potential for nebulization” <ref name="Longxing">PMID:32907861</ref>. When the LCB1 was modified to attach to a human IgG domain to enhance bioavailability (mini binders stay in the body longer and work more effectively), the results showed that LCB1 was less effective <ref name="Case">PMID:34192518</ref>. This can be explained by the proteins being much larger in size. The mini binders are also very stable, so they are able to be administered as a gel via nebulization <ref name="Longxing">PMID:32907861</ref>. Future directions of mini binders are to streamline the process of obtaining a sequence for pathogen neutralizing designs <ref name="Longxing">PMID:32907861</ref>. Given that there are only a small number of antibody therapies and vaccines approved for treatment of COVID, it is important to get this potential therapeutic approved to lay the foundation for other treatments for other viruses.Due to the mini binders being so effective, future directions of mini proteins should look to prevent viral entry of other viruses.

Sandbox Reserved 1849: Difference between revisions

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 These mini binders, <scene name='10/1075249/Ahb2_fullspikeprotein/1'>AHB2</scene>  and <scene name='10/1075249/Lcb1_fullspike_rotating/1'>LCB1</scene>, were designed from “scratch” (de novo) with the intention to mimic the binding of ACE2 to spike protein <ref name="Longxing">PMID:32907861</ref>. Using Rotamer Interaction Field (RIF) docking, the proteins were able to make the most efficient bonding using the ACE2 spike protein binding interface <ref name="Longxing">PMID:32907861</ref>. Using Site Saturation Mutagenesis (SSM), every residue in the minibinder’s helix scaffold will be substituted with each of the 20 amino acids, one at a time <ref name="Valleti">PMID:24970191</ref>. Forming SSM libraries, each of the libraries converged on a small number of closely related sequences, and from these libraries, the design was selected for AHB2 and LCB1 to find the sequence that yields a protein with a high affinity for the spike proteins receptor binding domain  <ref name="Longxing">PMID:32907861</ref>. AHB2 was designed using ACE2 helix scaffold, while LCB1 and LCB3 were designed full from scratch, attempting to make the best possible helix with the greatest affinity for the spike protein receptors <ref name="Longxing">PMID:32907861</ref>. Although LCB1 was designed before LCB3, LCB3 was less effective at neutralizing the viral response with a higher IC50 value <ref name="Longxing">PMID:32907861</ref>.
 == Implications ==
+Examining the IC50 values of the various mini binders gives quantitative data to the effectiveness of the proteins in preventing an immune response. The highest IC50 was AHB2 (15.5 nM) <ref name="Longxing">PMID:32907861</ref>. The higher IC50 indicates a larger amount of mini binder required to inhibit the biological process. Both LCB1 and LCB3 proved to be significantly more effective than AHB2, “LCB1 and LCB3 were within a factor of 3 of the most potent anti-Spike monoclonal antibodies described to date” <ref name="Longxing">PMID:32907861</ref>. The IC50 values of LCB1 and LCB3 are 23.54 pM and 48.1 pM, respectively<ref name="Longxing">PMID:32907861</ref>.
+Given that LCB1 proved to be the most effective mini binder, an experiment examined the effectiveness of the mini binder in mice. LCB1 was administered to the mice via nasal delivery. As expected, compared to control mini protein, the LCB1 was significantly more effective at reducing the viral burden, diminishing the immune cell infiltration, and inflammation <ref name="Case">PMID:34192518</ref>. The virus was not detected in the lungs 4-7 days post-infection, and the spleen, heart, and brain had viral RNA at very low concentrations <ref name="Case">PMID:34192518</ref>.
+The size of these mini binders is a large reason why they are so effective. The mini binders are “5% the molecular weight of a full antibody molecule with… 20-fold more potential for nebulization” <ref name="Longxing">PMID:32907861</ref>. When the LCB1 was modified to attach to a human IgG domain to enhance bioavailability (mini binders stay in the body longer and work more effectively), the results showed that LCB1 was less effective <ref name="Case">PMID:34192518</ref>. This can be explained by the proteins being much larger in size. The mini binders are also very stable, so they are able to be administered as a gel via nebulization <ref name="Longxing">PMID:32907861</ref>. Future directions of mini binders are to streamline the process of obtaining a sequence for pathogen neutralizing designs <ref name="Longxing">PMID:32907861</ref>. Given that there are only a small number of antibody therapies and vaccines approved for treatment of COVID, it is important to get this potential therapeutic approved to lay the foundation for other treatments for other viruses.Due to the mini binders being so effective, future directions of mini proteins should look to prevent viral entry of other viruses.