Study of new Zn(II)Prolinedithiocarbamate as a potential agent for breast cancer: Characterization and molecular docking

Irfandi, Rizal; Santi, Santi; Raya, Indah; Ahmad, Ahyar; AhmadFudholi,; Sari, Dewi Ratih Tirto; Prihantono, Prihantono

doi:10.1016/j.molstruc.2021.132101

Cited by 19 publications

(14 citation statements)

References 52 publications

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“…Low energy indicated tight interactions of ligandprotein complex. The binding energy score was affected by type of interactions, number of hydrogen and hydrophobic interactions [21,22,[24][25][26].…”

Section: Resultsmentioning

confidence: 99%

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Phaleria macrocarpa Flavonoid as a Potent MMP-1 Inhibitor for Endometriosis Therapy: In silico Study

Maharani

Sutrisno

2022

a-jhr

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Introduction: Endometriosis is a gynaecological disorder in women and causes infertility. Several therapeutic were developed to reduce endometriosis cases, one of them was matrix metalloproteinase (MMP) inhibitor. This study investigated the potential activity of the flavonoids in Phaleria macrocarpa fruit as MMP1 inhibitors for endometriosis. Methods: In silico modelling was used in this study. Six flavonoid structures were retrieved from PubChem NCBI database. A targeted protein, MMP1 was taken out from Protein Data Bank with ID 1CGE and predicted the active sites. Six flavonoids and MMP1 was interacted by molecular docking using Molegro virtual Docker version 5 and analyzed using PyMol 2.2 and Discovery Studio version 21.1.1. Three-dimensional complex structure of flavonoids – MMP1 showed interaction in the same active sites and performed an amino acid residue Glu219 as catalytic site. Results: Six flavonoids of Phaleria macrocarpa were divided into two patterns and generated varied binding energy. Glycitin and Catechin 7-O-beta-D-xyloside showed low score of binding energy and depicted similar structure with four aromatic rings. 8-Prenylnaringenin performed lower binding energy than naringenin, eriodictyol, and 5-O-methylgenistein. Conclusion: In silico analysis suggested that six flavonoids compounds is potent as MMP1 inhibitor and might be interfered endometriosis pathophysiology. In vivo and in vivo investigations are required for further analysis.

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Section: Resultsmentioning

confidence: 99%

“…Matrix metalloproteinase-1 (MMP1) was identified the active sites using Molegro Virtual Docker version 5.0 with van der Waals as a parameter [20][21][22][23]. Six flavonoids were interacted with MMP1 in the specific grid, which was X -2.92; Y 51.58; Z 52.09; radius 10.…”

Section: Docking Simulationmentioning

confidence: 99%

Phaleria macrocarpa Flavonoid as a Potent MMP-1 Inhibitor for Endometriosis Therapy: In silico Study

Maharani

Sutrisno

2022

a-jhr

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“…Fe (II) Isoleucine dithiocarbamate bound to several active sites of O6alkylguanine-DNA alkyltransferase that not identified on cisplatin. A recent report revealed that Zn (II) prolinedithiocarbamate altered the conformational structure of MGMT by binding ARG147, LEU102, VAL106, ILE76, and GLU77 (Irfandi et al, 2022). Antitumor agent, combinitrosourea prodrug 3-(3-(2-amino-9H-purin-6-yl) oxy) methyl)benzyl)-1-(2-chloroethyl)-1-nitrosourea, reported inhibit the O6alkylguanine-DNA alkyltransferase at Try114, Cys145, Val148, and Ser159 (Sun et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

A New Complex Design of Fe (II) Isoleucine Dithiocarbamate as a Novel Anticancer and Antivirus against SARSCOV-2 (COVID-19)

Irfandi

Riswandi

Raya

et al. 2022

Asian Pac J Cancer Prev

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Background: This study was carried out to synthesize a new complex of Fe(II) with isoleucine dithiocarbamate ligand and to determine its potential as an anticancer and antiviral agent for SARSCOV-2. Methods: The synthesized complexes were then characterized by UV-vis and FT-IR spectroscopy and their melting points. The value of the conductivity of the complex compound is also determined. Anti-cancer activity was tested in vitro and molecular docking. Its potential as an antiviral against SARSCOV-2 was also carried out by molecular docking. Pharmacokinetics/ ADMET properties were also carried out on the complex. Result: Spectral results showed the successful synthesis of Fe(II) isoleucine dithiocarbamate complex. The complex produced UV-vis spectra at 268 and 575 nm, and the IR data at 399-599 cm-1 showed the coordination between the Fe(II) atoms with sulphur, nitrogen and oxygen of the isoleucine dithiocarbamate ligand. Fe(II) isoleucine dithiocarbamate had a cytotoxicity effect on the MCF-7 cell line (IC 50 =613 µg/mL). The complex significantly caused morphological changes in the breast cancer cell line, finally leading to cell apoptosis. Conclusion: Cytotoxic test of Fe(II) isoleucine dithiocarbamate showed moderate anticancer activity on MCF-7 cancer cells and showed antiviral activity against SARSCOV-2 by interfering with spike glycoprotein -ACE2 receptors, and inhibiting major proteases and 3Clpro.

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“…The protein alanine racemase (4WR3) [9] and transglycosylase (1SLY) [12] as receptors were downloaded from the PDB database. Alanine racemase and transglycosylase predicted their binding cavities using Molegro virtual docker version 5 with the molecular surface by van der Waals as a parameter [16][17][18][19].…”

Section: Protein Retrieval and Binding Cavities Predictionmentioning

confidence: 99%

“…The receptors were docked to ligands by using Molegro Virtual Docker 5 with a specific area for alanine racemase as follows, X=43.87; Y=2.45; Z=2.99; Radius 9 and transglycosylase X=10.52 Y=47.19; Z=57.06 Radius 13. The parameters for docking were MolGrid 0.3A, 10x docking repetitions, and RMSD < 2 [17][18][19][20]. To validate the docking result of S. myrtifolium leaf, receptors were docked with antibacterial control Sodium Benzoate (CID243) from PubChem, Pyridoxal-5'-Phosphate (PDB ID 4WR3) for alanine racemase, and 4-O-(4-O-Sulfonyl-N Acetylglucosamininyl)-5-Methylhydroxy-L-Proline-Taurine (PDB ID 1SLY) for transglycosylase.…”

Section: Molecular Docking Simulationmentioning

confidence: 99%

IN SILICO SCREENING OF Syzygium myrtifolium FLAVONOID COMPOUNDS AS ANTI-BACTERIAL ACTIVITY

Permatasari

Witoyo²,

Masruri³

et al. 2022

J.Trop Life Science

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Bacterial infection and antibiotic resistance are popular issues nowadays. Several previous reports performed antibacterial screening activities involving natural herbs and synthetic drugs. Alanine racemase and transglycosylase are essential proteins for peptidoglycan membrane synthesis in bacteria and an alternative target for antibacterial performance. This study identified six flavonoid compounds in Syzygium myrtifolium to perform the antibacterial activity. In silico study was conducted for modelling flavonoids – protein complexes. Five flavonoids from S. myrtifolium were taken out of the canonical smiles from the PubChem database and modelled three-dimensional structure using ChemDraw and molView. Targeted protein, alanine racemase and transglycosylase were downloaded from Protein Data Bank with ID 4WR3 and 1SLY. Ligands and proteins were interacted by Molegro virtual Docker 5.0 and visualized by Discovery studio version 21.1.1. Five flavonoids showed inhibition with alanine racemase and transglycosylase in the same active sites of control and sodium benzoate. According to the binding energy, calopiptin performed the lowest binding energy value in alanine racemase complexes, while 2-Propanone, 1,3-bis(5-nitro-2-furanyl) showed the lowest value of four other flavonoids at transglycosylase complexes. The type of interactions were electrostatic, hydrogen bonds, hydrophobic interactions and unfavorable ones. Low binding energy and varied interaction types indicated tight of ligand-protein interaction. In summary, five flavonoids inhibited alanine racemase and transglycosylase, and the peptidoglycane membrane synthesis in bacteria might be inferred. Keywords: Alanine racemase, Flavonoids, In silico, Transglycosylase

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Study of new Zn(II)Prolinedithiocarbamate as a potential agent for breast cancer: Characterization and molecular docking

Cited by 19 publications

References 52 publications

Phaleria macrocarpa Flavonoid as a Potent MMP-1 Inhibitor for Endometriosis Therapy: In silico Study

Phaleria macrocarpa Flavonoid as a Potent MMP-1 Inhibitor for Endometriosis Therapy: In silico Study

A New Complex Design of Fe (II) Isoleucine Dithiocarbamate as a Novel Anticancer and Antivirus against SARSCOV-2 (COVID-19)

IN SILICO SCREENING OF Syzygium myrtifolium FLAVONOID COMPOUNDS AS ANTI-BACTERIAL ACTIVITY

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