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1 SARS CoV-2 Protein Inhibitors (AHB2 and LCB1/LCB3)
- 1.1 References
  - 1.1.1 PDB Files
- 1.2 Student Contributors

SARS CoV-2 Protein Inhibitors (AHB2 and LCB1/LCB3)

1 Introduction
2 Vaccines
- 2.1 AHB2 and LCB1/LCB3 Specifically
  - 2.1.1 Their Discovery
3 Binding Site
4 Inhibitor Differences

Introduction

SARS-CoV-2 better known as Covid-19 sent the world into a global pandemic. In order to create a vaccine, it was essential to understand how SARS-CoV-2 infected us.

The enzyme angiotensin converting enzyme 2 (ACE2) is attached to our cell membranes and then can be bound to a receptor binding domain (RBD) ^[1]. The spike protein of SARS-CoV-2 enters our bodies and binds to the RBD, allowing the spike protein access to ACE2 and our host cells ^[2]. Once the spike protein has access to our host cells, it is able to further infect our cells and spread the virus throughout our bodies, causing us to get sick. In order to create an effective vaccine, the pathway between the spike protein and the RBD needed to be interrupted.

Vaccines

AHB2 and LCB1/LCB3 Specifically

Protein inhibitors were thought of as a new idea for creating vaccines ^[3]. These protein inhibitors are also referred to as mini-binders, they interact with the ACE2 receptor binding domain no longer allowing the viral cell to bind and enter our cells. The mini-binders were also found to be smaller and more stable compared to antibody vaccines making their usage preferred over antibodies ^[3].

Their Discovery

The first mini-binder to be created to combat COVID-19 is called AHB2. In order to ensure that the mini-binder would bind to the same RBD that the ACE2 was bound to, AHB2 was designed by looking at sequence of ACE2 alpha-helix that makes interactions with spike receptor binding domain. This design process is referred to as the Rosetta Blueprint protein design ^[3].

The use of the Rosetta Blueprint protein design to create the AHB2 inhibitor.

As the AHB2 inhibitors were tested and found to be effective, it was then time to manipulate the mini-binders to create a more effective vaccine. A rotamer interaction field docking with in silico mini-proteins were used by using a scaffold library to generate binders to more distinct regions of the RBD surface ^[3]. This method is known as the de novo protein design and it is how the LCB1 and LCB3 mini-binders were created.

The use of the De Novo protein design to create the LCB1 and LCB3 inhibitors.

Binding Site

Inhibitor Differences

References

Cao, L., Goreshnik, I., Coventry, B., Case, J.B., Miller, L., Kozodoy, L., Chen, R.E., Carter, L., Walls, A.C., Park, Y., Strauch, E., Stewart, L., Diamond, M.S., Veesler, D., & Baker, D. De novo design of picomolar SARS-CoV-2 mini protein inhibitors. Science 370, 426-431 (2020). https://doi.org/10.1126/science.abd9909

https://www.who.int/europe/emergencies/situations/covid-19

https://pmc.ncbi.nlm.nih.gov/articles/PMC9786537/#:~:text=The%20receptor%2Dbinding%20domain%20(RBD,that%20initiates%20the%20viral%20transmission.

https://www.nature.com/articles/s41580-021-00418-x#citeas

https://www.science.org/doi/10.1126/science.abd9909

PDB Files

[1]https://www.rcsb.org/structure/7UHB

Student Contributors

Giavanna Yowell
Shea Bailey
Matthew Pereira

Proteopedia Page Contributors and Editors (what is this?)

Elizabeth Yowell

Retrieved from "http://52.214.119.220/wiki/index.php/User:Elizabeth_Yowell/_SandboxFinal"

@@ Line 19: / Line 19: @@
 The first mini-binder to be created to combat COVID-19 is called AHB2. In order to ensure that the mini-binder would bind to the same RBD that the ACE2 was bound to, AHB2 was designed by looking at sequence of ACE2 alpha-helix that makes interactions with spike receptor binding domain. This design process is referred to as the Rosetta Blueprint protein design <ref name="Cao">DOI:10.1126/science.abd9909</ref>.
-[[Image:ACB1_Methodology.png|400 px|left|thumb|The use of the Rosetta Blueprint protein design to create the AHB2 inhibitor.]]
+[[Image:ACB1_Methodology.png|400 px|right|thumb|The use of the Rosetta Blueprint protein design to create the AHB2 inhibitor.]]
 As the AHB2 inhibitors were tested and found to be effective, it was then time to manipulate the mini-binders to create a more effective vaccine. A rotamer interaction field docking with in silico mini-proteins were used by using a scaffold library to generate binders to more distinct regions of the RBD surface <ref name="Cao">DOI:10.1126/science.abd9909</ref>. This method is known as the de novo protein design and it is how the LCB1 and LCB3 mini-binders were created.
-[[Image:LCB1_Methodology.png|400 px|left|thumb|The use of the De Novo protein design to create the LCB1 and LCB3 inhibitors.]]
+[[Image:LCB1_Methodology.png|400 px|right|thumb|The use of the De Novo protein design to create the LCB1 and LCB3 inhibitors.]]