1
|
Valiente P, Nim S, Lee J, Kim S, Kim PM. Targeting the Receptor-Binding Motif of SARS-CoV-2 with D-Peptides Mimicking the ACE2 Binding Helix: Lessons for Inhibiting Omicron and Future Variants of Concern. J Chem Inf Model 2022; 62:3618-3626. [PMID: 35875887 PMCID: PMC9344788 DOI: 10.1021/acs.jcim.2c00500] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 11/30/2022]
Abstract
The COVID-19 pandemic continues to spread around the world, with several new variants emerging, particularly those of concern (VOCs). Omicron (B.1.1.529), a recent VOC with many mutations in the spike protein's receptor-binding domain (RBD), has attracted a great deal of scientific and public interest. We previously developed two D-peptide inhibitors for the infection of the original SARS-CoV-2 and its VOCs, alpha and beta, in vitro. Here, we demonstrated that Covid3 and Covid_extended_1 maintained their high-affinity binding (29.4-31.3 nM) to the omicron RBD. Both D-peptides blocked the omicron variant in vitro infection with IC50s of 3.13 and 5.56 μM, respectively. We predicted that Covid3 shares a larger overlapping binding region with the ACE2 binding motif than different classes of neutralizing monoclonal antibodies. We envisioned the design of D-peptide inhibitors targeting the receptor-binding motif as the most promising approach for inhibiting current and future VOCs of SARS-CoV-2, given that the ACE2 binding interface is more limited to tolerate mutations than most of the RBD's surface.
Collapse
Affiliation(s)
- Pedro
A. Valiente
- Donnelly
Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Satra Nim
- Donnelly
Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - JinAh Lee
- Zoonotic
Virus Laboratory, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil
Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
| | - Seungtaek Kim
- Zoonotic
Virus Laboratory, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 beon-gil
Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
| | - Philip M. Kim
- Donnelly
Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department
of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department
of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| |
Collapse
|
2
|
Valiente PA, Wen H, Nim S, Lee J, Kim HJ, Kim J, Perez-Riba A, Paudel YP, Hwang I, Kim KD, Kim S, Kim PM. Computational Design of Potent D-Peptide Inhibitors of SARS-CoV-2. J Med Chem 2021; 64:14955-14967. [PMID: 34624194 PMCID: PMC8525337 DOI: 10.1021/acs.jmedchem.1c00655] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Indexed: 12/28/2022]
Abstract
Blocking the association between the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein receptor-binding domain (RBD) and the human angiotensin-converting enzyme 2 (ACE2) is an attractive therapeutic approach to prevent the virus from entering human cells. While antibodies and other modalities have been developed to this end, d-amino acid peptides offer unique advantages, including serum stability, low immunogenicity, and low cost of production. Here, we designed potent novel D-peptide inhibitors that mimic the ACE2 α1-binding helix by searching a mirror-image version of the PDB. The two best designs bound the RBD with affinities of 29 and 31 nM and blocked the infection of Vero cells by SARS-CoV-2 with IC50 values of 5.76 and 6.56 μM, respectively. Notably, both D-peptides neutralized with a similar potency the infection of two variants of concern: B.1.1.7 and B.1.351 in vitro. These potent D-peptide inhibitors are promising lead candidates for developing SARS-CoV-2 prophylactic or therapeutic treatments.
Collapse
Affiliation(s)
- Pedro A. Valiente
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, Toronto, Ontario M5S 3E1,
Canada
| | - Han Wen
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, Toronto, Ontario M5S 3E1,
Canada
| | - Satra Nim
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, Toronto, Ontario M5S 3E1,
Canada
| | - JinAh Lee
- Zoonotic Virus Laboratory, Institut
Pasteur Korea, 16, Daewangpangyo-ro 712 Beon-gil Bundang-gu, Seongnam-si,
Gyeonggi-do 13488, Republic of Korea
| | - Hyeon Ju Kim
- Zoonotic Virus Laboratory, Institut
Pasteur Korea, 16, Daewangpangyo-ro 712 Beon-gil Bundang-gu, Seongnam-si,
Gyeonggi-do 13488, Republic of Korea
| | - Jinhee Kim
- Zoonotic Virus Laboratory, Institut
Pasteur Korea, 16, Daewangpangyo-ro 712 Beon-gil Bundang-gu, Seongnam-si,
Gyeonggi-do 13488, Republic of Korea
| | - Albert Perez-Riba
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, Toronto, Ontario M5S 3E1,
Canada
| | - Yagya Prasad Paudel
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, Toronto, Ontario M5S 3E1,
Canada
| | - Insu Hwang
- Center for Convergent Research of Emerging Virus
Infection, Korea Research Institute of Chemical Technology,
Daejeon 34114, Republic of Korea
| | - Kyun-Do Kim
- Center for Convergent Research of Emerging Virus
Infection, Korea Research Institute of Chemical Technology,
Daejeon 34114, Republic of Korea
| | - Seungtaek Kim
- Zoonotic Virus Laboratory, Institut
Pasteur Korea, 16, Daewangpangyo-ro 712 Beon-gil Bundang-gu, Seongnam-si,
Gyeonggi-do 13488, Republic of Korea
| | - Philip M. Kim
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, Toronto, Ontario M5S 3E1,
Canada
- Department of Molecular Genetics,
University of Toronto, Toronto, Ontario M5S 3E1,
Canada
- Department of Computer Science,
University of Toronto, Toronto, Ontario M5S 3E1,
Canada
| |
Collapse
|
3
|
Maity A, Choudhury AR, Chakrabarti R. Effect of Stapling on the Thermodynamics of mdm2-p53 Binding. J Chem Inf Model 2021; 61:1989-2000. [PMID: 33830760 DOI: 10.1021/acs.jcim.1c00219] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein-protein interaction (PPI) is one of the key regulatory features driving biomolecular processes and hence is targeted for designing therapeutics against diseases. Small peptides are a new and emerging class of therapeutics owing to their high specificity and low toxicity. For achieving efficient targeting of the PPI, amino acid side chains are often stapled together, resulting in the rigidification of these peptides. Exploring the scope of these peptides demands a comprehensive understanding of their working principle. In this work, two stapled p53 peptides have been considered to delineate their binding mechanism with mdm2 using computational approaches. The addition of stapling agent protects the secondary structure of the peptides even in the case of thermal and chemical denaturation. Although the introduction of a stapling agent increases the hydrophobicity of the peptide, the enthalpic stabilization decreases. This is overcome by the lowering of the entropic penalty, and the overall binding affinity improves. The mechanistic insights into the benefit of peptide stapling can be adopted for further improvement of peptide therapeutics.
Collapse
Affiliation(s)
- Atanu Maity
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Asha Rani Choudhury
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| |
Collapse
|
4
|
Bluntzer MTJ, O'Connell J, Baker TS, Michel J, Hulme AN. Designing stapled peptides to inhibit
protein‐protein
interactions: An analysis of successes in a rapidly changing field. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24191] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | | | - Julien Michel
- EaStChem School of Chemistry The University of Edinburgh Edinburgh UK
| | - Alison N. Hulme
- EaStChem School of Chemistry The University of Edinburgh Edinburgh UK
| |
Collapse
|