Molecular Dynamic Simulation Analysis on Marine Fungi Compounds Against EGFR and VEGFR-2 Inhibitory Activity in Non-Small Cell Lung Cancer

Yanuar, Arry; Chavarina, Kinanti Khansa; Syahdi, Rezi Riadhi

doi:10.5530/jyp.2018.2s.6

Cited by 3 publications

(3 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Hydrogen bond interactions play an essential role in preserving the secondary structures of protein [38]. For the ligand-uPA complexes in the MD simulation, the amino acid residues Tyr94, His99, Ser190, Gly216, Gly219 showed a hydrogen bond with the ligand.…”

Section: Hydrogen Bond Interactionmentioning

confidence: 99%

Pharmacophore Modeling, Docking, and Molecular Dynamics Simulation of Flavonoids as Inhibitors of Urokinase-type Plasminogen Activator

Tjahjono

Sari

Ibrahim

2022

J. Math. Fund. Sci.

View full text Add to dashboard Cite

The urokinase-type plasminogen activator (uPA) system plays a significant role in the invasion and metastasis of cancer cells. The present study was conducted to investigate natural product compounds as inhibitors and hit molecules of uPA using in-silico analysis. A pharmacophore model was built to screen the Indonesian Herbal Database (HerbalDB) to obtain inhibitors of different scaffolds. Based on the molecular docking score, four ligands were selected as potential uPA inhibitors. Subsequently, the stability of the ligand-uPA complex was analyzed using molecular dynamics (MD) simulation. An RMSD graph of the backbone protein and the RMSF values of the amino acid residues were also determined. In addition, the MM-PBSA method was applied to calculate the free binding energy. According to the results, Model_3, characterized by aromatic rings 23 (F1 and F2), cationic H-bond donor (F3), and metal ligator (F4) features, had an adequate goodness-of-hit score (GH). The four top-ranked ligands, isorhamnetin, rhamnetin, quercetin, and kaempferol, showed higher docking scores compared to the others. This study confirmed that isorhamnetin, rhamnetin, and kaempferol build stable complexes with uPA with lower binding energy than quercetin.

show abstract

Section: Hydrogen Bond Interactionmentioning

confidence: 99%

Pharmacophore Modeling, Docking, and Molecular Dynamics Simulation of Flavonoids as Inhibitors of Urokinase-type Plasminogen Activator

Tjahjono

Sari

Ibrahim

2022

J. Math. Fund. Sci.

View full text Add to dashboard Cite

show abstract

“…The compounds (2a-e) were synthesized by the amino-alkylation of VA (1) through a Mannich reaction refers to the preparation of Mannich bases derivatives of curcumin analog and dehydrozingerone reported previously. [15][16] A mixture of formaldehyde solution (80 mmol) and corresponding secondary amines (80 mmol) was mixed with 18 mL solution of 1 (20 mmol) in ethanol, heated under reflux at ± 50°C during 30 min. It stirred until a completed reaction at 25°C for 12-24 h (TLC monitoring).…”

Section: Synthesis Of the Mannich Bases 2a-ementioning

confidence: 99%

Synthesis and Antioxidant Activity Study of New Mannich Bases Derived From Vanillic Acid

Hayun¹,

Gavrila²,

Silviana³

et al. 2020

RJC

View full text Add to dashboard Cite

We synthesized five new Mannich bases compounds from vanillic acid and evaluated for their antioxidant activities using a free-radical DPPH and FRAP methods. The compounds' structures were confirmed based on infrared, proton NMR, carbon NMR, and mass spectra. In this study, the compound 5-(pyrrolidin-1-ylmethyl)vanillic acid (2e) showed the best free-radical scavenger activity, while compound 2-[(diethylamino)methyl]vanillic acid (2c) showed the best as a ferric reductant. Mannich bases enhanced the free-radical scavenger activity but decreasing the ferric reduction potential of the parent compounds. The compounds were found to be moderate antioxidant agents.

show abstract

“…In silico analyses may offer valuable research information and reduce the costs of drug development by reducing sample numbers in in vitro and in vivo studies [11]. Several studies have shown that virtual screening could be performed for marine compounds to target various macromolecules such as epidermal growth factor receptor-TK, vascular EGFR-2, mouse double minute 2, and procaspase-3 [12][13][14]. Herein, we performed in silico molecular docking experiments to identify the most promising compounds that can be isolated from echinoderms as HIV-1 reverse transcriptase (RT) inhibitors.…”

Section: Introductionmentioning

confidence: 99%

In Silico Investigation of Echinodermata Secondary Metabolites as Human Immunodeficiency Virus Type 1 (Hiv-1) Reverse Transcriptase Inhibitors

Nazwir

Yanuar²,

Syahdi³

2020

Int J App Pharm

Self Cite

View full text Add to dashboard Cite

Objective: Human immunodeficiency virus (HIV) targets the immune system and weakens immune surveillance and defenses against infections,leading to acute immunodeficiency syndrome. Recent trends in drug discovery from natural sources emphasize investigations of compounds frommarine ecosystems.Methods: In this study, we compiled a database of chemical compounds from echinoderms and virtually screened for those that inhibit HIV-1 reversetranscriptase (RT). The database was generated from literature searches. Virtual screening analyses for inhibitors of HIV-1 RT were then performedusing AutoDock software.Results: Based on screening results, the top thirteen ranked compounds were nobilisidenol B, Ech_005, 17-deoxyholothurinogenin,22,25-oxidoholothurinogenin, Ech_022, Ech_026, Ech_021, nobilisidenol A, Ech_025, 5α-cholest-8(14)-ene-3ß,7α-diol, astropecten A, Ech_004, andphrygiasterol.Conclusion: The present in silico screening analyses of compounds from marine ecosystems can be used to identify candidate compounds with highpotential as drugs for the treatment of refractory HIV infections.

show abstract

Molecular Dynamic Simulation Analysis on Marine Fungi Compounds Against EGFR and VEGFR-2 Inhibitory Activity in Non-Small Cell Lung Cancer

Cited by 3 publications

References 10 publications

Pharmacophore Modeling, Docking, and Molecular Dynamics Simulation of Flavonoids as Inhibitors of Urokinase-type Plasminogen Activator

Pharmacophore Modeling, Docking, and Molecular Dynamics Simulation of Flavonoids as Inhibitors of Urokinase-type Plasminogen Activator

Synthesis and Antioxidant Activity Study of New Mannich Bases Derived From Vanillic Acid

In Silico Investigation of Echinodermata Secondary Metabolites as Human Immunodeficiency Virus Type 1 (Hiv-1) Reverse Transcriptase Inhibitors

Contact Info

Product

Resources

About