CASE STUDY 2 by Ahmad Hamidin https://padlet.com/ahmadhamidin09/Bookmarks Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants en-us 2022-06-01 02:46:35 UTC 2022-06-01 04:27:44 UTC hello@padlet.com 1. What questions do I hope this article will answer? ahmadhamidin09 https://padlet.com/ahmadhamidin09/Bookmarks/wish/2206903138 1. What are potential compounds that can be anti-viral for COVID-19?
2. Is the compound found effective in inhibiting the Covid-19 virus?
3. Why not use the same drugs that be used for SARS & MERS to treat covid-19?

]]> 2022-06-01 02:53:24 UTC https://padlet.com/ahmadhamidin09/Bookmarks/wish/2206903138 2. What do the authors conclude? ahmadhamidin09 https://padlet.com/ahmadhamidin09/Bookmarks/wish/2206903517 1. 3CLpro is an enzyme that controls coronavirus replication and conserved in SARS-CoV-2.

2. 3CLpro enzyme in SARS-CoV-2 is highly similar to bat SARS-like coronavirus 3CLpro with some differences from other beta-coronavirus.

3. The authors predicted the 3D structure of SARS-CoV-2 3CLpro enzyme through comparative modelling.

4. The authors had selected top nine compounds from 32,297 that was screened from a medicinal plant database that inhibits SARS-CoV-2 3CLpro enzyme activity and replication. Isoflavone was selected as the best compound for inhibition.]]> 2022-06-01 02:53:47 UTC https://padlet.com/ahmadhamidin09/Bookmarks/wish/2206903517 3. What date/results emerged from the study? ahmadhamidin09 https://padlet.com/ahmadhamidin09/Bookmarks/wish/2206903883 9 potential compound was found from medicinal plant database and isoflavone is the best compound after molecular docking with the highest binding affinity.]]> 2022-06-01 02:54:06 UTC https://padlet.com/ahmadhamidin09/Bookmarks/wish/2206903883 4. How did the authors do this study? ahmadhamidin09 https://padlet.com/ahmadhamidin09/Bookmarks/wish/2206904118 1) Data Collection
- collect from GISAID database
- Gene sequences of 3CLpro were extracted from the
whole-genome sequences and translated into protein sequences using the translate tool of the ExPASy server

2) Sequence Analyses
- using T-Coffee to analyze phylogenetic tree
- alignment figure was generated using ESPript3
- analyze physicochemical parameters of SARS-CoV-2 3CLpro using ProtParam tool of ExPASy

3) Structural Analyses
- To probe the molecular architecture of SARS-CoV-2 3CLpro, comparative homology modelling was performed 
using Modeller v9.11
- initial quality estimation, energy minimisation, mutation analyses, and image processing using Chimera v1.8.1 and PyMOL educational version.

4) Ligand database preparation and molecular docking
- potential anti-viral phytochemicals and traditional Chinese medicinal compounds was generated from multiple databases (pubchem)
- screened against the predicted SARS-CoV-2 3CLpro structure. Molecular operating environment (MOE) was used for molecular docking, ligand-protein interaction and drug likeness analyses
- The qualitative assessment of absorption, deposition, metabolism, excretion and toxicity (ADMET) profile of selected hits were predicted computationally by using ADMETsar server

5) Molecular Dynamic Stimulation
- to verify docking results and to analyse the binding
behaviour and stability of potential compounds using the predicted SARS-CoV-2 3CLpro homology model

]]> 2022-06-01 02:54:20 UTC https://padlet.com/ahmadhamidin09/Bookmarks/wish/2206904118 5. What is the significance of these findings? ahmadhamidin09 https://padlet.com/ahmadhamidin09/Bookmarks/wish/2206904330 1. Novel compound for further R&D for anti-viral covid-19

2. Whole-genome sequence has helped researchers to identify virus in patients using reverse-transcription polymerase chain reaction method (PCR).

3. To know which group the pathogen belongs to. (in this article, beta-coronavirus group)

4. To identify the protein drug target which is  3-chymotrypsin-like cysteine protease (3CLpro) enzyme.

5. To know the replication process of SARS-Cov-2. (cleaving process)]]> 2022-06-01 02:54:34 UTC https://padlet.com/ahmadhamidin09/Bookmarks/wish/2206904330 6. List of other articles cited here that I should read. ahmadhamidin09 https://padlet.com/ahmadhamidin09/Bookmarks/wish/2206904496 1.  T-coffee: a novel method for fast and accurate multiple sequence alignment1
https://doi.org/10.1006/jmbi.2000.4042

2. ESPript: Analysis of multiple sequence alignments in PostScript
10.1093/bioinformatics/15.4.305
]]> 2022-06-01 02:54:47 UTC https://padlet.com/ahmadhamidin09/Bookmarks/wish/2206904496