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2-Cinnamamido-4-Methylpentanamide and N-(2-Hydroxypropanoyl)Cinnamamide: Synthesis, Characterization, and Molecular Docking Studies Through PBP2a Protein Rasyid, Herlina; Ernawati, Teni; Monoarfa, Indah Muthmainnah
Molekul Vol 19 No 2 (2024)
Publisher : Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.jm.2024.19.2.10154

ABSTRACT. Cinnamic acid has been found in several types of plants and has a diverse spectrum of bioactivity. Derivatization of cinnamic acid related to the improving bioactivity of a compound. Cinnamic acid can be found as an acid or in conjugated form with amides, esters, aldehydes. This research focus on the synthesis of amide derivatives of cinnamic acid to improve the bioactivity. Two compounds namely 2-cinnamamido-4-methylpentanamide (1a) and N-(2-hydroxypropanoyl)cinnamamide (1b) were carried out through amidation reaction using carbodiimide coupling reagent for 24 hours. The synthesized target compounds were characterized using FT-IR, GCMS-MS, 1H-NMR and 13C-NMR spectroscopy. The compounds were evaluated their antibacterial activity by molecular docking simulation against PBP2a (PDB ID: 1MWT) using AutoDock4 and AutoDockTools software. PBP2a is one of the main proteins in MRSA that has evolved to resist β-lactam antibiotics and was proposed to be the most likely target of MRSA. The inhibitory process of this protein works through inhibition of the bacterial cell wall. The synthesis process of 1a and 1b produced yields of 22.13% and 25.20%. Molecular docking results showed that 1a and 1b had better energy (ΔGbinding -7.33 and -6.29 kcal/mol) than Streptomycin as the control positive. The compounds of 1a and 1b had interactions on PBP2a through hydrogen bond with Asn464, Thr600, and Tyr519. This present study showed that the synthesized compounds from cinnamic acid derivatives have a potential to be used as antibacterial agents. Keywords: Amidation, antibacterial, 2-cinnamamido-4-methylpentanamide, molecular docking, N-(2-hydroxypropanoyl) cinnamamide.

The Potential of Paku Gajah (Angiopteris evecta) as Antitumor Through In Vitro and In Silico Studies Rasyid, Herlina; Asmirah, Asmirah; Firdausiah, Syadza; Arief, Ihsanul; Soekamto, Nunuk Hariani
Molekul Vol 19 No 2 (2024)
Publisher : Universitas Jenderal Soedirman

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20884/1.jm.2024.19.2.10644

ABSTRACT. Paku gajah (Angiopteris evecta) is one of the largest ferns which has been used empirically by the Dayak tribe of Kalimantan, Indonesia as a traditional medicine to treat various diseases, one of which is tumors. This research aims to determine the potential utilization of A. evecta stem extract as an antitumor by secondary metabolites analysis, toxicity and antitumor assay. The methods used in this study were gradual maceration using three solvents (n-hexane, ethyl acetate, and methanol), phytochemical screening, toxicity test, antitumor activity assay with the Alamarblue method, Liquid Chromatography-Mass Spectrometry (LC-MS) analysis, and molecular docking analysis. This study indicated that A. evecta stem extract contained secondary metabolites such as flavonoids, saponins, tannins, and steroids. The ethyl acetate and methanol were found as toxic extracts with LC50 130.67 and 314.31 µg/mL, respectively. In line with the toxicity, the antitumor activity of the ethyl acetate extract was the highest with an IC50 of 240.94 µg/mL and phytochemical analysis revealed the presence of violanthin and angiopteroside in the extract. Molecular docking showed that the binding energy and inhibition constants of violanthin and angiopteroside against receptors were higher than standard ligand F82. The interaction between violanthin and the receptor results five hydrogen-bond (H-bond) with Lys920, Cys919, Asp1046, and Leu840, while the angiopteroside produces four H-bonds with Leu836, Leu834, and Arg831. Keywords: Antitumor, molecular docking, paku gajah (Angiopteris evecta).

Inhibition of Human Acetylcholinesterase (4EY7) using Bioactive Compound from Moringa oleifera: Molecular Docking and Dynamic Studies Utami, Wiji; Apriyanto, Apriyanto; Antari, Laila; Rasyid, Herlina; Fitriani, Ika Nur
Jurnal Kimia Valensi Jurnal Kimia VALENSI, Volume 10, No. 2, November 2024
Publisher : Syarif Hidayatullah State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v10i2.39840

Alzheimer's disease is a neurodegenerative disorder caused by acetylcholine hydrolysis that impairs cognitive brain function. This research aims to determine the interaction and dynamic of ligands from Moringa oleifera on AChE through Lipinski's Rule, ADMET properties, molecular docking calculations, and molecular dynamic simulations. Lipinski's Rule calculation provided ligand limits that adhere to druglikeness properties. ADMET results also showed that several ligands satisfy ADMET properties. Pterygospermine has lower binding energy than the ligand control (-10.28 kcal mol-1) with amino acid residues of TYR133 and GLU202. It indicates a favorable interaction between the AChE receptor and ligand in the inhibition process. Based on molecular docking calculations, pterygospermine inhibits the AChE receptor at the Long, narrow aromatic gorge active site. According to molecular dynamic simulations, the MMPBSA energy for pterygospermine is 37.377 kJ mol-1. The samples showed a total average RMSD of 2 Å, suggesting no significant conformational changes throughout the simulation. The sample's average RMSF value is around 2 Å, suggesting favorable interactions with the receptor during simulation. However, this data is different from the ligand control interaction mode. Molecular dynamic investigations of the pterygospermine ligand in the complex revealed the stability and unfolded effect on the protein. The results of this study propose a candidate anti-Alzheimer's ligand from Moringa oleifera against the AChE receptor. In practice, these results can contribute to research studies exploring natural ingredients from plants with medicinal potential in drug discovery. These results can be validated using further research in vitro and in vivo.

In Silico Study of Alkaloid Compounds from Sida rhombifolia (Sidaguri) as Antimalarial Agents Targeting Plasmodium falciparum Dihydrofolate Reductase Arfansyah, Arfansyah; Sepyana, Anisa; Bahrun, Bahrun; Artasasta, Muh Ade; Rasyid, Herlina
Indonesian Journal of Chemistry Vol 25, No 4 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.106340

Malaria, caused by the Plasmodium parasite, represents a significant global health challenge, with approximately 229 million cases reported in 2020. Current treatments include artemisinin-based combination therapy; however, drug resistance poses serious issues. Natural products, including alkaloids from Sida rhombifolia, particularly cryptolepine, effectively inhibit Plasmodium falciparum through DNA intercalation. Research indicates that mutations in the PfDHFR enzyme of P. falciparum contribute to drug resistance, highlighting the urgent need for new inhibitors. A literature review combined with SwissADME, toxicology predictions, and molecular docking methods identified 11-cryptolepine carboxylic acid (B1) and N-trans-feruloyl tyramine (B11) as potential new inhibitors. The compounds exhibited binding energies of −7.22 and −8.41 kcal/mol, which are close to the native ligand (−7.31 kcal/mol). Additionally, they demonstrate favorable drug-likeness properties, indicating their potential as viable candidates for drug development. The molecular dynamics simulation for 100 ns was conducted to observe molecular interactions in a specific system dynamically. It was found that ligand B1 has better stability compared to ligand B11. This compound demonstrates significant potential for advancing malaria treatment strategies. Further research and clinical evaluation are warranted to fully realize their potential and translate these findings into effective clinical interventions for combating malaria globally.

AVERAGE LINKAGE CLUSTERING METHOD AND MOLECULAR DOCKING STUDY ON DATE PALM (PHOENIX DACTYLIFERA L.) AS POTENTIAL ANTI-ANEMIA AGENT Siswanto, Siswanto; Rasyid, Herlina; Ramadhani, Nur Aliah; Caesar, Nadia Nazwadiah; Sunusi, Nurtiti; Zainuddin, Zaraswati Dwyana
BAREKENG: Jurnal Ilmu Matematika dan Terapan Vol 18 No 4 (2024): BAREKENG: Journal of Mathematics and Its Application
Publisher : PATTIMURA UNIVERSITY

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.30598/barekengvol18iss4pp2459-2470

Anemia, characterized by blood hemoglobin (Hb) levels below the World Health Organization's (WHO) normal limit, remains a significant health concern. Date fruit (Phoenix dactylifera L.) stands out as an herbal plant boasting the highest iron content at 13.7 mg, suggesting its potential as an anti-anemia agent. This study aimed to explore the anti-anemia potential of active compounds in date fruit using average linkage clustering and validated using molecular docking. Compounds from dates were gathered via GC-MS analysis and online databases, totaling 145 compounds—50 from GC-MS and 95 from Knapsack and Dr. Duke databases. Additionally, 5 lead compounds served as positive controls for comparison. SwissADME online servers assessed the compounds' properties, serving as materials for the clustering method. The average linkage clustering method was employed, yielding an excellent dendrogram with a cophenetic correlation of 0.711. Notably, a total of 17 date fruit compounds are in the same cluster as the lead compounds. Molecular docking revealed 4 date palm fruit-derived compounds as potential PHD enzyme inhibitors, promising for anemia treatment. In conclusion, the average linkage clustering method and validation using molecular docking approaches highlight date fruit's potential as an alternative anemia treatment, showcasing the significance of interdisciplinary methodologies in drug discovery.

Toxicity and α-Amylase Inhibitory Potential of Tagetes erecta Leaf Extract: In Vitro and In Silico Approaches Rasyid, Herlina; Soekamto, Nunuk Hariani; Musa, Bulkis; Siswanto, Siswanto; Labanni, Arniati; Suma, Artania Adnin Tri; Syahrir, Nur Hilal A; Bahrun, Bahrun; Badrawati, Kadek Susi; Yusuf, Mohammad Taufik
Indonesian Journal of Chemistry Vol 25, No 5 (2025)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijc.104489

Tagetes erecta is one of traditional herbs with a variety of pharmacological actions. This study attempted to assess the toxicity and antidiabetic activity of T. erecta leaf extract. The extraction was carried out by maceration, then continued with phytochemical analysis. Toxicity of the extract was conducted using the brine shrimp lethality test. The antidiabetic activity was evaluated by α-amylase inhibitory using the 3,5-dinitrosalicylic acid method. The phytochemical of the most active extract was identified using GC-MS and subjected to bind the α-amylase (PDB ID: 2QV4) employing molecular docking. The LC50 values of n-hexane, EtOAc, and MeOH extracts were 33.41, 14.00, and 35.03 ppm, respectively, indicating high toxicity. The antidiabetic activity showed that EtOAc extract has the lowest IC50 value (1053.95 mg/L). Molecular docking analysis revealed the compounds 1–5 has range of binding energy at −4.07 to −4.83 kcal/mol. Acarbose as a positive control showed the lower binding energy at −5.03 kcal/mol, indicated more effective α-amylase inhibitory. This study revealed that T. erecta leaf extract has significant cytotoxic potential, which may warrant further exploration for anticancer applications. However, the relatively weak α-amylase inhibitory and lower binding affinity compared to acarbose imply limited utility as an antidiabetic agent.

Inhibition of Human Acetylcholinesterase (4EY7) using Bioactive Compound from Moringa oleifera: Molecular Docking and Dynamic Studies Utami, Wiji; Apriyanto, Apriyanto; Antari, Laila; Rasyid, Herlina; Fitriani, Ika Nur
Jurnal Kimia Valensi Jurnal Kimia VALENSI, Volume 10, No. 2, November 2024
Publisher : Department of Chemistry, Faculty of Science and Technology Syarif Hidayatullah Jakarta State Islamic University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.15408/jkv.v10i2.39840

Alzheimer's disease is a neurodegenerative disorder caused by acetylcholine hydrolysis that impairs cognitive brain function. This research aims to determine the interaction and dynamic of ligands from Moringa oleifera on AChE through Lipinski's Rule, ADMET properties, molecular docking calculations, and molecular dynamic simulations. Lipinski's Rule calculation provided ligand limits that adhere to druglikeness properties. ADMET results also showed that several ligands satisfy ADMET properties. Pterygospermine has lower binding energy than the ligand control (-10.28 kcal mol-1) with amino acid residues of TYR133 and GLU202. It indicates a favorable interaction between the AChE receptor and ligand in the inhibition process. Based on molecular docking calculations, pterygospermine inhibits the AChE receptor at the Long, narrow aromatic gorge active site. According to molecular dynamic simulations, the MMPBSA energy for pterygospermine is 37.377 kJ mol-1. The samples showed a total average RMSD of 2 Å, suggesting no significant conformational changes throughout the simulation. The sample's average RMSF value is around 2 Å, suggesting favorable interactions with the receptor during simulation. However, this data is different from the ligand control interaction mode. Molecular dynamic investigations of the pterygospermine ligand in the complex revealed the stability and unfolded effect on the protein. The results of this study propose a candidate anti-Alzheimer's ligand from Moringa oleifera against the AChE receptor. In practice, these results can contribute to research studies exploring natural ingredients from plants with medicinal potential in drug discovery. These results can be validated using further research in vitro and in vivo.

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