@article {2105, title = {Hepatitis E Inhibited by Rosmarinic Acid Extract from Clove Plant (Syzygium Aromaricum) through Computational Analysis}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {August 2023}, pages = {518-523}, type = {Original Article }, chapter = {518}, abstract = {

This study aims to evaluate the potential of Rosmarinic Acid as an inhibitor against Hepatitis E by interacting with the active site of the Tyrosine FYN protein. Computational approaches were employed to predict the molecular interactions between Rosmarinic Acid and Tyrosine FYN. The research methodology involved the use of software such as Pymol, Pyrex, Protein Plus, and the Lepinski Rule. Docking analysis was conducted using Pymol to obtain information about the binding energy between Rosmarinic Acid and Tyrosine FYN. The results of the analysis showed that Rosmarinic Acid exhibited a Binding Affinity of -8.3, -8, and -7.9, indicating a strong affinity towards the target protein. Additionally, Root Mean Square Deviation (RMSD) values of 0, 15.905, and 17.014 were used to assess the stability of the formed protein-ligand complex. Analysis using Protein Plus revealed interactions between Rosmarinic Acid and Tyrosine FYN. Furthermore, analysis using the Lepinski Rule to examine the physicochemical properties of Rosmarinic Acid indicated that the molecule had a mass of 360, 5 hydrogen bond donors, 8 hydrogen bond acceptors, a log P value of 1.76, and a molar reactivity of 89.8. These findings highlight the potential of Rosmarinic Acid as an inhibitor of Hepatitis E through its interaction with the Tyrosine FYN protein, providing a basis for the development of potential new therapies in the treatment of this disease.

}, keywords = {Hepatitis E, Molecular Docking., Rosmarinic acid, Syzygium aromaricum, Tyrosine FYN}, doi = {10.5530/pj.2023.15.112}, author = {Sunadi and Saddam Al Aziz and Fadhilah Fitri and Devni Prima Sari and Muhammad Raffi Ghifari and Rismi Verawati and Nita Yessirita and Oski Illiandri and Riso Sari Mandeli and Devi Purnamasari and Putri Azhari and Rahadian Zainul and Viol Dhea Kharisma and Vikash Jakhmola and Maksim Rebezov and ANM Ansori} } @article {2104, title = {In Silico Study of Rhamnocitrin Extract from Clove Syzygium Aromaricum in Inhibiting Adenosine A1 Adenylate Cyclase Interaction}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {August 2023}, pages = {512-517}, type = {Original Article }, chapter = {512}, abstract = {

This study aims to analyze the potential of Rhamnocitrin, a compound found in clove extract (Syzygium aromaticum), as an inhibitor of Adenylate Cyclase through an in-silico approach. The research method involves the use of software such as Pymol, PyRx, Protein Plus, and Lipinski Rule for molecular interaction analysis and physicochemical characterization of Rhamnocitrin. The analysis results show that Rhamnocitrin has significant affinity towards Adenosine A1 with Binding Affinity values of -6.1, -5.8, and -5.7. RMSD analysis indicates good stability of the formed protein-ligand complexes, with RMSD values of 0, 3.129, and 3.696. Analysis using Protein Plus software reveals the interaction between Rhamnocitrin and Adenosine A1, while the lipinski analysis shows physicochemical characteristics of Rhamnocitrin that meet important criteria, such as a mass of 300, 3 hydrogen bond donors, 6 hydrogen bond acceptors, log P of 2.6, and molar reactivity of 77.27. These findings provide new insights into the development of potential therapies involving clove extract and Rhamnocitrin as inhibitors of Adenylate Cyclase, and further research is needed to validate their effectiveness and safety.

}, keywords = {Adenosine A1, Adenylate Cyclase inhibition, Molecular Docking., Rhamnocitrin, Syzygium aromaricum}, doi = {10.5530/pj.2023.15.111}, author = {Nita Yessirita and Rismi Verawati and Devi Purnamasari and Rollando Rollando and Riso Sari Mandeli and Muhammad Thoriq Albari and Putri Azhari and Rahadian Zainul and Viol Dhea Kharisma and Vikash Jakhmola and Maksim Rebezov and ANM Ansori} } @article {2013, title = {Molecular Docking and ADME Studies of Centella Asiatica as Anti Hyperuricemia}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {April 2023}, pages = {384-389}, type = {Research Article}, chapter = {384}, abstract = {

Centella asiatica is a traditional natural medicine used in a number of Southeast Asian nations. (also known as Centella asiatica L., Urb., or Gotu Kola). The aim of this study is to determine the antihyperuricemia properties of Centella asiatica extract and the possibility that they will interact with the XDH enzyme. The XDH enzyme is one of three enzymes that can influence the onset of hyperuricemia with the other two are SLC22A12 and ABCG2. In this research, we employ a computational method in collaboration with a number of applications and databases. ADME analysis was carried on for some Centella asiatica constituents to determine their similarities to the drug and bioavailability components. The analysis continued on with molecular docking between the chemical compounds and several enzymes related to hyperuricemia. According to the findings, Centella asiatica contains active constituents that can be used as an alternative therapy for hyperuricemia.

}, keywords = {Centella asiatica, Hyperuricemia, Molecular Docking.}, doi = {10.5530/pj.2023.15.59}, author = {Ahmad Shobrun Jamil and Prayogi Galie Saputro} } @article {2073, title = {Phytochemical Compounds Identification From 70\% Ethanol Extract of Arcangelesia Flava (L.) Merr Stems Using LC-MS/MS and In-Silico Molecular Docking Approach as Inhibitor Interleukin-1β}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {August 2023}, pages = {528-534}, type = {Research Article}, chapter = {528}, abstract = {

Arcangelisia flava (L.) Merr has been traditionally used to treat jaundice, liver disease, diarrhea, fever, and inflammation. Judging from its potential, scientific evidence of this plant extract as an inhibitor of interleukin-1β is still lacking. This study aims to investigate the phytochemical compounds present in the 70\% ethanol extract of Arcangelesia flava stems by LC-MS/MS and to elucidate the ligand-protein interactions through in-silico studies. The extract was found to contain alkaloids, flavonoids, furanoditerpene, hydroxyquinoline, phenylpropanoid, phenol, and fatty acids. According to molecular docking of the 15 compounds analyzed by LC-MS/MS, the compounds 3-hydroxy-3{\textquoteright},4{\textquoteright},5{\textquoteright}-trimethoxyflavone (ΔG=-7.72 kcal/mol), fisisaine (ΔG=-6,91 kcal/mol), and demethyleneberberine (ΔG=-6.85 kcal/mol), which demonstrated the highest affinity for binding to the protein target. In addition, active amino acids contribute to this interaction by creating strong hydrogen bonds, such as MET148, LYS 103, and THR300. Phytochemical compounds from Arcangelesia flava may serve as adjunctive therapy or a promising source of advanced structures in drug discovery for treatments targeting interleukin-1β

}, keywords = {Arcangelisia flava (L.) Merr, Inhibitor interleukin-1β, LC-MS/MS, Molecular Docking.}, doi = {10.5530/pj.2023.15.114}, author = {Rizki Rahmadi Pratama and Irawati Sholikhah and Sukardiman and Ram Kumar Sahu and Retno Widyowati} } @article {2084, title = {Stimulation of Emodin from Aloe Vera on Protein Kinase PIM1 in the Central Nervous System Through In Silico Analysis}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {August 2023}, pages = {587-592}, type = {Research Article}, chapter = {587}, abstract = {

This study aims to investigate the potential of Emodin, a compound found in Aloe vera, as a stimulator of Protein Kinase PIM1 in the central nervous system using an in-silico approach. The research method involves the use of software such as Pymol, Pyrex, Protein Plus, and Lepinski Rule. Firstly, the protein structure of the target Protein Kinase PIM1 was obtained from a protein database and prepared using Pymol. Next, the molecular structure of Emodin was imported into Pyrex and subjected to geometry optimization. Docking analysis using Pymol was performed to predict the molecular interactions between Emodin and Protein Kinase PIM1. Additionally, RMSD analysis was conducted to evaluate the stability of the protein-ligand complex formed. The docking analysis results showed that Emodin exhibited significant Binding Affinity, with values of -8.4, -8.3, and -8.2, indicating a strong affinity between Emodin and Protein Kinase PIM1. The RMSD analysis indicated the stability of the protein-ligand complex, with RMSD values of 0, 1.101, and 1.122. Furthermore, analysis using Protein Plus revealed the presence of interactions between Emodin and Protein Kinase PIM1 through hydrogen bonding and hydrophobic contacts. The results of the Lepinski Rule analysis demonstrated that Emodin fulfilled several important criteria in drug design, including a molecular weight of 270, 3 hydrogen bond donors, 5 hydrogen bond acceptors, a log p value of 1.887220, and a molar reactivity of 64.480385. These findings indicate the potential of Emodin as a stimulator of Protein Kinase PIM1 in the central nervous system and provide an important foundation for the development of potential therapies for central nervous system-related disorders.

}, keywords = {Central Nervous System, Emodin, Molecular Docking., PIM1 Kinase, Stimulation}, doi = {10.5530/pj.2023.15.124}, author = {Rahadian Zainul and Rismi Verawati and Ritbey Ruga and Muhammad Arya Ghifari and Devi Purnamasari and Putri Azhari and Viol Dhea Kharisma and Vikash Jakhmola and Maksim Rebezov and ANM Ansori} } @article {1800, title = {Utilization of Secondary Metabolites in Algae Kappaphycus alvarezii as a Breast Cancer Drug with a Computational Method}, journal = {Pharmacognosy Journal}, volume = {14}, year = {2022}, month = {June 2022}, pages = {536-543}, type = {Original Article}, chapter = {536}, abstract = {

Breast cancer is one of the worst diseases that affect female people. Long-term treatment with therapy or surgery has a detrimental impact on the patient. The algae Kappaphycus alvarezii has gotten a lot of interest as a breast cancer medication because it contains chemicals that are expected to be anti-cancer. The objectives of this paper were to see how secondary metabolites in algae interact with the Nuclear Factor- kappaB protein kinase in breast cancer. The ligands and proteins were obtained from the PubChem and PDB websites, respectively. Swiss ADME was then used to assess the Pharmacokinetics and Drug likeness Properties. The last stage involved using molecular docking with PyRx and molecular dynamics to identify the interaction and visualization between the ligand and the target protein. The findings of the test revealed that the maraniol chemical had a superior binding capacity with NF kB protein kinase because it has a chromone group that controls transport efficiently in preventing breast cancer proliferation.

}, keywords = {Breast cancer, K. alvarezii, Molecular Docking., NF kB protein kinase}, doi = {10.5530/pj.2022.14.68}, author = {AF Dibha and S Wahyuningsih and ANM Ansori and VD Kharisma and MH Widyananda and AA Parikesit and MT Sibero and RT Probojati and AAA Murtadlo and JP Trinugroho and TH Sucipto and DDR Turista and I Rosadi and ME Ullah and V Jakhmola and R Zainul} } @article {327, title = {Identification and Characterization of Berberine in Tinospora cordifolia by Liquid Chromatography Quadrupole Time of Flight Mass Spectrometry (LC MS/MS Q-tof) and Evaluation of its anti Inflammatory Potential}, journal = {Pharmacognosy Journal}, volume = {9}, year = {2017}, month = {April 2017 }, pages = {350-355}, type = {Original Article}, chapter = {350}, abstract = {

Introduction: Tinospora cordifolia (Willd.) Miers ex Hook F and Thomas commonly called as gudduchi or amrita is a widely used plant in traditional medicinal system of Ayurveda. A UPLC MS/MS Q-tof method for the identification and characterization of berberine in Tinospora cordifolia (Willd.) Miers. ex HooK.F. and Thomas. and to evaluate the anti inflammatory potential of bioactive fraction. Materials and Methods: The presence of berberine in Tinospora cordifolia was determined by HPLC and was subsequently isolated by HPTLC. The anti inflammatory property of the fraction containing berberine was demonstrated to have an inhibitory activity on 5 lipoxygenase, an enzyme involved in inflammatory pathway and its IC50 value was obtained. The binding interactions between berberine and 5-LOX were demonstrated by docking studies. Result: The presence of berberine in Tinospora cordifolia methanolic extract was identified by HPLC and HPTLC analysis and confirmed by UPLC MS/ MS Q-tof. The fraction containing berberine inhibited 5-LOX with an IC50 of 0.041\± 0.0003\μg/mL as compared to that of NDGA (positive control) which showed an IC50 of 2.75 \± 0.05 \μg/mL. Molecular docking of berberine with 5-LOX showed a binding energy of -8.942 \± 0.039665 kcal/mol and Ki of 273.16 \± 3.026 nM as compared to the NDGA which has a binding energy of -7.186 \± 0.170503 kcal/mol and Ki 5.604\± 1.618 \μM. Conclusion: Tinospora cordifolia can be used as a source of berberine and possible anti inflammatory activity of Tinospora cordifolia may be attributed to the presence of berberine.

}, keywords = {5 Lipoxygenase, Berberine, Mass spectrometry, Molecular Docking., Tinospora cordifolia}, doi = {10.5530/pj.2017.3.59}, url = {/files/PJ-9-3/10.5530pj.2017.3.59}, author = {Mohind C. Mohan and Anu P. Abhimannue and Prakash Kumar B} }