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

SARS-CoV-2 virus has caused pandemic disease since the end of 2019. Virus transmission occurs through droplet and infects the host's respiratory tract rapidly. Viral propagation occurs through translation process of genome +ssRNA, then it being replicated forming some new body parts of virus and assemblied into virions that ready to infect. During the replication process, the translated viral genome in the form of polyprotein will be cut into smaller components by proteases, which one is 3CLpro. The presence of the 3CLpro receptor is used in drug development through in-silico molecular docking process to minimize failures before laboratory test. The antivirus compounds that used to inhibit the 3CLpro receptor are from gletang plant (Tridax procumbens Linn.). This study aim is to determine the value of binding affinity, the interaction between compounds and receptor, and the effect of drug components. The research was conducted by in-silico through the molecular docking process of 3CLpro receptor and antivirus compounds of gletang (Tridax procumbens Linn.), including betulinic acid, kaempferol and lignan. The results showed that the binding affinity of betulinic acid was -6.6 kcal/mol, kaempferol was -5.6 kcal/ mol and lignan was -5.4 kcal/mol. The interaction form of compounds and receptor was hydrogen bond, electrostatic, hydrophobic, and van der Waals. Compared to baicalein compound as a positive control with the value of binding affinity was -6.7 kcal/mol and its interaction with 3CLpro receptor, showed betulinic acid, kaempferol and lignan have smaller ability but they have the potential to inhibit the 3CLpro receptor.

Section: Resultsmentioning

confidence: 99%

The Potential of Antivirus Compounds in Gletang (Tridax procumbens Linn.) in Inhibiting 3CLpro Receptor of SARS-CoV-2 Virus by In Silico

Islamiati¹,

Suryani²,

Adawiyah³

et al. 2023

“…42 There are also pi-cation, pi-alkyl, pi-stacked amide, vdw, and unfavorable donor-donor bonds that form a relatively negative binding affinity. [43][44][45][46][47][48][49][50]…”

Section: Resultsmentioning

confidence: 99%

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

Aini¹,

Kharisma²,

Widyananda³

et al. 2022

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.

“…The case of COVID 19 has enlarged widely to 213 countries and it caused more than 270 million infections over 5 million cases and those numbers still rising. 3 WHO confirmed the symptoms of COVID 19 were fever, dry cough, respiratory disorders, and olfactory and taste disorders. [4][5][6][7] The human coronavirus (HCoV) was positivestranded RNA virus.…”

Section: Introductionmentioning

confidence: 97%

“…9 M pro has the main role in SARS-CoV-2 transcription and replication. 10,11 Hence, M pro and RdRp were the best candidates for designing antiviral drugs to find therapeutics agents against SARS-CoV-2.…”

Section: Introductionmentioning

confidence: 99%

In Silico Study of Entry Inhibitor from Moringa oleifera Bioactive Compounds against SARS-CoV-2 Infection

Mawaddani¹,

Sutiyanti²,

Widyananda³

et al. 2022

Pterygospermin, Quercetin, Rutin, and β-amyrin which has an antiviral potential compounds against COVID 19 by inhibiting M pro and RdRp activity. [15][16][17][18] Besides all the compounds above, Oleic acid was most found at around 84% in M. Oleifera. 19 M. oleifera was the most appropriate candidate for an antiviral agent against SARS-CoV-2. The aim of this study was to screen bioactive compounds of Moringa oleifera and to identify the antiviral potential compounds toward SARS-CoV-2 through an entry inhibitor mechanism. METHODS Data mining of sampleThe bioactive compounds of M. oleifera which consist of anthraquinone, apigenin, aurantiamide acetate, benzyl isothiocyanate, chlorogenic acid, chrysin, dibutyl phthalate, ellagic acid, hesperidin, isorhoifolin, myricetin, pterygospermin, quercetin, rutin, and vitex. The bioactive compounds of M. oleifera were retrieved format from PubChem database (https://pubchem.ncbi.nlm.nih.gov/) in sdf format. 20 Protein modelingThe structure of M pro and RdRp as the target proteins which were not available in the RCSB PDB database was modeled based on their amino acid sequence. The NCBI (https://www.ncbi.nlm.nih.gov/) database was used to retrieve sequences of amino acids with fasta format. Furthermore, protein modeling is made through the SWISSMODEL site (https://swissmodel. expasy.org/). The selection of protein models was selected from several parameters such as QMQE value, QMEAN value, coverage value, local quality value, and comparison plot. In addition, the protein