Sandbox Reserved 1847: Difference between revisions
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==Introduction== | ==Introduction== | ||
===What are the SARS-CoV2 Minibinders?=== | ===What are the SARS-CoV2 Minibinders?=== | ||
These mini proteins target the interaction between ACE2 and SARS-CoV-2 spike protein <ref name="Longxing">PMID:32907861</ref>. The mini binders are small proteins designed to bind to the SARS-CoV-2 spike protein with a greater affinity than ACE2 <ref name="Longxing">PMID:32907861</ref>. These mini binders reduce the viral burden of SARS-CoV-2 in mice <ref name="Case">PMID:34192518</ref>. Minibinders were de novo | These mini proteins target the interaction between ACE2 and SARS-CoV-2 spike protein <ref name="Longxing">PMID:32907861</ref>. The mini binders are small proteins designed to bind to the SARS-CoV-2 spike protein with a greater affinity than ACE2 <ref name="Longxing">PMID:32907861</ref>. These mini binders reduce the viral burden of SARS-CoV-2 in mice <ref name="Case">PMID:34192518</ref>. Minibinders were "de novo" designed to mimic the ACE2 helix, but have a lower dissociation constant, yielding a greater affinity for the spike protein <ref name="Longxing">PMID:32907861</ref>. The binding region between <scene name='10/1075251/Ace2_and_rbd/3'>spike protein and ACE2</scene> (PDB: [https://www.rcsb.org/structure/8K4U 8K4U]) makes it seem like binding region is telling how these proteins were designed. Taking a closer look at the SARS-CoV-2 disease pathway shows where the minibinders target the interaction between ACE2 and SARS-CoV-2 spike protein. | ||
[[Image:Minibinders RBD.jpg|500 px|right|thumb|Figure 1. Image of the individual helices of AHB2, LCB1, and LCB3, respectively, bound to the RBD of the spike protein.]] | [[Image:Minibinders RBD.jpg|500 px|right|thumb|Figure 1. Image of the individual helices of AHB2, LCB1, and LCB3, respectively, bound to the RBD of the spike protein.]] | ||
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===Design=== | ===Design=== | ||
AHB2 is a Series A Helix Binder which is a miniprotein that binds specifically to the alpha helix of the protein. LCB1 and LCB3 are long chain bases that are longer in length which allow for more contact between the RBD, increasing the binding affinity. These mini binders, AHB2 and LCB1, were designed de novo | AHB2 is a Series A Helix Binder which is a miniprotein that binds specifically to the alpha helix of the protein. LCB1 and LCB3 are long chain bases that are longer in length which allow for more contact between the RBD, increasing the binding affinity. These mini binders, AHB2 and LCB1, were designed "de novo" with the intention to mimic the binding of ACE2 to the 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 was substituted with each of the 20 amino acids, one at a time, computationally choosing the best sequence <ref name="Valleti">PMID:24970191</ref>. Forming SSM libraries,experimental tests were run on each of the libraries to converge on a small number of closely related sequences <ref name="Valleti">PMID:24970191</ref>. From these libraries, one of these was selected for each design, AHB2 or LCB1-LCB8<ref name="Longxing">PMID:32907861</ref>. | Using Site Saturation Mutagenesis (SSM), every residue in the minibinder’s helix scaffold was substituted with each of the 20 amino acids, one at a time, computationally choosing the best sequence <ref name="Valleti">PMID:24970191</ref>. Forming SSM libraries,experimental tests were run on each of the libraries to converge on a small number of closely related sequences <ref name="Valleti">PMID:24970191</ref>. From these libraries, one of these was selected for each design, AHB2 or LCB1-LCB8<ref name="Longxing">PMID:32907861</ref>. | ||
AHB2 was designed using an ACE2 helix scaffold, while LCB1 and LCB3 were designed completely from scratch, attempting to make the best possible helix with the greatest affinity for the spike protein receptors . Although LCB1 was designed before LCB3, LCB3 was less effective at neutralizing the viral response with a high IC50 !SUBSCRIPT! Value <ref name="Longxing">PMID:32907861</ref> . | AHB2 was designed using an ACE2 helix scaffold, while LCB1 and LCB3 were designed completely from scratch, attempting to make the best possible helix with the greatest affinity for the spike protein receptors . Although LCB1 was designed before LCB3, LCB3 was less effective at neutralizing the viral response with a high IC50 !SUBSCRIPT! Value <ref name="Longxing">PMID:32907861</ref> . | ||
