In Silico Screening of Bioactive Compounds from Garcinia mangostana L. Against SARS-CoV-2 via Tetra Inhibitors

The global COVID-19 pandemic caused by SARS-CoV-2 has been the resulted of massive human deaths since early 2020. The purpose of this study was to determine the potential of mangosteen (Garcinia mangostana L.) as an inhibitor of RBD spike, helicase, Mpro, and RdRp activity of SARS-CoV-2 with an in silico approach. The samples were obtained from PubChem and RCSB PDB. Analysis of the similarity of the drug was carried out with the Swiss ADME on the basis of Lipinski rule of five. Prediction of antivirus probabilities was carried out using PASS Online. Molecular screening was performed using PyRx through molecular docking. Discovery Studio was used for visualization. The bioactive compounds with the highest antiviral potential were indicated with the lowest binding affinity to the targeted proteins RBD spike, helicase, Mpro, and RdRp of SARS-CoV-2. The results indicated that mangiferin has the greatest potential as a potential antiviral. However, more research is required to validate the results of these computational predictions. Copyright © 2022 Phcogj.Com.

Bioactive Compounds from Purslane (Portulaca oleracea L.) and Star Anise (Illicium verum Hook) as SARS-CoV-2 Antiviral Agent via Dual Inhibitor Mechanism: In Silico Approach

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the COVID-19 pandemic that infects humans and attacks the body's immune system. The purpose of the study was to identify the potential of bioactive compounds in purslane (Portulaca oleracea L.) and star anise (Illicium verum Hook) via a dual inhibitor mechanism against SARS-CoV-2 proteases with an in silico approach. The samples were obtained from PubChem and RSCB PDB. Antivirus probability prediction was performed on PASS Online. Virtual screening was performed with PyRx via molecular docking. Visualization was used by PyMol and Discovery Studio. Compounds with the best antiviral potential are indicated by the low binding affinity value to the target proteins, namely SARS-CoV-2 TMPRSS2 and PLpro. The results showed that purslane luteolin has the best antiviral potential. However, further studies are required to validate this computational prediction. © 2022 Phcogj.Com.

In Silico Screening of Bioactive Compounds from Syzygium cumini L. and Moringa oleifera L. Against SARS-CoV-2 via Tetra Inhibitors

The global pandemic of COVID-19 has caused disastrous consequences for both humans and the economy. The purpose of this study was to determine the potential of juwet (Syzygium cumini L.) and moringa (Moringa oleifera L.) as inhibitors of RBD spike, helicase, Mpro, and RdRp activity of SARS-CoV-2 with an in-silico approach. Samples were obtained from PubChem and RSCB PDB databases. The drug similarity analysis was determined using Swiss ADME and the Lipinski rule of five. Prediction of antivirus probabilities is carried out with PASS Online. Molecular screening is performed by molecular docking using PyRx. Visualization was used using PyMol and Discovery Studio. The bioactive compounds with the best antiviral potential had the lowest affinity bonds to the target proteins against RBD spike, helicase, Mpro, and RdRp of SARS-CoV-2. Results show that ellagic acid from java plum and myricetin from moringa have the best potential as potential antivirals. However, more research is required to validate the results of these computational predictions.

In Silico Phytochemical Compounds Screening of Allium sativum Targeting the Mpro of SARS-CoV-2

The global pandemic of coronavirus disease is still widely spread across the world causing catastrophic effect in both human life and global economy. By the end of year 2021, it has caused a total of 5.437.636 deaths across the world. Indonesia has rich plant biodiversity including medicinal plants that may be used for combating the virus. One of the commonly used medicinal plants comes from Allium species and it has been proved to have antiviral activity. Conducting an in silico study, we screened bioactive compounds that came from Allium sativum to fight against coronavirus through the inhibition of 3CL-Pro, one of the major protease that have an active role for viral replication. Molecular docking of compounds from Allium sativum to 3CL-Pro resulting in the discovery of 5 compounds that have the best binding affinity to 3CL-Pro, which are squalene, 1,4-dihydro-2,3-benzoxathiin 3-oxide, 1,2,3-propanetriyl ester, trans-13-octadecenoic acid and methyl-11-hexadecenoate with binding affinity of -7, -6.5, -5.9, -5.7 and -5.6 kcal/mol, respectively. It is very likely that these compounds can be candidates for therapeutic agents and these candidates need to be studied further.

Bioactive compounds from mangosteen (Garcinia mangostana L.) as an antiviral agent via dual inhibitor mechanism against SARSCoV- 2: an in silico approach

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes COVID-19 which is responsible for respiratory illness infection in humans. The virus was first identified in China in 2019 and later spread to other countries worldwide. This study aims to identify the bioactive compounds from mangosteen (Garcinia mangostana L.) as an antiviral agent via dual inhibitor mechanisms against two SARS-CoV-2 proteases through the in silico approach. The three-dimensional structure of various bioactive compounds of mangosteen from the database was examined. Furthermore, all the target compounds were analyzed for drug, antiviral activity prediction, virtual screening, molecular interactions, and threedimensional structure visualization. It aimed to determine the potential of the bioactive compounds from mangosteen that can serve as antiviral agents to fight SARS-CoV-2. Results showed that the bioactive compounds from mangosteen have the prospective to provide antiviral agents that contradict the virus via dual inhibitory mechanisms. In summary, the binding of the various bioactive compounds from mangosteen results in low binding energy and is expected to have the ability to induce any activity of the target protein binding reaction. Therefore, it allows various bioactive compounds from mangosteen to act as dual inhibitory mechanisms for COVID-19 infection.

Anti-inflammatory potential of λ-carrageenan by inhibition of IL-6 receptor: in silico study

In some cases, the immune system in COVID-19 patients leads to the release of excess cytokine production (cytokine storm), which will potentially develop into pneumonia. Interleukin 6 (IL-6) plays the role of pro-inflammatory cytokine, it is a receptor mediated signalling system. Macroalgae is well known as a source of valuable bioactive substances with potential biological activities. Among them is the sulphated polysaccharide lambda-carrageenan λ-CGN which has been reported as an anti-inflammatory agent. However, its mechanism of action against IL-6 production is currently unknown. This study aims to predict potential molecular mechanisms of λ-CGN chemical compound against IL-6 expression through in silico study. Chemical compound of λ-CGN and target protein in this study were obtained from the pubchem and protein data bank (PDB). The molecular docking prediction was conducted with PyRx software, the result is λ-CGN compound showing strong binding energy to bind target protein IL-6 receptor with the value of -5.9 kcal/mol. Based on the results of in silico study, the sulphated polysaccharide λ-CGN potentially inhibits IL-6R expression by binding ligand pocket with six conventional hydrogen bonds (amino acid residus: His256, His 257, Trp 219, Arg 231, and Asp 221) and two carbon hydrogen bonds (amino acid residus: THR 218 and GLN 220). Binding with these amino acid residues potentially contributes to IL-6 receptor structural change which could result in functional change. Hence, further studies related to in vitro and in vivo investigations would be interesting to further understand the inhibitory mechanism of λ-CGN against IL-6.

Potential vaccine targets for COVID-19 and phylogenetic analysis based on the nucleocapsid phosphoprotein of Indonesian SARS-CoV-2 isolates

Recently, the world is facing outbreaks of severe acute respiratory syndrome coronavirus 2 or SARS-CoV-2 and the number of infected patients is increasing every day. Researchers are doing their best to find the most effective treatment to tackle this deathly virus. Several approaches had been proposed to be tested in the lab for efficacy but none of them are qualified to be used as the treatment of the COVID-19. Therefore, this study aimed to design a vaccine based on epitope, which was obtained from the nucleocapsid phosphoprotein (N protein). 38 samples of SARS-CoV-2 isolates were retrieved from the GISAID Database and NCBI GenBank. These samples were used to check the evolutionary relationship of the SARS-CoV-2 and determine whether these nucleocapsid proteins are well-conserved with less or even no mutations occur at all, and whether there was any evolutionary relationship between the recent coronavirus with the previous coronavirus by conducting the phylogenetic analysis. Then, it is desirable to see the molecular interaction between the human BCR/FAB receptor with the predicted peptides through the molecular docking process. All of the peptides were generated by the IEDB analysis tools and have already been tested for antigenicity, so the one that was being docked is the peptide that has antigen properties. Based on the analysis that had been done, the PEP1 was recommended as an epitope-based peptide vaccine candidate to deal with the SARS-CoV-2 outbreaks. Copyright © 2020 THE AUTHOR(S).

Concept of sars-cov-2 vaccine design to fight covid-19 pandemic: A review insight

Cluster of pneumonia infection emerged in Wuhan, China due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Additionally, more than 190 countries have confirmed 82 million cases of SARS-CoV-2 infection. Currently, there is a SARS-CoV-2 epidemic, and no effective prophylactic methods are available. A vaccine is considered as an effective method to restrict an epidemic. Several vaccine designing techniques have been established, which is enabling researchers from various institutes for developing vaccine towards SARS-CoV-2 infections. In this review, we condense the development of vaccine research against SARS-CoV-2.