Phycobilins as potent food bioactive broad-spectrum inhibitor compounds against M pro and PL pro of SARS-CoV-2 and other coronaviruses: A preliminary Study
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Abstract
In the twenty first century, we have witnessed three corona virus outbreaks; SARS in 2003, MERS in 2012 and ongoing pandemic COVID-19. To prevent outbreaks by novel mutant strains, we need broad-spectrum antiviral agents that are effective against wide array of coronaviruses. In this study, we scientifically investigated potent food bioactive broad-spectrum antiviral compounds by targeting M pro and PL pro proteases of CoVs using in silico and in vitro approaches. The results revealed that phycocyanobilin (PCB) showed potential inhibitor activity against both proteases. PCB had best binding affinity to M pro and PL pro with IC 50 values of 71 μm and 62 μm, respectively. In addition, in silico studies of M pro and PL pro enzymes of other human and animal CoVs indicated broad spectrum inhibitor activity of the PCB. Like PCB, other phycobilins such as phycourobilin (PUB), Phycoerythrobilin (PEB) and Phycoviolobilin (PVB) showed similar binding affinity to SARS-CoV-2 M pro and PL pro
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SciScore for 10.1101/2020.11.21.392605: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Due to limitation on availability of crystal PDB structures of PLpro, both dimer and monomeric forms were used in docking studies. For Mpro, docking scores are in the range of −8.3 to −9.3 K.cal/mol. PCB showed higher binding …
SciScore for 10.1101/2020.11.21.392605: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
No key resources detected.
Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Due to limitation on availability of crystal PDB structures of PLpro, both dimer and monomeric forms were used in docking studies. For Mpro, docking scores are in the range of −8.3 to −9.3 K.cal/mol. PCB showed higher binding affinity with docking score (−9.3 K.cal/mol) for MERS Mpro followed by HCoV NL63 (−9.0 K.cal/mol) and IBV (−8.9 K.cal/mol). For PLpro, docking scores were in the range of −8.9 to −7.6 K.cal/mol. The results revealed that PCB had higher binding affinity to dimer form of PLpro enzymes than monomeric forms. When compared monomers only, PCB had best docking score for MERS-CoV (−8.5 K.cal/mol) followed by TGEV (−8.1 K.cal/mol) and SARS-CoV-2 (−8.0 K.cal/mol). Figure S2 and S3 show polar contacts of PCB with binding pocket key amino acid residues of Mpro and PLpro enzymes of human and animal CoVs. Surprisingly the docking results suggest PCB as a promising broad-spectrum food bioactive inhibitor compound against CoVs proteases. The computed physical properties of phycocyanobilin show rotatable bond count of 10, hydrogen bond donor count of 5 and hydrogen bond acceptor count of 7 (NCBI, 2020), which makes multiple hydrogen bond interactions between the compound and specific amino acid residues located at the active site of the pocket of the protease enzymes. Molecular docking studies indicated that propionic carboxyl and lactam ring carbonyl oxygens of PCB are involved in polar interactions with aminoacid residues of proteases. 3.4 Inhibitor activities of other...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
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