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

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Anti-viral chimeric protein RetroMAD1™ potently block SARS-CoV-2 viral entry and propagation

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Chan, Lee-Chin, Yassim, Aini Syahida Mat, Leow, Thean Chor, Sabri, Suriana, Yahaya, Radin Shafierul Radin, Bakar, Awang Muhammad Sagaf Abu·2023·Scientific Reports
DOI 10.21203/rs.3.rs-2712307/v1PMC PMC10656507

Preprint — published as 10.1038/s41598-023-47511-z · Paper page

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Abstract

COVID-19 is a disease caused by the highly transmissible and pathogenic SARS-CoV-2 virus. Since its first case was documented in 2019, it has rapidly widespread and has caused millions of deaths worldwide. Many intervention strategies targeting these proteins have been developed. However, frequently mutation of SARS-CoV-2 poses a challenge to the effectiveness of current treatments. Therefore, it is critical to develop new therapeutic drugs against this disease. In this present study, in silico approach was used to study the interaction between RetroMAD1™and SARS-CoV-2 proteins including Spike proteins (S), 3-chymotrypsin-like protease (3CL pro) and papain-like protease (PL pro). The interaction of these viral proteins and RetroMAD1™ was performed through HDOCK server and visualised using PyMOL. Docking results revealed that all the complexes of SARS-CoV-2 proteins binding with RetroMAD1™ have relatively high docking scores. The binding energy of RetroMAD1™ complexes with SARS-CoV-2 S, 3CL pro, PL pro were − 15, -12.3 and − 15.4, respectively. RetroMAD1™antiviral efficiency and cytotoxicity was also evaluated using EpiAirway™ Model. In vitro validation of viral inhibitory effect of RetroMAD1™was performed with 3CL pro Inhibition Assay. The outcome showed that RetroMAD1™ represents a potential drug candidate against SARS-CoV-2 for its promising viral inhibitory effect.

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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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Metadata

Authors
Chan, L.-C., Yassim, A. S. M., Leow, T. C., Sabri, S., Yahaya, R. S. R., & Bakar, A. M. S. A.
Affiliations
  • Biovalence Sdn. Bhd.
  • Universiti Sains Malaysia (MY)
  • Universiti Putra Malaysia (MY)
  • Jabatan Perkhidmatan Veterinar (MY)
Corresponding author
  • Yassim, Aini Syahida Mat
  • Bakar, Awang Muhammad Sagaf Abu
ORCID
Venue
Scientific Reports
Publisher
Research Square Platform LLC
Published
2023-04-05
Volume
13
Issue
1
Pages
20178-20178
ISSN
2045-2322 (ISSN-L)
DOI
10.21203/rs.3.rs-2712307/v1
PMC
PMC10656507
OpenAlex
W4388751591
Cited by
5
References
1
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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CoChat. (2026). Citation check: Anti-viral chimeric protein RetroMAD1™ potently block SARS-CoV-2 viral entry and propagation. https://app.cochat.ai/papers/10.21203/rs.3.rs-2712307/v1
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Chan, L.-C., Yassim, A. S. M., Leow, T. C., Sabri, S., Yahaya, R. S. R., & Bakar, A. M. S. A. (2023). Anti-viral chimeric protein RetroMAD1™ potently block SARS-CoV-2 viral entry and propagation. Scientific Reports. https://doi.org/10.21203/rs.3.rs-2712307/v1

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