Feeds:
Posts
Comments

Posts Tagged ‘therapeutic proteins’


Miniproteins against the COVID-19 Spike protein may be therapeutic

Reporter: Stephen J. Williams, PhD

Computer-designed proteins may protect against coronavirus

At a Glance

  • Researchers designed “miniproteins” that bound tightly to the SARS-CoV-2 spike protein and prevented the virus from infecting human cells in the lab.
  • More research is underway to test the most promising of the antiviral proteins.

 

 

 

 

 

 

 

An artist’s conception of computer-designed miniproteins (white) binding coronavirus spikes. UW Institute for Protein Design

The surface of SARS-CoV-2, the virus that causes COVID-19, is covered with spike proteins. These proteins latch onto human cells, allowing the virus to enter and infect them. The spike binds to ACE2 receptors on the cell surface. It then undergoes a structural change that allows it to fuse with the cell. Once inside, the virus can copy itself and produce more viruses.

Blocking entry of SARS-CoV-2 into human cells can prevent infection. Researchers are testing monoclonal antibody therapies that bind to the spike protein and neutralize the virus. But these antibodies, which are derived from immune system molecules, are large and not ideal for delivery through the nose. They’re also often not stable for long periods and usually require refrigeration.

Researchers led by Dr. David Baker of the University of Washington set out to design synthetic “miniproteins” that bind tightly to the coronavirus spike protein. Their study was funded in part by NIH’s National Institute of General Medical Sciences (NIGMS) and National Institute of Allergy and Infectious Diseases (NIAID). Findings appeared in Science on September 9, 2020.

The team used two strategies to create the antiviral miniproteins. First, they incorporated a segment of the ACE2 receptor into the small proteins. The researchers used a protein design tool they developed called Rosetta blueprint builder. This technology allowed them to custom build proteins and predict how they would bind to the receptor.

The second approach was to design miniproteins from scratch, which allowed for a greater range of possibilities. Using a large library of miniproteins, they identified designs that could potentially bind within a key part of the coronavirus spike called the receptor binding domain (RBD). In total, the team produced more than 100,000 miniproteins.

Next, the researchers tested how well the miniproteins bound to the RBD. The most promising candidates then underwent further testing and tweaking to improve binding.

Using cryo-electron microscopy, the team was able to build detailed pictures of how two of the miniproteins bound to the spike protein. The binding closely matched the predictions of the computational models.

Finally, the researchers tested whether three of the miniproteins could neutralize SARS-CoV-2. All protected lab-grown human cells from infection. Candidates LCB1 and LCB3 showed potent neutralizing ability. These were among the designs created from the miniprotein library. Tests suggested that these miniproteins may be more potent than the most effective antibody treatments reported to date.

“Although extensive clinical testing is still needed, we believe the best of these computer-generated antivirals are quite promising,” says Dr. Longxing Cao, the study’s first author. “They appear to block SARS-CoV-2 infection at least as well as monoclonal antibodies but are much easier to produce and far more stable, potentially eliminating the need for refrigeration.”

Notably, this study demonstrates the potential of computational models to quickly respond to future viral threats. With further development, researchers may be able to generate neutralizing designs within weeks of obtaining the genome of a new virus.

—by Erin Bryant

Source: https://www.nih.gov/news-events/nih-research-matters/computer-designed-proteins-may-protect-against-coronavirus

Original article in Science

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors

 

  1. View ORCID ProfileLongxing Cao1,2
  2. Inna Goreshnik1,2
  3. View ORCID ProfileBrian Coventry1,2,3
  4. View ORCID ProfileJames Brett Case4
  5. View ORCID ProfileLauren Miller1,2
  6. Lisa Kozodoy1,2
  7. Rita E. Chen4,5
  8. View ORCID ProfileLauren Carter1,2
  9. View ORCID ProfileAlexandra C. Walls1
  10. Young-Jun Park1
  11. View ORCID ProfileEva-Maria Strauch6
  12. View ORCID ProfileLance Stewart1,2
  13. View ORCID ProfileMichael S. Diamond4,7
  14. View ORCID ProfileDavid Veesler1
  15. View ORCID ProfileDavid Baker1,2,8,*

See all authors and affiliations

Science  09 Sep 2020:
eabd9909
DOI: 10.1126/science.abd9909

Abstract

Targeting the interaction between the SARS-CoV-2 Spike protein and the human ACE2 receptor is a promising therapeutic strategy. We designed inhibitors using two de novo design approaches. Computer generated scaffolds were either built around an ACE2 helix that interacts with the Spike receptor binding domain (RBD), or docked against the RBD to identify new binding modes, and their amino acid sequences designed to optimize target binding, folding and stability. Ten designs bound the RBD with affinities ranging from 100pM to 10nM, and blocked ARS-CoV-2 infection of Vero E6 cells with IC 50 values between 24 pM and 35 nM; The most potent, with new binding modes, are 56 and 64 residue proteins (IC 50 ~ 0.16 ng/ml). Cryo-electron microscopy structures of these minibinders in complex with the SARS-CoV-2 spike ectodomain trimer with all three RBDs bound are nearly identical to the computational models. These hyperstable minibinders provide starting points for SARS-CoV-2 therapeutics.

 

RESEARCH ARTICLE

De novo design of picomolar SARS-CoV-2 miniprotein inhibitors

  1. View ORCID ProfileLongxing Cao1,2
  2. Inna Goreshnik1,2
  3. View ORCID ProfileBrian Coventry1,2,3
  4. View ORCID ProfileJames Brett Case4
  5. View ORCID ProfileLauren Miller1,2
  6. Lisa Kozodoy1,2
  7. Rita E. Chen4,5
  8. View ORCID ProfileLauren Carter1,2
  9. View ORCID ProfileAlexandra C. Walls1
  10. Young-Jun Park1
  11. View ORCID ProfileEva-Maria Strauch6
  12. View ORCID ProfileLance Stewart1,2
  13. View ORCID ProfileMichael S. Diamond4,7
  14. View ORCID ProfileDavid Veesler1
  15. View ORCID ProfileDavid Baker1,2,8,*

See all authors and affiliations

Science  09 Sep 2020:
eabd9909
DOI: 10.1126/science.abd9909

Abstract

Targeting the interaction between the SARS-CoV-2 Spike protein and the human ACE2 receptor is a promising therapeutic strategy. We designed inhibitors using two de novo design approaches. Computer generated scaffolds were either built around an ACE2 helix that interacts with the Spike receptor binding domain (RBD), or docked against the RBD to identify new binding modes, and their amino acid sequences designed to optimize target binding, folding and stability. Ten designs bound the RBD with affinities ranging from 100pM to 10nM, and blocked ARS-CoV-2 infection of Vero E6 cells with IC 50 values between 24 pM and 35 nM; The most potent, with new binding modes, are 56 and 64 residue proteins (IC 50 ~ 0.16 ng/ml). Cryo-electron microscopy structures of these minibinders in complex with the SARS-CoV-2 spike ectodomain trimer with all three RBDs bound are nearly identical to the computational models. These hyperstable minibinders provide starting points for SARS-CoV-2 therapeutics.

 

SARS-CoV-2 infection generally begins in the nasal cavity, with virus replicating there for several days before spreading to the lower respiratory tract (1). Delivery of a high concentration of a viral inhibitor into the nose and into the respiratory system generally might therefore provide prophylactic protection and/or therapeutic benefit for treatment of early infection, and could be particularly useful for healthcare workers and others coming into frequent contact with infected individuals. A number of monoclonal antibodies are in development as systemic treatments for COVID-19 (26), but these proteins are not ideal for intranasal delivery as antibodies are large and often not extremely stable molecules and the density of binding sites is low (two per 150 KDa. antibody); antibody-dependent disease enhancement (79) is also a potential issue. High-affinity Spike protein binders that block the interaction with the human cellular receptor angiotensin-converting enzyme 2 (ACE2) (10) with enhanced stability and smaller sizes to maximize the density of inhibitory domains could have advantages over antibodies for direct delivery into the respiratory system through intranasal administration, nebulization or dry powder aerosol. We found previously that intranasal delivery of small proteins designed to bind tightly to the influenza hemagglutinin can provide both prophylactic and therapeutic protection in rodent models of lethal influenza infection (11).

Design strategy

We set out to design high-affinity protein minibinders to the SARS-CoV-2 Spike RBD that compete with ACE2 binding. We explored two strategies: first we incorporated the alpha-helix from ACE2 which makes the majority of the interactions with the RBD into small designed proteins that make additional interactions with the RBD to attain higher affinity (Fig. 1A). Second, we designed binders completely from scratch without relying on known RBD-binding interactions (Fig. 1B). An advantage of the second approach is that the range of possibilities for design is much larger, and so potentially a greater diversity of high-affinity binding modes can be identified. For the first approach, we used the Rosetta blueprint builder to generate miniproteins which incorporate the ACE2 helix (human ACE2 residues 23 to 46). For the second approach, we used RIF docking (12) and design using large miniprotein libraries (11) to generate binders to distinct regions of the RBD surface surrounding the ACE2 binding site (Fig. 1 and fig. S1).

 

 

 

 

 

 

 

 

 

 

 

Download high-res image

Fig. 1 Overview of the computational design approaches.

(A) Design of helical proteins incorporating ACE2 helix. (B) Large scale de novo design of small helical scaffolds (top) followed by rotamer interaction field (RIF) docking to identify shape and chemically complementary binding modes.

For full article please  go to Science at https://science.sciencemag.org/content/early/2020/09/08/science.abd9909

 

Read Full Post »