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All Journal Jurnal Farmasi Galenika (Galenika Journal of Pharmacy) Indonesian Journal of Chemistry Molekul: Jurnal Ilmiah Kimia
Saipul Maulana
Department Of Pharmacy, Faculty Of Mathematics And Natural Sciences, Tadulako University, Palu 94118, Indonesia
Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Health Professions Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology

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In Vitro and In Silico Studies of Quercetin and Daidzin as Selective Anticancer Agents Muhammad Sulaiman Zubair; Syariful Anam; Saipul Maulana; Muhammad Arba
Indonesian Journal of Chemistry Vol 21, No 2 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.53552

Abstract

Quercetin and daidzin are flavonoid and flavonoid glycoside type compounds that have been found in many plants and nutraceuticals. This study aims to examine the in vitro cytotoxic and selectivity properties of quercetin and daidzin on breast and cervical cancers and to study their molecular interaction and stability on epidermal growth factor receptor tyrosine kinase (EGFR-TK) by applying molecular docking and molecular dynamics (MD) simulations. In vitro anticancer activity was performed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method on breast cancer cell (T47D), cervical cancer cells (HeLa), and Vero normal cells, while molecular docking and MD simulation were done by using AutoDock Vina and Amber18 package software, respectively. Quercetin and daidzin showed potent cytotoxic and high selectivity on both cell lines. Daidzin was found to has a higher IC50 and selectivity index than quercetin. Docking and MD results showed that both compounds prefer to interact with epidermal growth factor receptor tyrosine kinase (EGFR-TK). Daidzin showed better interaction than quercetin with a docking score of -9.6 kcal/mol. Also, daidzin was found more stable than quercetin with low RMSD and RMSF values.
Synthesis and Antidiabetic Evaluation of N’-Benzylidenebenzohydrazide Derivatives by In Silico Studies Yusuf Syaril Alam; Pratiwi Pudjiastuti; Saipul Maulana; Nur Rahmayanti Afifah; Fahimah Martak; Arif Fadlan; Tutik Sri Wahyuni; Syukri Arief
Indonesian Journal of Chemistry Vol 23, No 4 (2023)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.82073

Abstract

Two new of N’-benzylidenebenzohydrazide (NBB) derivatives were successfully synthesized and yielded 50–58%. FTIR, ESI-MS, 1H-NMR and 13C-NMR were used to investigate the characteristic of NBB derivates. The structure and relationship of NBB derivatives into α-glucosidase and α-amylase as good targets for diabetes treatment were evaluated using in silico screening. Molecular Mechanics-Poisson Boltzmann/Generalized Born Surface Area (MM-PB/GBSA) was used to calculate the free binding energy (ΔGbind (MM-GBSA)) of NBB to α-glucosidase and α-amylase receptors showed that the results of −0.45 and −20.79 kcal/mol respectively. In the ortho position, NBB derivatives exhibited electron donating groups (EDG like -OCH3, -OH and -Cl with binding free energies of −21.94, −6.71 and 21.94, respectively, and acarbose, a native ligand energy of 32.62 kcal/mol. In addition, the binding free energy of N-2-(-OCH3, -OH and -Cl)-NBB to the α-amylase receptor showed the number of −39.33, −43.96, −42.81, respectively and −46.51 kcal/mol in comparing with a native ligand. As a result, it was found that all the NBB derivatives were able to interact with several amino acids in the α-glucosidase cavity as well as the native ones, including Ala281, Asp282, and Asp616.  NBB and native ligand showed similar interaction between α-amylase with Gly110 amino acid residue.
Penambatan Molekuler dan Simulasi Dinamika Molekuler Senyawa Dari Genus Nigella Terhadap Penghambatan Aktivitas Enzim Protease HIV-1: Molecular Docking and Molecular Dynamics Simulation of Compounds from Nigella Genus on Protease HIV-1 Enzyme Inhibitors Zubair, Muhammad Sulaiman; Maulana, Saipul; Mukaddas, Alwiyah
Jurnal Farmasi Galenika (Galenika Journal of Pharmacy) (e-Journal) Vol. 6 No. 1 (2020): (March 2020)
Publisher : Universitas Tadulako

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (551.855 KB) | DOI: 10.22487/j24428744.2020.v6.i1.14982

Abstract

Nigella plant genus has potential as anti-HIV. One species of Nigella, Nigella sativa has been reported to have HIV-1 protease enzyme inhibitory activity. This research aims to determine the compounds of the Nigella genus that have activity as HIV-1 protease enzyme inhibitory activity through molecular docking method by Autodock Vina and to compare interaction stability through molecular dynamics simulations by AMBER. The metabolite of the Nigella genus was obtained from the KnapSack website, and enzyme model was obtained from the Protein Data Bank (3NU3). The results of molecular docking found the lowest affinity energy of Nigella compound is Nigellidine 4-O-sulfite (-13.4 kcal/mol). Meanwhile, the affinity energy of the ligand native (Amprenavir) was -12.1 kcal/mol. The lowest affinity energy of Nigellidine 4-O-sulfite might be predicted to have potency as an HIV-1 Protease inhibitor. Molecular dynamics simulation showed Root Mean Square Fluctuation (RMSF) value of Nigellidine 4-O-sulfite with the amino acid active site is 0.4064 Ã… for ASP:25 and 0.5667 Ã… for ASP: 125. Whereas RMSF ligand native with the amino acid active site, ASP: 25 is 0.3647 Ã… and ASP: 125 is 0.3639 Ã…. The higher RMSF value of Nigellidine 4-O-sulfite describes the lower interaction stability than the ligand native.
Docking Study of Naphthalene Compounds from Eleutherine Bulbosa as Antidiabetic Agents on Multiple Receptors Anam, Syariful; Yuyun, Yonelian; Yusriadi, Yusriadi; Sultan, Asriana; Pakaya, David; Maulana, Saipul; Zubair, Muhammad Sulaiman
Molekul Vol 20 No 1 (2025)
Publisher : Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.jm.2025.20.1.10942

Abstract

ABSTRACT. Diabetes Mellitus is a severe disease to the world health community; it is estimated that 700 million people worldwide will suffer from it. The approach taken to this disease includes improving lifestyle and pharmacological therapy. Recent pharmacological therapeutic approaches include inhibiting the α-glucosidase enzyme, the dipeptidyl peptidase 4 (DPP-4) enzyme, and the sodium-glucose co-transporter-2 (SGLT-2) protein. This research aims to conduct a docking study on three naphthalene compounds from Eleutherine bulbosa against three receptors: α-glucosidase, the DPP-4, and the SGLT-2 protein. The methods used are protein structure preparation, docking protocol validation, preparation of E. bulbosa test ligand structures, and molecule docking for test compounds. Validation was carried out by calculating the Root Mean Square Deviation (RMSD) values using PyMOL software; the results showed that the RMSD value of native ligands was <2Å. Molecular docking of the test compounds was conducted using Autodock Vina 1.2.3 ver 2020. Eleutherinoside A showed the highest binding against the α-glucosidase and DPP-4 protein. Eleuthoside B has the most increased binding to SGLT-2 protein. The research concluded that three naphthalene compounds from E. bulbosa can be used as an antidiabetic agent. Keywords: Antidiabetic; Docking study; Eleutherine bulbosa; Naphthalene; α-glucosidase; DPP-4; SGLT-2
Co-Authors Alwiyah Mukaddas Arba, Muhammad Asriana Sultan David Pakaya Fadlan, Arif Fahimah Martak Muhammad Sulaiman Zubair Nur Rahmayanti Afifah Pratiwi Pudjiastuti Sugeng, Santoso Syariful Anam Tutik Sri Wahyuni Yonelian Yuyun Yusriadi Yusriadi Yusuf Syaril Alam