Article by Mohammad Rizki Fadhil Pratama
Asian Journal of Pharmaceutical and Clinical Research, 2018
Objectives: Akar kuning (Arcangelisia flava) was known to have various pharmacological activities... more Objectives: Akar kuning (Arcangelisia flava) was known to have various pharmacological activities including as antibacterial. Several Gram-positive and Gram-negative bacteria show response to akar kuning secondary metabolites, although the type of metabolites that inhibit the growth of each type of bacteria not yet known. This study aims to obtain the prediction of metabolites from akar kuning with the greatest antibacterial potential against various types of antibacterial receptors. Methods: Molecular docking was performed using Autodock Vina 1.1.2 on several secondary metabolites of akar kuning against active site of several antibacterial receptors that were known for many antibiotics including as cell wall, protein, nucleic acid synthesis inhibitors, and antimetabolites. The main parameter used was the free energy of binding as affinity marker. Results: The docking results show that among 11 metabolites studied, 6-hydroxyfibraurin, berberine, and fibleucin provided the lowest free energy of binding between 11 antibacterial receptors compared with natural substrates or inhibitors from each receptor. Interesting results show by berberine as inhibitor of protein synthesis with possibility of allosteric site discovery. Berberine also shows more than 75% similarity with natural substrate of cell wall inhibition receptor, indicating possible similar type of interaction. Conclusion: Overall, it seems that for the selected secondary metabolites of akar kuning, the main mechanism of action was the inhibition of protein and cell wall synthesis, which was shown by berberine.
Asian Journal of Pharmaceutical and Clinical Research, 2018
Objectives: Lupeol, a triterpenoid isolated from Kasturi (Mangifera casturi) fruit has been known... more Objectives: Lupeol, a triterpenoid isolated from Kasturi (Mangifera casturi) fruit has been known for having several pharmacological activities, including anticancer properties. Lupeol showed antiproliferative activity toward many cancer cells line including breast cancer. Lupeol showed promising potency as both ER-α and HER2 inhibitors, although still lower than known ER-α and HER2 Inhibitors. Chemical structure optimization of lupeol was predicted could increase the affinity of lupeol derivatives against ER-α and HER2. This study aims to determine lupeol derivative with the highest affinity against ER-α and HER2. Methods: All ligands were sketched and optimized using Gaussian 03W with Hartree–Fock method basis set 3-21G. Molecular docking was performed using Autodock 4.2.6 on several modified chemical structure of lupeol against active site of ER-α and HER2. The main parameter used was the free energy of binding and inhibition constants as affinity marker. Results: The docking results show that lupeol derivative with an amine group (Lupeol-2) and ethyl group (Lupeol-4) at position C3 provide the highest affinity with the free energy of binding and dissociation constant −12.24 kcal/mol and 1.07 nM for ER-α also −9.63 kcal/mol and 86.94 nM for HER2, respectively. Interestingly, although lupeol derivatives showed higher affinity toward ER-α, their amino acid residues were closer to the interaction on HER2. Conclusion: These results predict that lupeol have greater potential to be developed as a HER2 inhibitor. Further, derivate lupeol-4 should be potential to be developed as HER2-positive breast cancer therapy.
Asian Journal of Pharmaceutical and Clinical Research, 2017
Objectives: This study aims to find the relationship between artemisinins and neuraminidase (NA) ... more Objectives: This study aims to find the relationship between artemisinins and neuraminidase (NA) with molecular docking study and also to determine the most potent NA inhibitor from artemisinin and derivatives. Methods: All ligands were sketched and optimized using Gaussian 03W with Hartree-Fock method basis sets 6-311G. Molecular docking was performed using AutoDock 4.2.3 toward NA in complexes with oseltamivir as co-crystal ligand. The main parameters used were the free energy of binding (∆G) and dissociation constant (K i) as affinity marker. Results: Artesunate provided most negative free ∆G and lowest K i toward NA with −9.55 kcal/mol and 100.66 nM, respectively. Artesunate shows higher affinity than oseltamivir with interactions between artesunate and amino acids at position 246 had important influences on artesunate affinity toward NA from H5N1. Conclusion: In silico molecular docking results indicated that artesunate could be considered as NA inhibitor and should be potential to be developed as anti-influenza particularly to H5N1 with oseltamivir resistance.
Research Journal of Microbiology, 2015
Lactobacillus plantarum species often harbor several plasmids. These plasmids may encoded importa... more Lactobacillus plantarum species often harbor several plasmids. These plasmids may encoded important traits such as phages or antibiotics resistances, lactose catabolism and production of proteolytic enzyme and also bacteriocins that named plantaricin. Lactobacillus plantarum IBL-2 that isolated from strawberry of Bali plantation have the highest anti-microorganism activity among the L. plantarum isolate collection of BTCC Indonesia. Only few study carried out to examine the antifungal activity of bacteriocin from L. plantarum. This study focus on anti-Candida activity of plasmid associated with bacteriocin production from L. plantarum IBL-2. The isolates were confirmed by the 16S rRNA analysis by PCR and the phylogenetic tree was built based on references sequences and one outgroups from database. The plantaricin gene screening then performed in plasmid that was isolated from L. plantarum IBL-2 by PCR using five pairs or plantaricin gene primer. The anti-Candida potential of plantaricin observed were analyzed by in silico by docking analysis between the plantaricin and receptors of apoptosis proteins. PlnB and PlnEF were observed in the L. plantarum plasmid. Only PlnEF become the focus of study. Analysis of docking study predicted that PlnEF have interactions with apoptosis proteins regulator in eukaryotic cells. PlnEF that encoded by plasmid of L. plantarum may exert anti-Candida potential through interactions with apoptosis proteins regulator.
Papers by Mohammad Rizki Fadhil Pratama
Social Science Research Network, Dec 1, 2015
Human Epidermal growth factor Receptor 2 (HER2), an epidermal protein involved in signalling of c... more Human Epidermal growth factor Receptor 2 (HER2), an epidermal protein involved in signalling of cycle cell process is a potential target for breast cancer therapy by prevent proliferative cells activity from MAPK pathway. Artemisinin, a group of anti-malarial compound and its derivatives are known to have cytotoxic activity associated with termination of proliferation cells process. The present study aims to determine the most potent artemisinin derivatives as HER2 inhibitor. Molecular docking against HER2 showed that artesunate provide most negative free energy of binding and lowest inhibition constants -10.59 kcal/mol and 17.36 nM, respectively. Artesunate show higher affinity towards tyrosine kinase site of HER2 compared to TAK-285, potent dual inhibitor EGFR/HER2 with amino acids interactions at position 726 until 734 had important influences towards affinity of artesunate. This results predicted artesunate has antiproliferative activity as HER2 inhibitor and should be potential to be developed as breast cancer therapy.
Social Science Research Network, Jul 1, 2016
ChemistrySelect, 2022
Ten novel compounds of 3-alkyl / aryl-6-S-( 2',3',4',6'-tetra-O-acetyl-β-D-glcopy... more Ten novel compounds of 3-alkyl / aryl-6-S-( 2',3',4',6'-tetra-O-acetyl-β-D-glcopyranosyl)-1,2,4-triazolo[3,4-b]-1,3,4-thiadiazoles were designed and synthesized from 3-alkyl / aryl-4-amino-5-mercapto-1,2,4-triazoles. The structures of all the compounds were confirmed by means of1 H NMR,13 C NMR,HRMS and IR. The preliminary bioassay showed that all target compounds possessed efficient antibacterial activities on Escherichia coli,Staphylococcus aureus,Bacillus subtilis and Monilia albican. Especially,the compound 3c had strong antibacterial by the lowest minimal inhibitory concentration( MIC) values on the four tested strains which were close to those of the controlled drug fluconazole. The interaction and binding free energy of the target compounds( 3a—3j) with FabⅠ were studied by Auto Dock 4.0.
Substansi Naskah<br> (Workshop Persiapan Reakreditasi Jurnal Poltekkes Jakarta III)
Jurnal Farmasi Sains dan Praktis, 2021
Topical agents indicated for the treatment of acne have the potential to cause irritation or alle... more Topical agents indicated for the treatment of acne have the potential to cause irritation or allergic contact dermatitis. This study investigates the irritancy potential of anti-acne cream of bawang dayak (Eleutherine bulbosa (Mill.) Urb.) previously tested for microbiological effectiveness with the lowest concentration of 5% and the highest concentration of 20%. The method used in this study is the human patch test. A total of 20 volunteers were recruited for the patch test study, testing the cream. The result showed that all volunteers did not experience irritation both in the 5% or 20% bawang dayak extract cream formulations. However, the interview results were found that some volunteers experienced a slight itching without any significant skin adverse reactions on the cream application. Therefore, based on these initial findings it can be safely concluded that the cream of bawang dayak does not cause significant skin adverse reaction and good enough for further development for a...
Dataset: A Mini-Review of the Molecular Docking Study of SARS-CoV-2 with Phytochemicals from Medi... more Dataset: A Mini-Review of the Molecular Docking Study of SARS-CoV-2 with Phytochemicals from Medicinal Plants
Bibliometric Analysis of Research on <em>Boesenbergia Rotunda</em>, Pinostrobin, and ... more Bibliometric Analysis of Research on <em>Boesenbergia Rotunda</em>, Pinostrobin, and Their Derivatives using VOSviewer
Journal of Advanced Pharmaceutical Technology & Research, 2021
The estrogen hormone dependent accounts for a major cause in the incidence of women breast cancer... more The estrogen hormone dependent accounts for a major cause in the incidence of women breast cancer. Thus, their receptor, especially the estrogen receptor α (ER-α), is becoming a target in endocrine treatment. These ligand-inducible nuclear functions are regulated by an array of phytochemical and synthetic compounds, such as 17 β-estradiol and tamoxifen (4-hydroxytamoxifen [4OHT]). The Chinaberry (Melia azedarach) leaves are known naturally for relieving internal and external diseases. Previous studies revealed the potency of Melia's ethanolic extract and ethyl acetate fractions as anticancer; furthermore, this study aimed to resolve possible ER-α antagonist's mechanism and safety from M. azedarach leaves ethyl acetate fraction contents. Melia's phytochemical content was analyzed with electrospray ionization liquid chromatography-mass spectrometry, while its ER-α antagonist's potency was investigated by in silico. The computational docking was used to 3ERT (a human ER...
Asian Journal of Pharmaceutical and Clinical Research, 2018
Objectives: Lupeol, a triterpenoid isolated from Kasturi (Mangifera casturi) fruit has been known... more Objectives: Lupeol, a triterpenoid isolated from Kasturi (Mangifera casturi) fruit has been known for having several pharmacological activities, including anticancer properties. Lupeol showed antiproliferative activity toward many cancer cells line including breast cancer. Lupeol showed promising potency as both ER-α and HER2 inhibitors, although still lower than known ER-α and HER2 Inhibitors. Chemical structure optimization of lupeol was predicted could increase the affinity of lupeol derivatives against ER-α and HER2. This study aims to determine lupeol derivative with the highest affinity against ER-α and HER2.Methods: All ligands were sketched and optimized using Gaussian 03W with Hartree–Fock method basis set 3-21G. Molecular docking was performed using Autodock 4.2.6 on several modified chemical structure of lupeol against active site of ER-α and HER2. The main parameter used was the free energy of binding and inhibition constants as affinity marker.Results: The docking resul...
Borneo Journal of Pharmacy, 2018
This study aims to obtain the profile of Thin-Layer Chromatography (TLC) and Ultraviolet-Visible ... more This study aims to obtain the profile of Thin-Layer Chromatography (TLC) and Ultraviolet-Visible (UV-Vis) spectrophotometry from ethanol extract of akar kuning stems (Arcangelisia flava) from Central Kalimantan. The TLC method is used with the orientation phase of the combination of polar-non-polar solvents resulting from orientation, while ethanol is used as the solvent for UV-Vis spectrophotometers. TLC results showed the formation of 3 stains on a combination of polar solvents chloroform : methanol : water while in a non-polar solvent combination n-hexane : ethyl acetate did not show any stains. Comparison of retention factor (Rf) values show the best combination of polar solvents to separate stains at a ratio of 5 : 2 : 1, respectively. Separation in 2-dimensional TLC with polar solvents showed a similar pattern with 1-dimensional separation in the form of 3 stains. UV-Vis spectrophotometer results showed 4 main peaks with wavelength 227.2; 267.4; 345.2; and 425.3 nm, respective...
Asian Journal of Pharmaceutical and Clinical Research, 2018
Objectives: Akar kuning (Arcangelisia flava) was known to have various pharmacological activities... more Objectives: Akar kuning (Arcangelisia flava) was known to have various pharmacological activities including as antibacterial. Several Gram-positive and Gram-negative bacteria show response to akar kuning secondary metabolites, although the type of metabolites that inhibit the growth of each type of bacteria not yet known. This study aims to obtain the prediction of metabolites from akar kuning with the greatest antibacterial potential against various types of antibacterial receptors.Methods: Molecular docking was performed using Autodock Vina 1.1.2 on several secondary metabolites of akar kuning against active site of several antibacterial receptors that were known for many antibiotics including as cell wall, protein, nucleic acid synthesis inhibitors, and antimetabolites. The main parameter used was the free energy of binding as affinity marker.Results: The docking results show that among 11 metabolites studied, 6-hydroxyfibraurin, berberine, and fibleucin provided the lowest free ...
Asian Journal of Pharmaceutical and Clinical Research, 2017
Objectives: This study aims to find the relationship between artemisinins and neuraminidase (NA) ... more Objectives: This study aims to find the relationship between artemisinins and neuraminidase (NA) with molecular docking study and also to determine the most potent NA inhibitor from artemisinin and derivatives.Methods: All ligands were sketched and optimized using Gaussian 03W with Hartree-Fock method basis sets 6-311G. Molecular docking was performed using AutoDock 4.2.3 toward NA in complexes with oseltamivir as co-crystal ligand. The main parameters used were the free energy of binding (ΔG) and dissociation constant (Ki) as affinity marker.Results: Artesunate provided most negative free ΔG and lowest Ki toward NA with −9.55 kcal/mol and 100.66 nM, respectively. Artesunate shows higher affinity than oseltamivir with interactions between artesunate and amino acids at position 246 had important influences on artesunate affinity toward NA from H5N1.Conclusion: In silico molecular docking results indicated that artesunate could be considered as NA inhibitor and should be potential to ...
Biointerface Research in Applied Chemistry, 2020
Peganum harmala is known to have active metabolites such as alkaloids, which can affect the centr... more Peganum harmala is known to have active metabolites such as alkaloids, which can affect the central nervous system. One of the various alkaloids is thought to be related to their activity as dopamine receptor antagonists, which can be developed in the therapy of various neurological diseases. This study aims to determine the alkaloid from P. harmala, which has the highest potential as the dopamine receptor antagonist. The method used was molecular docking against dopamine receptors with risperidone as the reference ligand. The results showed that among the known alkaloids from P. harmala, dipegine, harmalanine, and harmalacinine showed the highest potency in terms of both free energy of binding and similarity of ligand-receptor interactions. The results of this investigation anticipate that some alkaloids from P. harmala have the potential as the dopamine receptor antagonist.
Akar kuning (Arcangelisa flava) diketahui memiliki berbagai aktivitas farmakologi seperti antikan... more Akar kuning (Arcangelisa flava) diketahui memiliki berbagai aktivitas farmakologi seperti antikanker. Beberapa metabolit sekunder akar kuning menunjukkan aktivitas antiproliferasi sel kanker. Overproliferasi pada sel kanker salah satunya disebabkan oleh kelainan pada EGFR, kelompok reseptor yang berperan pada saat inisiasi proliferasi sel. Inhibisi pada EGFR dapat menghambat proses proliferasi sel kanker. Penelitian ini bertujuan mengetahui metabolit sekunder dari akar kuning dengan potensi paling besar sebagai inhibitor berbagai EGFR. Metode yang digunakan adalah molecular docking beberapa metabolit sekunder akar kuning terhadap EGFR-1, EGFR-2, EGFR-3, dan EGFR-4. Hasil docking menunjukkan berberin memberikan energi bebas ikatan paling negatif dan konstanta inhibisi paling kecil pada seluruh EGFR, dengan afinitas paling tinggi ditunjukkan pada EGFR-2 dengan ΔG dan ki secara berturut-turut sebesar -9,34 kcal/mol dan 141,81 nM. Over-ekspresi aktivitas dari EGFR-2 sendiri seringkali t...
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Article by Mohammad Rizki Fadhil Pratama
Papers by Mohammad Rizki Fadhil Pratama