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Cited by 5SARS-CoV-2 and COVID-19 ResearchComputational Drug Discovery Methodsvaccines and immunoinformatics approaches

The DOI matches its Crossref record; 92 of the 92 references it cites were found in a registry or an index.

Inhibition of SARS-CoV-2 3CL protease by the anti-viral chimeric protein RetroMAD1

Open access
Chan, Lee-Chin, Mat Yassim, Aini Syahida, Ahmad Fuaad, Abdullah Al Hadi, Leow, Thean Chor, Sabri, Suriana, Radin Yahaya, Radin Shafierul, Abu Bakar, Awang Muhammad Sagaf·2023·Scientific Reports
DOI 10.1038/s41598-023-47511-zPMC PMC10656507

Published version of a preprint

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Abstract

COVID-19 results from SARS-CoV-2, which mutates frequently, challenging current treatments. Therefore, it is critical to develop new therapeutic drugs against this disease. This study explores the interaction between SARS-CoV-2 3CL pro and RetroMAD1, a well-characterized coronavirus protein and potential drug target, using in-silico methods. The analysis through the HDOCK server showed stable complex formation with a binding energy of -12.3, the lowest among reference drugs. The RetroMAD1-3CL pro complex underwent a 100 ns molecular dynamics simulation (MDS) in an explicit solvation system, generating various trajectories, including RMSD, RMSF, hydrogen bonding, radius of gyration, and ligand binding energy. MDS results confirmed intact interactions within the RetroMAD1-3CL pro complex during simulations. In vitro experiments validated RetroMAD1's ability to inhibit 3CL pro enzyme activity and prevent SARS-CoV-2 infection in human bronchial cells. RetroMAD1 exhibited antiviral efficacy comparable to Remdesivir without cytotoxicity at effective concentrations. These results suggest RetroMAD1 as a potential drug candidate against SARS-CoV-2, warranting further in vivo and clinical studies to assess its efficiency.

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Crossref · 10.1038/s41598-023-47511-z

Cites

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Statistics

Figures

Figure 1 3D Structural Model of RetroMAD1. The predicted structure consists of complete domain of Retrocyclin- 101, MAP-30 and Dermaseptin S-1 model.
Figure 1 3D Structural Model of RetroMAD1. The predicted structure consists of complete domain of Retrocyclin- 101, MAP-30 and Dermaseptin S-1 model.CC BY · PubMed Central
Figure 2 Binding of RetroMAD1 with 3CLpro. (A) Structure of SARS-CoV-2 3CLpro monomer (PDB ID 6LU7). (B) Red colour indicates the active site of SARS-CoV-2 3CLpro (Novak et al., 2021). The catalytic dyad, His41 and Cys145 depicted in yellow and dark blue respectively. The binding complex of 3CLpro with (C) RetroMAD1, (D) Andrographolide, (E) Ivermectin and (F) Remdesivir. Figure was made by using Pymol.
Figure 2 Binding of RetroMAD1 with 3CLpro. (A) Structure of SARS-CoV-2 3CLpro monomer (PDB ID 6LU7). (B) Red colour indicates the active site of SARS-CoV-2 3CLpro (Novak et al., 2021). The catalytic dyad, His41 and Cys145 depicted in yellow and dark blue respectively. The binding complex of 3CLpro with (C) RetroMAD1, (D) Andrographolide, (E) Ivermectin and (F) Remdesivir. Figure was made by using Pymol.CC BY · PubMed Central
Figure 3 Initial YASARA MD snapshot, subsequent to YASARA's energy minimization, is depicted in red (0 ns), while the conformation following 100 ns of simulation is illustrated in blue, and the averaged structural snapshots is represented in green. The superimpositions were executed with respect to Domains I and II of the 3CLpro using PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC. It was discerned that interaction regions were consistently preserved throughout the computational simulation period.
Figure 3 Initial YASARA MD snapshot, subsequent to YASARA's energy minimization, is depicted in red (0 ns), while the conformation following 100 ns of simulation is illustrated in blue, and the averaged structural snapshots is represented in green. The superimpositions were executed with respect to Domains I and II of the 3CLpro using PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC. It was discerned that interaction regions were consistently preserved throughout the computational simulation period.CC BY · PubMed Central
Figure 4 The molecular dynamics analysis of the 3CLpro-RetroMAD1 complex over 100 ns simulations. (A) The graph displays the root mean square deviation (RMSD) of the Cα atoms (blue), backbone atoms (red), and average RMSD (green). The trajectory reveals a stable binding interaction throughout the simulation, with fluctuation within permissible limit; (B) The root mean square fluctuation (RMSF) shows the per residue flexibility of 3CLpro (blue) and RetroMAD1 (orange). Minor fluctuations at less 2 Å were observed for the contact residues; (C) RetroMAD1 conformation RMSD change compared to initial binding pose via HDOCK. The ligand shows little variation throughout the simulations; (D) Bound illustration of 3CLpro (orange)-RetroMAD1 (blue) complex. Also highlighted in this cartoon representation in green, representing flexible structure and, in red, the 3CLpro residues bearing less than 5 Å contact distance to RetroMAD1. The insets in Subfigures (B) and (D) show the relationships between the high RMSF residues and the structural locality of the high RMSF regions within the bound structures: Residues 18–35 (α), 280–300 (γ) and 315–335 (δ) of RetroMAD1 and residues 210–280 (β) of 3CLpro display highest flexibility relative to the overall binding dynamics of the complex.
Figure 4 The molecular dynamics analysis of the 3CLpro-RetroMAD1 complex over 100 ns simulations. (A) The graph displays the root mean square deviation (RMSD) of the Cα atoms (blue), backbone atoms (red), and average RMSD (green). The trajectory reveals a stable binding interaction throughout the simulation, with fluctuation within permissible limit; (B) The root mean square fluctuation (RMSF) shows the per residue flexibility of 3CLpro (blue) and RetroMAD1 (orange). Minor fluctuations at less 2 Å were observed for the contact residues; (C) RetroMAD1 conformation RMSD change compared to initial binding pose via HDOCK. The ligand shows little variation throughout the simulations; (D) Bound illustration of 3CLpro (orange)-RetroMAD1 (blue) complex. Also highlighted in this cartoon representation in green, representing flexible structure and, in red, the 3CLpro residues bearing less than 5 Å contact distance to RetroMAD1. The insets in Subfigures (B) and (D) show the relationships between the high RMSF residues and the structural locality of the high RMSF regions within the bound structures: Residues 18–35 (α), 280–300 (γ) and 315–335 (δ) of RetroMAD1 and residues 210–280 (β) of 3CLpro display highest flexibility relative to the overall binding dynamics of the complex.CC BY · PubMed Central
Figure 5 Analysis of interaction via hydrogen bonding counts and radius of gyration. (A) The hydrogen bonding is categorized as follows: intrinsic molecular hydrogen bonds are denoted in blue, bonds formed with the adjacent 3CLpro are in green, and those engaged with the aqueous environment are represented in red. Cumulative hydrogen bonds is depicted in gray. (B) The radius of gyration of RetroMAD1-3CLpro complex corresponds to 100 ns molecular dynamics simulation at 298 K.
Figure 5 Analysis of interaction via hydrogen bonding counts and radius of gyration. (A) The hydrogen bonding is categorized as follows: intrinsic molecular hydrogen bonds are denoted in blue, bonds formed with the adjacent 3CLpro are in green, and those engaged with the aqueous environment are represented in red. Cumulative hydrogen bonds is depicted in gray. (B) The radius of gyration of RetroMAD1-3CLpro complex corresponds to 100 ns molecular dynamics simulation at 298 K.CC BY · PubMed Central
Figure 6 Concentration–response curve for determining the half-maximal inhibitory concentration (IC50) of RetroMAD1 against 3CL protease enzyme activity, assayed using the Untagged 3CL Protease (SARS-CoV-2) Assay Kit (BPS Bioscience #78,042). The calculated IC50 value for RetroMAD1, inhibiting 3CLpro activity, was found to be 86.89 μg/mL.
Figure 6 Concentration–response curve for determining the half-maximal inhibitory concentration (IC50) of RetroMAD1 against 3CL protease enzyme activity, assayed using the Untagged 3CL Protease (SARS-CoV-2) Assay Kit (BPS Bioscience #78,042). The calculated IC50 value for RetroMAD1, inhibiting 3CLpro activity, was found to be 86.89 μg/mL.CC BY · PubMed Central

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Citations

Cites

Research works printed but not linked: 1

  1. Satpathy, R. In silico prediction of anti–SARS-CoV-2 effect of dermaseptin peptides from amphibian origin. Trends Peptide Protein Sci. 5, 1–9 (2020).

Metadata

Authors
Chan, L.-C., Mat Yassim, A. S., Ahmad Fuaad, A. A. H., Leow, T. C., Sabri, S., Radin Yahaya, R. S., & Abu Bakar, A. M. S.
Affiliations
Universiti Putra Malaysia (MY)
ORCID
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2023-11-17
Volume
13
Issue
1
Pages
20178-20178
ISSN
2045-2322 (ISSN-L)
DOI
10.1038/s41598-023-47511-z
PMC
PMC10656507
OpenAlex
W4388751591
Cited by
5
References
92
Citations by year
2026: 1 · 2025: 1 · 2024: 3
FWCI
1.03
Type
journal article
Language
en
Open access
Licence
Locations
  • Scientific Reports (publishedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Universiti Putra Malaysia Institutional Repository (Universiti Putra Malaysia) (submittedVersion, cc-by)
  • Greater South Information System
Funders
Utah State University
Topics
  • Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
  • Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
Keywords
SARS-CoV-2, COVID-19 pandemic, main protease, main protease inhibition, fusion protein, antiviral drug candidates, protein-protein complex stability, molecular dynamics simulation, human bronchial epithelial cells, cytotoxicity
MeSH terms
COVID-19, SARS-CoV-2, Antiviral Agents, Cysteine Endopeptidases, Humans, Peptide Hydrolases, Protease Inhibitors, Recombinant Fusion Proteins, Viral Nonstructural Proteins

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