Novel anti-SARS-CoV-2 mechanisms of fusion broad range anti- infective protein ricin A chain mutant-pokeweed antiviral protein 1 (RTAM-PAP1) in silico

10.21203/rs.3.rs-32952/v2 ◽

2020 ◽

Author(s):

Yasser Hassan ◽

Sherry Ogg ◽

Hui Ge

Keyword(s):

In Silico ◽

Protein Structures ◽

Ligand Docking ◽

Pokeweed Antiviral Protein ◽

Antiviral Protein ◽

Ricin A Chain ◽

High Affinity ◽

A Chain ◽

Binding Mechanisms ◽

Ricin A

Abstract A deadly pandemic named COVID-19 caused by a new coronavirus SARS- CoV-2 has emerged in 2019 and is still spreading globally at a dangerous pace. As of today, there are no proven vaccines, therapies or even strategies to fight off this virus. Here, we describe the in silico results of a novel broad range anti-infective fusion protein RTAM-PAP1 against the various key pro- teins of SARS-CoV-2 using the latest protein-ligand docking software. RTAM-PAP1 was compared against the SARS-CoV-2 B38 antibody, ricin A chain, pokeweed antiviral protein from leaves and the lectin griffithsin using CoDockPP special COVID-19 version. These experiments revealed novel binding mechanisms of RTAM-PAP1 with high affinity to numerous targets with anti-SARS-CoV-2 effects. RTAM-PAP1 was further characterized in a preliminary toxicity study in mice and was found to likely be a potent anti- SARS-CoV-2 agent. These findings might lead to the discovery of novel SARS-CoV-2 targets and therapeutic protein structures.

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Novel Binding Mechanisms of Fusion Broad Range Anti-Infective Protein Ricin A Chain Mutant-Pokeweed Antiviral Protein 1 (RTAM-PAP1) against SARS-CoV-2 Key Proteins in Silico

Toxins ◽

10.3390/toxins12090602 ◽

2020 ◽

Vol 12 (9) ◽

pp. 602

Author(s):

Yasser Hassan ◽

Sherry Ogg ◽

Hui Ge

Keyword(s):

In Silico ◽

Protein Structures ◽

Ligand Docking ◽

Pokeweed Antiviral Protein ◽

Antiviral Protein ◽

Ricin A Chain ◽

In Silico Docking ◽

A Chain ◽

Binding Mechanisms ◽

Ricin A

The deadly pandemic named COVID-19, caused by a new coronavirus (SARS-CoV-2), emerged in 2019 and is still spreading globally at a dangerous pace. As of today, there are no proven vaccines, therapies, or even strategies to fight off this virus. Here, we describe the in silico docking results of a novel broad range anti-infective fusion protein RTAM-PAP1 against the various key proteins of SARS-CoV-2 using the latest protein-ligand docking software. RTAM-PAP1 was compared against the SARS-CoV-2 B38 antibody, ricin A chain, a pokeweed antiviral protein from leaves, and the lectin griffithsin using the special CoDockPP COVID-19 version. These experiments revealed novel binding mechanisms of RTAM-PAP1 with a high affinity to numerous SARS-CoV-2 key proteins. RTAM-PAP1 was further characterized in a preliminary toxicity study in mice and was found to be a potential therapeutic candidate. These findings might lead to the discovery of novel SARS-CoV-2 targets and therapeutic protein structures with outstanding functions.

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Major Structural Differences between Pokeweed Antiviral Protein and Ricin A-Chain do not Account for their Differing Ribosome Specificity

European Journal of Biochemistry ◽

10.1111/j.1432-1033.1996.00159.x ◽

1996 ◽

Vol 235 (1-2) ◽

pp. 159-166 ◽

Cited By ~ 20

Author(s):

John A. Chaddock ◽

Arthur F. Monzingo ◽

Jon D. Robertus ◽

J. Michael Lord ◽

Lynne M. Roberts

Keyword(s):

Pokeweed Antiviral Protein ◽

Antiviral Protein ◽

Ricin A Chain ◽

Structural Differences ◽

A Chain ◽

Ricin A

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The Action of Pokeweed Antiviral Protein and Ricin A-chain on Mutants in the α-Sarcin Loop ofEscherichia coli23S Ribosomal RNA

Journal of Molecular Biology ◽

10.1006/jmbi.1995.0660 ◽

1995 ◽

Vol 254 (5) ◽

pp. 848-855 ◽

Cited By ~ 21

Author(s):

Alan Marchant ◽

Martin R. Hartley

Keyword(s):

Ribosomal Rna ◽

Pokeweed Antiviral Protein ◽

Antiviral Protein ◽

Ricin A Chain ◽

A Chain ◽

Ricin A

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Post-Infection Entry Mechanism of Ricin A Chain-Pokeweed Antiviral Proteins (RTA-PAPs) Chimeras is Mediated by Viroporins

10.1101/2021.06.17.448882 ◽

2021 ◽

Author(s):

Yasser Hassan

Keyword(s):

Post Infection ◽

Chimeric Protein ◽

Ligand Docking ◽

Host Cell Membrane ◽

Ricin A Chain ◽

Infected Cells ◽

Antiviral Proteins ◽

A Chain ◽

Ricin A

The limitations of virus-specific antiviral drugs became apparent during the current COVID-19 pandemic. The search for broad range antiviral proteins of a new kind to answer current and future pandemics has become an even more pressing matter. Here, the author further describes the expected anti-SARS-CoV-2 mechanisms of a novel broad range antiviral chimeric protein constructed between ricin A chain and pokeweed antiviral proteins. The latest in protein-ligand docking software were used to determine binding affinity of RTA-PAPs to SARS-CoV-2 frameshift stimulation element and elucidate the preferential post-infection entry mechanisms of RTA-PAPs into virus infected cells over non-infected ones, by doing a comparative analysis between in vitro and in silico results on numerous viruses. The results obtained strongly suggest that the post-infection preferential entry of RTA-PAPs into infected cells is mediated by the presence of viroporins integrated into the host cell membrane. The discovery of this mechanism revealed RTA-PAPs, and proteins like them, to be a new class of broad range antivirals that target with high specificity viroporin producing viruses, and with gain of functions in antiviral activities, post-infection.

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Gene cloning and construction of prokaryotic and plant expression vectors of RICIN-A-Chain/PAP-S1 fusion protein and its inhibition of protein synthesis

10.1101/046060 ◽

2016 ◽

Cited By ~ 3

Author(s):

Yasser S. Hassan ◽

Sherry L. Ogg

Keyword(s):

Fusion Protein ◽

Expression Vectors ◽

Single Chain ◽

Antiviral Protein ◽

Ricin A Chain ◽

C Terminus ◽

N Terminus ◽

A Cell ◽

A Chain ◽

Ricin A

AbstractPokeweed antiviral protein (PAP) is a single-chain ribosome-inactivating protein that exists in several forms isolated from various organs and at different stages of development of Phytolacca americana (pokeweed). In this study, PAP-S1, one of the two known isoforms found in seeds, was isolated and PCR amplified using primers based on the known mRNA of PAP-S2, the other known form found in seeds. The complete cDNA encoding PAP-S1 was determined here for the first time. PAP-S1 is a potent antiviral protein with many potential clinical applications. However, it was found to be dosage dependent with observed side effects at high dosage. In this study, we report the production of a recombinant antiviral peptide-fusion protein between Ricin A-chain and PAP-S1. The peptide-fusion recombinant proteins Ricin-A-Chain/PAP-S1 and PAP-S1/Ricin-A-Chain were generated by joining the Nterminus of PAP-S1 to the C-terminus of Ricin A-chain and the C-terminus of PAP-S1 to the N-terminus of Ricin A-chain respectively, and were expressed in an Escherichia coli cell free expression systems. The peptide-fusion recombinant protein Ricin-A-Chain/PAP-S1 (F2) was found to be more active than the PAPS1/Ricin-A-chain (F1) and similar to PAP-S1 in a cell free prokaryotic environment, and both showed much stronger activity in a cell free eukaryotic environment. The DNA sequence of the complete cDNA of PAP-S1 and of the peptide-fusion protein Ricin-A-Chain/PAP-S1 with the PAP-S1 signal peptide at the N-terminus of Ricin Achain were inserted in plant destination binary vectors for A. tumefaciens mediated transformation. It is the authors’ opinion that additional research should be done in order to determine both cytotoxicity and selectivity of fusion protein F2 compared to PAP-S1, as it could be a viable, more potent and less cytotoxic alternative to PAPS1 alone at high dosage, for both agricultural and therapeutic applications.

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