Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2

Fatriansyah, Jaka Fajar; Rizqillah, Raihan Kenji; Yandi, Muhamad Yusup; Fadilah, Fadilah; Sahlan, Muhamad

doi:10.1016/j.jksus.2021.101707

Cited by 36 publications

(19 citation statements)

References 32 publications

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“…The system that has been set is then ready for molecular dynamics simulation with the Desmond Molecular Dynamics feature. Molecular dynamics simulation was carried out for 20 ns, with a trajectory record of 20 ps, in an npt ensemble [ 7 ]. In addition, we conducted ligand torsion analysis.…”

Section: Methodsmentioning

confidence: 99%

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Molecular Dynamics Simulation of Ligands from Anredera cordifolia (Binahong) to the Main Protease (Mpro) of SARS-CoV-2

Fatriansyah

Boanerges

Kurnianto

et al. 2022

Journal of Tropical Medicine

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COVID-19 in Indonesia is considered to be entering the endemic phase, and the population is expected to live side by side with the SARS-CoV 2 viruses and their variants. In this study, procyanidin, oleic acid, methyl linoleic acid, and vitexin, four compounds from binahong leaves-tropical/subtropical plant, were examined for their interactions with the major protease (Mpro) of the SARS-CoV 2 virus. Molecular dynamics simulation shows that procyanidin and vitexin have the best docking scores of −9.132 and −8.433, respectively. Molecular dynamics simulation also shows that procyanidin and vitexin have the best Root Mean Square Displacement (RMSD) and Root Mean Square Fluctuation (RMSF) performance due to dominant hydrogen, hydrophobic, and water bridge interactions. However, further strain energy calculation obtained from ligand torsion analyses, procyanidin and vitexin do not conform as much as quercetin as ligand control even though these two ligands have good performance in terms of interaction with the target protein.

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Section: Methodsmentioning

confidence: 99%

“…Particularly when they are repeatedly employing the trial and error approach. To simulate the performance and efcacy of medications in treating COVID-19, the in silico method may be a preliminary step and can be very important to speed up drug discovery [5][6][7][8][9].…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Simulation of Ligands from Anredera cordifolia (Binahong) to the Main Protease (Mpro) of SARS-CoV-2

Fatriansyah

Boanerges

Kurnianto

et al. 2022

Journal of Tropical Medicine

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“…Molecular docking between fi mH and chamomile give high degree of binding (docking score is -9.4), as compared to molecular docking with D-mannose with a score of -5.5. Th is means a lower energy needed for molecule binding (ligand and target) to form a more stable complex than with D-mannose [39].…”

Section: Fast Identifi Cation System By Vitek-2 Compact Systemmentioning

confidence: 99%

Suggestion of a fimH Inhibitor by a Molecular Docking Method for Escherichia coli Isolated from Clinical Samples of Patients with UTI

Alnuaimi¹,

Alsaeid²,

Abolmaali³

2023

Mikrobiol. Z.

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E. coli is one of the most important organisms that cause urinary tract infection (UTI) in more than 95% of patients with UTI. The aim of this study was to search for inhibitors of (fimH) by a docking method using computer programs and websites specialized for this purpose. Methods. This study involved 63 samples with positive E. coli collected from patients with UTI from February 2021 to October 2021 at the Iraqi hospital in Karbala. Full laboratory investigation for E. coli was made to detect FimH and predictsuitable inhibitors. The Fast Identification System VITEK-2, compact DNA extraction system, and PCR Molecular docking were used. Studies of FimH inhibitor for animals were performed as well. Results. FimH was found in most E. coli isolates, namely in 61 (96.82%) of 63 samples. The principle of the experiment is dependent on activated infection on animals with/without feeding with our drug (chamomile), and then the counted E. coli in their urine chamomile appears to be a good FimH inhibitor, with a docking score of -9.4, and to be able to reduce UTI in roughly 50 percent of rats examined. Conclusions. The chamomile was predicted as a suitable inhibitor of (fi mH) and then tested on rats. The results showed its good inhibitory properties.

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“…Molecular docking studies (a type of in silico research) indicate that rutin and CAPE have the highest affinity with ACE2 among common propolis components [ 140 ]. Another study based on molecular docking suggests that sulabiroin-A ( Figure 2 , XII ) may be an inhibitor of SARS-CoV-2 [ 141 ]. Sulabiroin-A is a podophyllotoxin derivative recently isolated from propolis of the stingless bee Tetragonula aff.…”

Section: Antiviral Activitymentioning

confidence: 99%

Perspectives for Uses of Propolis in Therapy against Infectious Diseases

Salatino

2022

Molecules

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Propolis has gained wide popularity over the last decades in several parts of the world. In parallel, the literature about propolis composition and biological properties increased markedly. A great number of papers have demonstrated that propolis from different parts of the world is composed mainly of phenolic substances, frequently flavonoids, derived from plant resins. Propolis has a relevant role in increasing the social immunity of bee hives. Experimental evidence indicates that propolis and its components have activity against bacteria, fungi, and viruses. Mechanisms of action on bacteria, fungi, and viruses are known for several propolis components. Experiments have shown that propolis may act synergistically with antibiotics, antifungals, and antivirus drugs, permitting the administration of lower doses of drugs and higher antimicrobial effects. The current trend of growing resistance of microbial pathogens to the available drugs has encouraged the introduction of propolis in therapy against infectious diseases. Because propolis composition is widely variable, standardized propolis extracts have been produced. Successful clinical trials have included propolis extracts as medicine in dentistry and as an adjuvant in the treatment of patients against COVID-19. Present world health conditions encourage initiatives toward the spread of the niche of propolis, not only as traditional and alternative medicine but also as a relevant protagonist in anti-infectious therapy. Production of propolis and other apiary products is environmentally friendly and may contribute to alleviating the current crisis of the decline of bee populations. Propolis production has had social-economic relevance in Brazil, providing benefits to underprivileged people.

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Molecular docking and dynamics studies on propolis sulabiroin-A as a potential inhibitor of SARS-CoV-2

Cited by 36 publications

References 32 publications

Molecular Dynamics Simulation of Ligands from Anredera cordifolia (Binahong) to the Main Protease (Mpro) of SARS-CoV-2

Molecular Dynamics Simulation of Ligands from Anredera cordifolia (Binahong) to the Main Protease (Mpro) of SARS-CoV-2

Suggestion of a fimH Inhibitor by a Molecular Docking Method for Escherichia coli Isolated from Clinical Samples of Patients with UTI

Perspectives for Uses of Propolis in Therapy against Infectious Diseases

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