@article {2493, title = {Andrographolide and Resveratrol as Potential Modulators of AIM2 and IFI16 Inflammasomes in Periodontitis: A Docking Study}, journal = {Pharmacognosy Journal}, volume = {17}, year = {2025}, month = {April 2025}, pages = {179-187}, type = {Original Article}, chapter = {179}, abstract = {

Background: Proinflammatory cytokines play a critical role in the destruction of periodontal tissues. DNAsensing inflammasomes, such as AIM2 and IFI16, are key mediators in the secretion of IL-1 and IL-18 and facilitate pyroptosis in periodontitis. Andrographolide and resveratrol are phytocompounds known for their anti-inflammatory effects, though their precise mechanisms of action remain uncertain. This study aimed to elucidate the molecular interactions of andrographolide and resveratrol with AIM2 and IFI16 inflammasomes using a computational approach. Methods: Ten phytocompounds were selected and analyzed via molecular docking. Protein-ligand docking was conducted with AutoDock 4.2.6. Binding affinities and hydrogen bond interactions were assessed. Andrographolide and resveratrol complexes with AIM2 and IFI16 were further subjected to 100 ns molecular dynamics simulations using GROMACS software to assess complex stability. Results: Both andrographolide and resveratrol complexes demonstrated stability throughout the simulations, with adequate inter-hydrogen bonding. Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) analysis revealed that AIM2-andrographolide (-112.100 {\textpm} 18.106 kJ/mol) and IFI16-andrographolide (-50.047 {\textpm} 27.076 kJ/mol) complexes exhibited higher binding energies compared to AIM2-resveratrol (-15.328 {\textpm} 2.539 kJ/mol) and IFI16-resveratrol (-12.534 {\textpm} 20.184 kJ/mol) complexes. Conclusion: Molecular docking and dynamics analyses indicate that andrographolide demonstrates a stronger binding affinity to AIM2 and IFI16 inflammasomes compared to resveratrol. This suggests andrographolide as a promising host modulatory candidate for the therapeutic management of periodontitis.

}, keywords = {AIM2 inflammasome, Andrographolide, IFI16 inflammasome, Molecular docking, Periodontitis, Resveratrol}, doi = {10.5530/pj.2025.17.22}, author = {Lalitha Tanjore Arunachalam and Snophia Suresh and Vamsi Lavu and Shankarram Vedamanickam and Nissanthe Nagarajan} } @article {2477, title = {In Vitro Antibacterial Activity, In-Silico Molecular Docking and Pharmacokinetic Profile of a Phytosterol Isolated from The Leaves of Carissa Bispinosa}, journal = {Pharmacognosy Journal}, volume = {17}, year = {2025}, month = {January 2025}, pages = {99-106}, type = {Research Article}, chapter = {99}, abstract = {

Carissa bispinosa (L.) Desf. Ex-Brenan is a medicinal plant widely used in South Africa. The study reports on the isolation of a phytosterol from C. bispinosa along with molecular docking and pharmacokinetic studies. The phytochemicals were extracted with hexane, dichloromethane, acetone and methanol. The compound was isolated following a bioactivity-guided isolation protocol using column-chromatography and thin-layer chromatography. Nuclear magnetic resonance (NMR) was used for compound characterisation. The antimicrobial activity was assessed using bioautography and micro-broth dilution assays. AutoDock vina, SwissADME and ADMET lab were used for molecular docking, pharmacokinetic and toxicological properties, respectively. Drug-likeness was evaluated based on Lipinski{\textquoteright}s rule of five (Ro5). The isolated compound was identified as β-sitosterol. It had an anti-S. aureus activity of (0.31 mg/mL). It revealed binding scores of -7.2 and -6.4 kcal/mol against penicillin-binding protein and DNA gyrase, respectively. It violated one of Ro5 (MLOGP \> 4.15). It has no inhibitory effects against isoforms of cytochrome P450. Moreover, it demonstrated no adverse effect on skin, non-carcinogenic and non-hepatotoxic effects. Based on the results, β-sitosterol can be considered as potential anti-S. aureus drug. Further studies may focus on ascertaining the mechanism of action in-vitro and investigating the synergistic effects of the compound with conventional drugs.

}, keywords = {Antimicrobial, Carissa bispinosa, Molecular docking, Pharmacokinetics}, doi = {10.5530/pj.2025.17.14}, author = {Wanda Shekwa and Mashilo Mash Matotoka and Tsolanku Sydney Maliehe and Peter Masoko} } @article {2528, title = {In-Silico Study of Bioactive Compounds from Moringa oleifera Fruit as Anti Premature Senescence Agents in Cardiac Cells: A Study on the p53 Protein}, journal = {Pharmacognosy Journal}, volume = {17}, year = {2025}, month = {August 2025}, pages = {497-505}, type = {Original Article}, chapter = {497}, abstract = {

Background: Cellular senescence, characterized by irreversible cell cycle arrest, contributes significantly to the pathogenesis of cardiovascular diseases through mechanisms involving oxidative stress and activation of p53-mediated signaling. Moringa oleifera, widely recognized for its antioxidant properties, has demonstrated anti-aging effects; however, the specific bioactive compounds within its fruit and their mechanisms of action remain poorly understood. Objective: This study aimed to investigate the potential of M. oleifera fruit-derived compounds as anti-premature senescence agents targeting the p53 protein using in-silico molecular docking approaches. Methods: Bioactive compounds from M. oleifera fruit were screened via molecular docking against the human p53 protein, with Nutlin-3 used as a positive control. Binding affinities, hydrogen bonding, and hydrophobic interactions were analyzed to determine ligand{\textendash} receptor interactions. Results: Niacin and oxalic acid exhibited stronger binding affinities ({\textendash}5.90 and {\textendash}6.00 kcal/mol, respectively) compared to Nutlin-3 ({\textendash}5.64 kcal/mol). Niacin formed stable hydrogen bonds and hydrophobic interactions with key residues within the p53 active site, suggesting a capacity to modulate p53 activity. Oxalic acid demonstrated the highest binding affinity but lacked hydrogen bonding, indicating potential instability despite strong interaction. These findings support previous studies highlighting M. oleifera{\textquoteright}s role in ROS suppression and p53 modulation, pointing to its therapeutic relevance in mitigating cellular aging. Conclusion: Niacin and oxalic acid from M. oleifera exhibit promising binding characteristics as modulators of the p53 pathway. Their anti-senescence potential warrants further validation through molecular dynamics simulations and biological assays. This study supports the development of natural compound-based therapeutics for age-related cardiac degeneration.

}, keywords = {Antioxidant, cellular senescence, in silico, Molecular docking, Moringa oleifera, p53 protein}, doi = {10.5530/pj.2025.17.62}, author = {Tiwuk Susantiningsih and Ichwan Baihaki and Maria Selvester Thadeaus and Yuni Setyaningsih and Mila Citrawati} } @article {2523, title = {Moringa oleifera Fruit Secondary Metabolites Role in Sarcopenic Obesity via Fat Mass and Obesity-Associated Protein: An In Silico Analysis}, journal = {Pharmacognosy Journal}, volume = {17}, year = {2025}, month = {August 2025}, pages = {450-457}, type = {Original Article}, chapter = {450}, abstract = {

Background: Sarcopenic obesity (SO) refers to the coexistence of sarcopenia and obesity, pathogenic interaction between loss of skeletal muscle and function and fat-mass accumulation. Fat mass and obesityassociated (FTO) protein is one of the proteins that involved in pathophysiology of SO. Moringa oleifera is one of potential drug candidates for degenerative diseases due to its various bioactive metabolites from most parts of this plant. Objective: An in silico study, employing computational methods to simulate molecular interactions through molecular docking, aims to investigate the potential of Moringa oleifera fruit secondary metabolites to interact with FTO protein. Methodology: This study was carried out the molecular docking analysis of Moringa oleifera fruit secondary metabolites that was retrieved from database and have been screened for drug-likeness and toxicity for FTO protein inhibitor candidates. Molecular docking was using Pyrx v0.8, AutoDock 4.2.6 by AutoDockTools 1.5.7, and BIOVIA Discovery studio client 2025 as visualization tools. Results: This study showed 9 bioactive compounds from Moringa oleifera fruit is bioavailable and safe for oral drugs according to Lipinski Rule of 5 (RO5) and Oral Rat Acute Toxicity (LD50). Molecular docking results showed riboflavin is the most potential compound as FTO protein inhibitor as its strongest affinity and interaction in active site compared to FTO protein native ligands 3-methylthymidine (DT). Conclusion: Therefore, Moringa oleifera fruit is potential for SO therapy candidates through regulation of FTO protein activity.

}, keywords = {and riboflavin, FTO protein, Molecular docking, Moringa oleifera fruit, sarcopenic obesity (SO)}, doi = {10.5530/pj.2025.17.57}, author = {Mila Citrawati and Assyafiya Salwa and Yuni Setyaningsih and Cut Fauziah and Tiwuk Susantiningsih} } @article {2333, title = {Comparative Analysis Molecular Simulation IL6R Alpha with TCZ and HIL6: Mechanism in Inflammatory Responses}, journal = {Pharmacognosy Journal}, volume = {16}, year = {2024}, month = {August 2024}, pages = {738-743}, type = {Original Article}, chapter = {738}, abstract = {

Introduction: In cases of inflammation, there is typically a connection between IL6R and HIL6. If there is an excessive level of activity in this connection, it can lead to a cytokine storm. Tocilizumab (TCZ), also known as AntiIL-6R, is a biologic drug that is a recombinant humanized monoclonal antibody. It is specifically used to treat inflammatory and autoimmune diseases that are associated with cytokine storms. Method: This study utilizes in silico analysis to assess the ability of TCZ, a biosimilar, to block IL6R and compares it to the blocking effect of HIL6. Validation of the 3D structure of the IL6R was performed using a Ramachandran plot. Results: The IL6R alpha subunit had a validation score of 97.86\%, while the IL6R beta subunit had a validation value of 95.54\%. The molecular docking analysis reveals that the TCZ light chain forms a complex with IL6R, yielding a docking score of -16.4 kcal mol-1. Similarly, the TCZ heavy chain also interacts with IL6R, resulting in a docking value of -15.5 kcal mol-1. Notably, both scores are higher than the docking score of the control, which involves IL6R with HIL6, measuring -12.5 kcal mol- 1. The root mean square fluctuation (RMSF) value of the IL6R protein in the presence of TCZ (Tocilizumab) is consistently below 2, with an average range of 0.04-0.09. Conclusion: The affinity between IL6R and TCZ is greater than the affinity between IL6R and HIL6.

}, keywords = {Binding affinity, HIL6, IL6, IL6R, Molecular docking, Molecular dynamics.}, doi = {10.5530/pj.2024.16.123}, author = {Engla Merizka and Septelia Inawati Wanandi and Budiman Bela and Silvia Tri Widyaningtyas and Fadilah Fadilah} } @article {2219, title = {Screening and Identification of Metabolites from Sambiloto (Andrographis paniculata) Ethanol Extract for Pro-Inflammatory Cytokines Inhibitory through In Silico and In Vitro Approaches}, journal = {Pharmacognosy Journal}, volume = {16}, year = {2024}, month = {February 2024}, pages = {131-140}, type = {Research Article}, chapter = {131}, abstract = {

Objective: Andrographis paniculata has long been a traditional medicinal plant in Indonesia. This study is intended to evaluate the anti-pro-inflammatory cytokines of 98\% ethanol extract of A. paniculata by in vitro and in silico approaches. Inhibition of pro-inflammatory cytokines is also one of the therapies in treating COVID-19. Methods: The molecular docking approach was utilized as a first screening to evaluate the potential for suppression of macrophage cell activation; an ADMET prediction test was performed to determine the pharmacological, pharmacokinetic, and toxicity as a therapeutic target. TNF-α, IL-1{\ss}, and IL-6 levels were measured using an ELISA method to investigate anti-cytokine pro-inflammatory activity in LPS-induced RAW 264.7 macrophage cells. LC-MS/MS was used to identify additional metabolite compounds. Results: Ethanol extract containing particular metabolites 14-Deoxyandrographoside and 14-Deoxy-17-hydroxyandrographolide inhibited TNF-α and IL-1β by 100\% and IL-6 by 85.59\%, respectively. While compared to the Dexamethasone molecule as a positive control, preliminary screening and ADMET prediction for the metabolite compound 14-Deoxyandrographoside exhibited relatively high binding stability to the CD14 receptor by -7.5 kcal/mol and was safe against various ADMET indications. Conclusions: This study reveals that the compound 14-Deoxyandrographoside in pure ethanol extract is a potential anticytokine agent candidate for treating pro-inflammatory cytokines, including COVID-19 infection.

}, keywords = {LC-MS/MS, Molecular docking, Pro-inflammatory cytokines, Sambiloto}, doi = {10.5530/pj.2024.16.18}, author = {Evul Winoto Lukito and Dyah Iswantini and Budhi Antariksa and Mohamad Rafi and Setyanto Tri Wahyudi} } @article {2208, title = {Unveiling Potential Therapies: Molecular Docking Analysis of CAMKK2 and Its Mutant Variants with CAMKK2 Inhibitors in Indonesian Patients with HIV-Sensory Neuropathy}, journal = {Pharmacognosy Journal}, volume = {16}, year = {2024}, month = {February 2024}, pages = {46-51}, type = {Original Article}, chapter = {46}, abstract = {

HIV sensory neuropathy (HIV-SN) is one among many complications that impair patients{\textquoteright} quality of life. Studies in Asian and African populations found that single nucleotide polymorphisms (SNPs) of calcium/ calmodulin-dependent protein kinase 2 (CAMKK2) influence the risk of HIV-SN. This study attempts to explain the influence of CAMKK2 mutations on HIV SN by studying bioinformatics interactions between CAMKK2, its mutants, and their inhibitors by molecular docking with AutoDock in order to observe their interactions with CAMKK2 inhibitors. Results showed that CAMKK2{\textquoteright}s binding energy with its native ligand (ATP) is stronger than the mutant variant of CAMKK2MT85 and CAMKK2MT363. Conversely, interaction between CAMKK2 and its inhibitors (KN-93, STO-609, and trifluoperazine) have the lowest mean binding energy compared to CAMKK2MT85 and CAMKK2MT363. This indicates that the mutant variants have weaker interactions with the native ligand and the inhibitors, therefore disrupting the normal function of CAMKK2, its interactions with the inhibitors, while increasing the likelihood of HIV-SN.

}, keywords = {CAMKK2 inhibitors, HIV-SN, Molecular docking, mutation, SNP}, doi = {10.5530/pj.2024.16.7}, author = {Ahmad Yanuar Safri and Salim Harris and Putera Dewa Haryono and Ariane Benina Budiwan and Eugenia Isadora and Aisyah Fitriannisa Prawiningrum and Fadilah Fadilah} } @article {1992, title = {Antibacterial and Anti-quorum Sensing Activities of Erianthemum dregei{\textquoteleft}s Leaf Extract and Molecular Docking}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {April 2023}, pages = {279-285}, type = {Original Article }, chapter = {279}, abstract = {

Background: The increasing incidence of multi-drug resistance among pathogens has propelled researchers to search for novel antimicrobial and anti-quorum sensing agents characterised by different mechanisms and high potency. Objective: The study aimed at investigating the antibacterial and antiquorum sensing properties of compounds from Erianthemum dregei and their molecular interactions with the target proteins. Methods: The methanolic leaf extract from E. dregei was evaluated for its chemical composition and antibacterial activity using gas chromatography-mass spectrophotometry (GC-MS) and micro-dilution method, respectively. The inhibition of violacein production in Chromobacterium violaceum (ATCC 07) was assayed as anti-quorum sensing activity using micro-dilution method. The molecular docking of the GC-MS ligands and penicillin-binding protein 2x (PDP2) and CviR was executed using AutoDock Vina. Results: The two volatile compounds namely phytol (93.58\%) and 3-tetradecyn-1-ol (6.42\%) were shown by GC-MS. The extract exhibited antibacterial activity against the selected bacterial strains with minimum inhibitory concentration (MIC) values ranging from 1.56 to 3.125 mg/mL. The maximum inhibition of violacein production of 53.93\% was observed at 1.56 mg/mL. Both compounds had docking scores of more than -6.0 kcal/mol against the target proteins. Conclusion: The results revealed that the extract is a potential source of antibacterial and anti-quorum sensing compounds and thus can have pharmacological applicability.

}, keywords = {Anti-quorum sensing activity, Antibacterial activity, Erianthemum dregei, Molecular docking}, doi = {10.5530/pj.2023.15.39}, author = {Tsolanku Sidney Maliehe and Tlou Nelson Selepe and Nokuthula Nomusa Mthembu and Jabulani Siyabonga Shandu} } @article {1981, title = {Computational and Pharmacokinetic Investigation of Some Heterocyclic Amide Derivatives as Cyclooxygenase Inhibitors: An In-Silico Approach}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {March 2023}, pages = {194-207}, type = {Research Article}, chapter = {194}, abstract = {

The two most significant as well as historically important non-steroidal and anti-inflammatory medications (NSAIDs), aspirin and ibuprofen, are frequently used to treat fever, pain, and inflammation. By blocking the activity of cyclooxygenase (COX), it can prevent the production of prostaglandin. In an effort to examine the physiochemical and biological properties of some heterocyclic amide derivatives and quantum mechanical computations have been used to analyze the compounds. To clarify the thermochemical, molecular orbital, and equilibrium geometrical features in the gas phase, density functional theory (DFT) with the B3LYP/6- 31G basis set has been used. Binding affinities and modes of heterocyclic amide analogs have been investigated on human cyclooxygenase (COX-1 and COX-2) proteins (6Y3C and 5F19) using molecular docking as well as nonbonding interactions. Results from geometry and thermochemical analysis support the chemical sustainability of all the structures. Most of the compounds exhibited a significant affinity for binding to the receptor protein (5F19) than the standard drugs aspirin and ibuprofen. The improved pharmacokinetic features of certain derivatives with reduced acute oral toxicity were revealed by ADMET prediction. Overall, four heterocyclic amide analogs 3-6 were found to be more efficient in inhibiting COX- 2 (5F19) than COX-1 (6Y3C), suggesting that they may be useful as COX-2-related inflammation drug candidates.

}, keywords = {ADMET., Cyclooxygenase (COX), Heterocyclic amide derivatives, Molecular docking}, doi = {10.5530/pj.2023.15.29}, author = {Emranul Kabir and M. R. O. Khan Noyon and Monir Uzzaman} } @article {2066, title = {Computational Evaluation of the Potential of Salicylate Compound from Syzygium aromaticum on Carbonic Anhydrase I as a Gastric Acid Stimulant}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {August 2023}, pages = {489-493}, type = {Original Article }, chapter = {489}, abstract = {

This article explores the potential of the salicylate compound (Syzygium Aromaticum) as a stimulant for Carbonic Anhydrase I in gastric acid secretion, using a computational approach. The research methods include molecular modeling with Pymol and Pyrex, determination of compound structure and interactions with Protein Plus, and examination of physicochemical properties using the Lipinski Rule. The results show that the Binding Affinity of salicylate with Carbonic Anhydrase I ranges from -7.3 to -6.5, with RMSD values of 0, 2.102, and 2.212, indicating good modeling quality. The interaction between salicylate and Carbonic Anhydrase I is also supported by the findings from Protein Plus. Furthermore, the salicylate compound complies with the Lipinski Rule, with a molecular weight of 137, 1 hydrogen bond donor, 3 hydrogen bond acceptors, a log P value of 0.34, and a molar reactivity of 34.16. This study highlights the prospect of salicylate as a potential modulator of Carbonic Anhydrase I.

}, keywords = {Carbonic Anhydrase I, Gastric Acid Stimulant, Molecular docking, Salicylate, Syzygium Aromaticum.}, doi = {10.5530/pj.2023.15.107}, author = {Rahadian Zainul and Rismi Verawati and Rauza Sukma Rita and Fadhli Ranuharja and Musa Ghufron and Agariadne Dwinggo Samala and Herland Satriawan and Muhammad Raffi Ghifari and Devi Purnamasari and Riso Sari Mandeli and Amalia Putri Lubis and Viol Dhea Kharisma and Vikash Jakhmola and Maksim Rebezov and ANM Ansori} } @article {1986, title = {Curcumin from Curcuma longa L. as Dual Inhibitors Against Indonesian SARS-CoV-2 Isolates: A Molecular Docking Study}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {March 2023}, pages = {228-232}, type = {Research Article}, chapter = {228}, abstract = {

COVID-19 has become a global pandemic since 2020. The search for promising drugs based on the abundant herbal ingredients in Indonesia is one of the breakthroughs. Curcumin is a chemical compound with various potentials such as antioxidant, anti-inflammatory and antiviral. We conducted a molecular docking analysis to determine the potential of curcumin against SARS-CoV-2 non-structural and structural proteins, such as the main protease and spike protein. This study used the compound of curcumin (PubChem CID: 969516) from Curcuma longa L. or turmeric and two Indonesian SARS-CoV-2 isolates that have been deposited in the GISAID database (hCoV-19/Indonesia/JI-PNF-217315/2021 - EPI_ ISL_12777089 or lineage B.1.617.2 and hCoV-19/Indonesia/JI-PNF-211373/2021 - EPI_ISL_6425649 or lineage B.1.470). In addition, we used molnupiravir (PubChem CID: 145996610) as a drug control. We performed molecular docking analysis with PyRx software 0.9.9 (academic license) and visualization of molecular docking results with PyMOL software 2.5.4 (academic license). The results of this study found that curcumin had good potential against main protease and spike protein compared to the drug (control). In summary, we suggested that curcumin is a potential drug candidate against SARS-CoV-2. However, there is a need for future wet laboratory-based pre-clinical research such as in vitro and in vivo.

}, keywords = {COVID-19, Curcumin, Indonesia, Molecular docking, SARS-CoV-2}, doi = {10.5530/pj.2023.15.34}, author = {Chairul A. Nidom and Arif N. M. Ansori and Astria N. Nidom and Setyarina Indrasari and Reviany V. Nidom} } @article {2123, title = {Evaluation of In vivo Analgesic and Anti-inflammatory Activity of Oroxyulum indicum, Baicalein, Chrysin with Phytochemical Analysis and Molecular Docking Study}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {October 2023}, pages = {811-822}, type = {Research Article}, chapter = {811}, abstract = {

Background: Oroxyulum indicum (OIE) is a native medicinal plant that has been widely employed in Ayurvedic medicine for thousands of years. Though studies have been published citing the analgesic and anti-inflammatory activity of Oroxyulum indicum and chrysin and Baicalein, there has been no comparative study comparing their activittes and confirming them with molecular docking results. Molecular docking study of two phytochemicals Chrysin (PubChem CID 5281607) and Baicalein (PubChem CID 5281605) into the active sites of cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2). Evaluation and validation of Anti-inflammatory and Analgesic effects of a methanolic extract of the stem bark of Oroxylum indicum and its two constituents Chrysin and Baicalein in Charles foster rats with analysis of the phytoconstituent of Oroxyulum indicum through HRMS analysis. Methodology: UHPLC-HRMS/MS analyses were performed on a Dionex Ultimate 3000 RS Series UHPLC system combined with a Q Exactive Plus High-Resolution Accurate Mass Spectrometry System. Hot plate and Tal flick model are used for screening of analgesic activity. TNF-alpha and IL-6 inflammatory markers were examined. Carrageenan model is used for antiinflammatory analysis. Result: Interesting results has been obtained in the docking studies of Chrysin and Baicalein with COX-1 (PDB ID: 1EQG). The hydrogen bond interaction established between the Chrysin and Baicalein with the important amino acid, includes Arg 120, Tyr 355, Ser 530, Met 522 (Figure 1). The binding free energy of the Chrysin and Baicalein with target COX-1 was found to be -7.88 and -7.26 Kcal/mol. Conclusion: There is marked reduction in the TNF Alpha expression in the OIE group which is followed by Baicalein and Chrysine. The Baicalein group shows the most marked cumulative increase in reaction time for tail flick among all the groups of the intervention group followed by Chrysine and OIE.

}, keywords = {Baicalein, Chrysine, Molecular docking, Oroxylum indicum, TNF alpha.}, doi = {10.5530/pj.2023.15.156}, author = {Bhairav Kumar Pathak and Kamlesh M. Palandurkar and Meenakshi Singh and Anshuman Trigunayat and Amit Singh and Reena Giri and Kiran Rajendra Giri} } @article {2081, title = {In Silico Study on the Inhibition of Sitogluside from Clove Plant (Syzygium aromaticum) on Interleukin 2 in B and T Cell Proliferation}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {August 2023}, pages = {575-580}, type = {Research Article}, chapter = {575}, abstract = {

This research discusses an in-silico study of sitogluside found in the clove plant (Syzygium aromaticum) as a potential inhibitor of B and T cell proliferation through interaction with Interleukin-2. This study utilizes methods such as Swiss Target Prediction, Pymol, Pyrex, Protein Plus, and Lipinski{\textquoteright}s Rule to predict the biological activity and pharmacokinetic characteristics of sitogluside. From the docking simulation results, sitogluside exhibited strong interactions with interleukin-2 with RMSD values of 0, 1.637, and 2.299, and Binding Affinities of -5.7, -5.5, and -5.5, indicating its potential effectiveness as an inhibitor. In addition, sitogluside fulfills Lipinski{\textquoteright}s rule with a molecular mass of 520, 4 hydrogen bond donors and acceptors, a log P value of 2.3, and a molar reactivity of 133, indicating a high potential for good bioavailability in biological systems. These results suggest that sitogluside from the clove plant holds potential as a new therapy in inhibiting B and T cell proliferation, however further research is needed to validate these findings and explore its potential in clinical treatments.

}, keywords = {Cell Proliferation, Interleukin-2, Molecular docking, Sitogluside, Syzygium.}, doi = {10.5530/pj.2023.15.122}, author = {Linda Rosalina and Devi Purnamasari and Rismi Verawati and Okta Suryani and Muhammad Arya Ghifari and Amalia Putri Lubis and Rahadian Zainul and Riso Sari Mandeli and Viol Dhea Kharisma and Vikash Jakhmola and Maksim Rebezov and ANM Ansori} } @article {2067, title = {In Silico Study on the Potential of Guaiacol Extract from Green Tea (Camellia sinensis) as a Stimulant for Carbanoic Anhydrase II in Renal Tubular Acidosis}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {August 2023}, pages = {494-499}, type = {Original Article }, chapter = {494}, abstract = {

This study explores the potential of Guaiacol, a green tea extract from Camellia sinensis, as a stimulant in renal tubular acidosis through in-silico investigation on the Carbanoic Anhydrase II enzyme. Utilizing comprehensive computational tools including PyMOL, PyRx, Protein Plus, and the Lipinski{\textquoteright}s Rule of Five, a detailed examination of the molecular structure and its interactions with the target enzyme was conducted. The results from Protein Plus revealed interactions between Guaiacol and Carbanoic Anhydrase II. Quantitative parameters were determined with Binding Affinity values of -5, -4.7, and -4.5, along with RMSD values of 0, 0.956, and 1.412. The Lipinski{\textquoteright}s Rule of Five was employed to evaluate the compound{\textquoteright}s drug-like properties, with the findings indicating a molecular weight of 124, one hydrogen bond donor, two hydrogen bond acceptors, a log P of 1.4, and a molar reactivity of 34.65. Overall, these findings suggest that Guaiacol holds promising therapeutic potential in the treatment of renal tubular acidosis.

}, keywords = {Camellia sinensis., Carbanoic Anhydrase II, Guaiacol, Molecular docking, Renal Tubular Acidosis}, doi = {10.5530/pj.2023.15.108}, author = {Rahadian Zainul and Rismi Verawati and Agus Suprijono and Riso Sari Mandeli and Asri Peni Wulandari and Dony Novaliendry and Ritmaleni and Linda Rosalina and Muhammad Arya Ghifari and Amalia Putri Lubis and Viol Dhea Kharisma and Vikash Jakhmola and Maksim Rebezov and ANM Ansori} } @article {2083, title = {Interaction of Cynaroside from Orthosiphon Aristatus Plant Extract on TNF Alpha as a Stimulant in Malaria and Asthma}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {August 2023}, pages = {581-586}, type = {Research Article}, chapter = {581}, abstract = {

This research aims to investigate the interaction between cynaroside, a natural compound found in Orthosiphon aristatus plant extract, with TNF Alpha as a stimulant in the context of malaria and asthma. The research method involved an in-silico approach using software such as Pymol, PyRx, Protein Plus, and the Lepinski Rule. The results of the study showed that cynaroside has a significant interaction with TNF Alpha, as indicated by high Binding Affinity values of -9.6, -9.3, and -9.2. Analysis using Protein Plus confirmed the interaction between cynaroside and TNF Alpha. Additionally, evaluation using the Lepinski Rule of Five revealed that cynaroside has physicochemical characteristics suitable as a potential drug compound, with a mass of 448, hydrogen bond donors of 7, hydrogen bond acceptors of 11, log p -0.401, and molar reactivity of 105.2. These findings provide a deeper understanding of the potential of cynaroside in regulating the immune response to malaria and asthma through its interaction with TNF Alpha. These results can serve as an important basis for further research in the development of more targeted and effective therapies for both of these diseases

}, keywords = {Asthma., Cynaroside, Malaria, Molecular docking, Orthosiphon aristatus, TNF Alpha}, doi = {10.5530/pj.2023.15.123}, author = {Rahadian Zainul and Rismi Verawati and Gemini Alam and Khoirun Nisyak and Trisna Kumala Sari and Muhammad Arya Ghifari and Ritbey Ruga and Putri Azhari and Romadhon and Himmatul Barroroh and Riso Sari Mandeli and Devi Purnamasari and Viol Dhea Kharisma and Vikash Jakhmola and Maksim Rebezov and ANM Ansori} } @article {2068, title = {Molecular Docking of Thaflavine from Camellia sinensis in Inhibiting B-Cell Lymphoma Through BCl2 Apoptosis Regulator: An In Silico Study}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {August 2023}, pages = {500-505}, type = {Original Article }, chapter = {500}, abstract = {

This study aims to analyze the potential of Thaflavine, a compound found in green tea (Camellia sinensis), as an inhibitor in inhibiting B-cell lymphoma through its interaction with the BCl2 apoptosis regulator using an in-silico approach. The research methodology involved the use of software tools such as PyMOL, PyRx, Protein Plus, and the Lepinski Rule. Through molecular docking analysis using PyMOL and PyRx, the findings of this study demonstrate significant interactions between Thaflavine and BCl2, with Binding Affinity values of -5.5, -4.6, and -4.6, and RMSD values of 0, 1.436, and 2.292. The analysis using Protein Plus indicates the presence of interactions between Thaflavine and BCl2. Additionally, the analysis using the Lepinski Rule of Five reveals that Thaflavine meets the criteria as a potential drug compound, with a molecular weight of 549, 9 hydrogen bond donors, 12 hydrogen bond acceptors, a log P value of -2.5, and a molar reactivity of 119.17. The findings of this study provide important contributions to the development of therapies for B-cell lymphoma through an in-silico approach. However, further research is needed for in vitro and in vivo validation.

}, keywords = {Apoptosis Regulator BCl2, B-cell Lymphoma, Camellia sinensis., In-Silico Thaflavine, Molecular docking}, doi = {10.5530/pj.2023.15.109}, author = {Rahadian Zainul and Rismi Verawati and Herland Satriawan and Teresa Liliana Wargasetia and Devi Purnamasari and Amalia Putri Lubis and Bahrun and Riso Sari Mandeli and Muhammad Thoriq Albari and Viol Dhea Kharisma and Vikash Jakhmola and Maksim Rebezov and ANM Ansori} } @article {2069, title = {Study on the Inhibition of Sinensetin Extract from Cat{\textquoteright}s Whiskers Plant (Orthosiphon aristatus) on ATP Binding Cassette Sub-Family G Member 2 in Uric Acid}, journal = {Pharmacognosy Journal}, volume = {15}, year = {2023}, month = {August 2023}, pages = {506-511}, type = {Original Article }, chapter = {506}, abstract = {

This study aims to investigate the potential of sinensetin, a compound found in the Cat{\textquoteright}s Whiskers plant (Orthosiphon aristatus), as an inhibitor in inhibiting uric acid through its interaction with ATP Binding Cassette Sub-Family G Member 2 (ABCG2). The in-silico approach was employed using software tools such as Pymol, PyRx, Protein Plus, and Lepinski Rule. The results of molecular docking analysis using PyRx demonstrated significant interactions between sinensetin and ABCG2, with Binding Affinity values of -6.8, -6.6, and -6.6, and RMSD values of 0, 0.785, and 1.379. The analysis using Protein Plus confirmed the interaction between sinensetin and ABCG2, supporting the previous docking findings. Furthermore, the evaluation of pharmacokinetic parameters using the Lepinski Rule of Five revealed that sinensetin meets the criteria as a potential drug compound, with a molecular weight of 372, no hydrogen bond donors, seven hydrogen bond acceptors, a log P value of 3.345, and a molar reactivity of 98.5. This research provides new insights into the development of uric acid therapy through an in-silico approach, and these findings can serve as a basis for further research involving in vitro and in vivo validation.

}, keywords = {ATP Binding Cassette, Molecular docking, Orthosiphon aristatus, Sinensetin, Uric Acid.}, doi = {10.5530/pj.2023.15.110}, author = {Anni Faridah and Rismi Verawati and Budhi Oktavia and Musa Ghufron and Devi Purnamasari and Muhammad Raffi Ghifari and Linda Rosalina and Putri Azhari and Rahadian Zainul and Viol Dhea Kharisma and Vikash Jakhmola and Maksim Rebezov and ANM Ansori} } @article {1943, title = {DFT and Pharmacokinetic Study of Some Heterocyclic Aspirin Derivatives as The Cyclooxygenase Inhibitors: An In-Silico Approach}, journal = {Pharmacognosy Journal}, volume = {14}, year = {2022}, month = {January 2023}, pages = {1005-1021}, type = {Research Article }, chapter = {1005}, abstract = {

Ibuprofen and aspirin are frequently used to relieve inflammation, pain, and fever. These are the two most significant non-steroidal and anti-inflammatory drugs (NSAIDs). They prevent the development of prostaglandin by blockampounds have been assessed by ibuprofen as well as quantum mechanical computations. Density functional theory (DFT) with the B3LYP/6-31G+ basis function has been used to elucidate the thermo-chemical, molecular orbital, and optimum geometrical aspects in the gas phase. Using molecular docking and non-bonding interactions, the binding affinities and behaviors of some heterocyclic aspirin analogs have been studied on human cyclooxygenase (COX-1 as well as COX-2) proteins (6Y3C and 5F19). The chemical stability of all structures is supported by geometry and thermo-chemical findings. In contrast to aspirin and ibuprofen, almost all tested analogs exhibited a substantial binding score to the receptor protein (5F19). The ADMET prediction revealed the enhanced pharmacokinetic properties of some derivatives with less acute oral toxicity. Overall, eight heterocyclic aspirin analogues 2-9 were shown to be more effective in inhibiting Cyclooxygenase-2 (5F19) than Cyclooxygenase-1 (6Y3C), indicating that they may be effective as COX-2-related inflammation therapeutic candidates.

}, keywords = {ADMET., Aspirin, DFT, Heterocyclic compound, Molecular docking}, doi = {10.5530/pj.2022.14.204}, author = {Emranul Kabir and M. R. O. Khan Noyon and Md. Amjad Hossain and Pranta Acharjee} } @article {1904, title = {In Silico Analysis and ADMET Prediction of Flavonoid Compounds from Syzigium cumini var. album on α-Glucosidase Receptor for Searching Anti-Diabetic Drug Candidates}, journal = {Pharmacognosy Journal}, volume = {14}, year = {2022}, month = {December 2022}, pages = {736-743}, type = {Original Article}, chapter = {736}, abstract = {

Background: One of the causes of death is diabetes. Anti-diabetic drugs currently available do not work optimally because some have been reported to have side effect and resistance. Objective: This study aimed to flavonoid compounds from Syzygium cumini var. album with the greatest anti-diabetic activity and lower toxicity than acarbose. Materials and Methods: This research is an in silico study of nine flavonoid compounds from Syzygium cumini var. album, starting with PASS online was used to predict the activity spectrum of substances, drug-likeness prediction using DruLiTo, ADMET prediction (absorption, distribution, metabolism, excretion, and toxicity) using pkCSM online. Molecular docking was carried out by the AutoDock 4.2.6 program on α-glucosidase targeting. Visualization is done with the Discovery Studio Visualizer software. Results: From the data obtained, D-(+)-Catechin has a high affinity for α-glucosidase with a free energy of binding (ΔG) -5.94 kcal/mol and an inhibition constant (Ki) of 44270 nm. Conclusion: Based on the results of the study, it can be concluded that the flavonoid compounds from Syzygium cumini var. album has the potential as a promising anti-diabetic drug candidate, where the best candidate is D- (+)-Catechin. However, further studies of flavonoid compounds from Syzygium cumini var. album are needed.

}, keywords = {Flavonoid., Molecular docking, PASS, Pharmacokinetics, α-glucosidase}, doi = {10.5530/pj.2022.14.161}, author = {Yanu Andhiarto and Suciati and Ersanda Nurma Praditapuspa and Sukardiman} } @article {1762, title = {The Potential Effect of Nigericin from Streptomyces hygroscopicus subsp. Hygroscopicus Against the Syndemic of Malaria and COVID-19 through Molecular Docking Perspective}, journal = {Pharmacognosy Journal}, volume = {14}, year = {2022}, month = {April 2022}, pages = {268-275}, type = {Original Article}, chapter = {268}, abstract = {

Background: Malaria is a constantly challenging problem, notably in the Coronavirus Disease-19 (COVID-19) pandemic. The syndemic condition, malaria-COVID-19 co-infections, had been reported. Our previous study successfully revealed several compounds from Streptomyces hygroscopicus subsp. Hygroscopicus, including nigericin that has both antimalarial and antiviral effects. In malaria infection, Plasmodium falciparum Chloroquine Resistance Transporter (PfCRT) is the potential target for eliminating Plasmodium. Meanwhile, for SARS-CoV-2 infection, MPro is an essential protein for SARS-CoV-2 survival. This research aims to examine the potential effect of nigericin towards Plasmodium and SARS-CoV-2 by assessing its molecular interaction with PfCRT and MPro through molecular docking study. Methods: The protein target PfCRT and MPro were obtained from Protein Data Bank. Nigericin and the control ligand (chloroquine and N3) were obtained from PubChem. The pharmacokinetic analysis was done using SwissADME. Specific molecular docking was conducted using PyRx 0.9 and was visualized using LigPlot and PyMOL. Results: Nigericin has a large molecular weight, leading to the non-fulfillment of the Lipinski rule for oral administration. Through molecular docking study, the binding affinity of the Nigericin-PfCRT complex was -8.1 kcal/mol, and Nigericin-MPro was -8.6 kcal/mol. These binding affinities were stronger than the control ligand. The interaction between Nigericin-PfCRT and Nigericin-MPro share a similar pocket-site and amino acid residues as the control ligands. Conclusion: Nigericin has potential antimalarial and anti-coronavirus effects through molecular docking perspective by assessing the binding affinity and similarity of amino acid residues compared to control. Administration of systemic route can be an option in giving nigericin.

}, keywords = {COVID-19, Malaria, Molecular docking, Nigericin}, doi = {10.5530/pj.2022.14.33}, author = {Faratisha IFD and Cahyono AW and Erwan NE and Putri AM and Ariel DG and Yunita KC and Nugraha RYB and Mardhiyyah K and Fitri LE} } @article {1608, title = {ADMET Prediction and In silico Analysis of Mangostin Derivatives and Sinensetin on Maltase-Glucoamylase Target for Searching Anti-Diabetes Drug Candidates}, journal = {Pharmacognosy Journal}, volume = {13}, year = {2021}, month = {July 2021}, pages = {883-889}, type = {Original Article}, chapter = {883}, abstract = {

Background: Diabetes mellitus (DM) is a complex chronic disease with hyperglycemia, which is glucose levels above normal whose number of sufferers is increasing. By inhibiting the human maltase-glucoamylase enzyme which is included in the starch-digestion pathway are used to delay glucose production and thus aid in the treatment of type II diabetes. Aims and Methods: To analyze the potential of mangostin derivatives (alpha-mangostin, betamangostin, gamma-mangostin) and sinensetin as anti-diabetes through ADMET prediction and in silico tests against human maltase-glucoamylase targets using the docking method with miglitol was used as a control. Result: The ligands ɑ, β, γ-mangostin and sinensetin have good interactions with macromolecules and form hydrogen bonds also van der Waals on the macromolecule active side of human maltase-glucoamylase. Conclusion: The ADMET of mangostin derivatives (ɑ, β, and γ), and sinensetin can be predicted by the pkCSM online tool, and they showed good affinity on maltase-glucoamylase target compared to standard drugs like miglitol.

}, keywords = {Anti-diabetes, Maltase-glucoamylase, Mangostin derivatives, Molecular docking, Sinensetin}, doi = {10.5530/pj.2021.13.113}, author = {Intan Kris Prasetyanti and Sukardiman and Suharjono} } @article {1424, title = {Evaluation of Acute toxicity, In-vitro, In-vivo Antidiabetic Potential of the Flavonoid Fraction of the plant Chenopodium album L}, journal = {Pharmacognosy Journal}, volume = {13}, year = {2021}, month = {May 2021}, pages = {765-779}, type = {Research Article}, chapter = {765}, abstract = {

Background: The Chenopodium album L. commonly recognized as Bathua, is widely distributed globally and contains various phytoconstituents that help treat several diseases. However, until now, aerial parts{\textquoteright} antidiabetic potential and the plant{\textquoteright}s acute toxicity at fraction level have never been established. Objectives: To investigate the acute toxicity, the in-vitro, in-vivo antidiabetic potential of the plant at fraction level. Materials and Methods: The aerial parts of the plant were fractionated into different fractions, i.e., flavonoid fraction (CAFF), tannin fraction (CATF), alkaloid fraction (CAAF), saponin fraction (CASF), and were analyzed for in-vitro alpha-amylase inhibition assay. The CAFF, CATF, and CAAF were selected based on in-vitro alpha-amylase inhibition assay results and were further screened for its acute toxicity and in vivo antidiabetic activity using a high-fat diet and streptozotocin-induced diabetes model. The CAFF was characterized by LC-MS, and a molecular docking study was carried out. Results: The in-vitro alpha-amylase inhibition assay revealed that CAFF was found to be more potent than standard Acarbose having IC50 values 122.18 {\textpm} 1.15 and 812.83{\textpm} 1.07 μg/ml, respectively. The CAFF fraction was found to possess potent antidiabetic activity in a dose-dependent manner in both in vitro and in vivo diabetic models and did not produce any sign of severe toxicity. Furthermore, the bioactive CAFF fraction was characterized by LC-MS, showed the presence of quercetin 3-O-(2{\textquoteright}{\textquoteright},6{\textquoteright}{\textquoteright}-di-O-rhamnosyl) glucoside (QRG) or quercetin 3-O-(2{\textquoteright}{\textquoteright},6{\textquoteright}{\textquoteright}-di-Orhamnosyl) galactoside (QRGa) and quercetin 3-O-rutinoside (rutin) (QR). It is predicted from the molecular docking study that the CAFF fraction primarily acts as an alphaamylase inhibitor. Conclusion: The CAFF fraction was found to poses dose-dependent potent antidiabetic activity and did not produce any sign of severe toxicity and primarily act as an alpha-amylase inhibitor.

}, keywords = {Acute toxicity, Alpha-amylase, Antidiabetic activity, Chenopodium album, Lc-Ms, Molecular docking}, doi = {10.5530/pj.2021.13.98}, author = {Neeraj Choudhary and Pranav Kumar Prabhakar and Gopal L Khatik and Subba Rao Chamakuri and Devesh Tewari and Ashish Suttee} } @article {1643, title = {In Silico Analysis of Pinostrobin Derivatives from Boesenbergia pandurata on ErbB4 Kinase Target and QSPR Linear Models to Predict Drug Clearance for Searching Anti-Breast Cancer Drug Candidates}, journal = {Pharmacognosy Journal}, volume = {13}, year = {2021}, month = {September 2021}, pages = {1143-1149}, type = {Original Article}, chapter = {1143}, abstract = {

Background: ErbB4 is a member of ErbB family of receptor tyrosine kinases (RTKs) and plays an important role in resistance to ErbB2 inhibitors. Objective: This study aimed to design a pinostrobin derivative with activity as an ErbB4 inhibitor and to establish a quantitative structure-property relationship (QSPR) of pinostrobin and its derivatives to predict drug clearance. Materials and Methods: In this research, an in silico study was conducted on pinostrobin and its derivatives by predicting the prediction of activity spectra for substances (PASS) with PASS online, followed by molecular docking using the AutoDockTools 4.2.6 program on ErbB4 protein kinase and visualizing the docking results using the Discovery Studio Visualizer software. While the study of QSPR pinostrobin and its derivatives was determined using physicochemical parameters with clearance (CLtot) using SPSS. Results: From the data obtained, 5-O-2- phenylacetylpinostrobin has a high affinity for ErbB4 protein with a free energy of binding (ΔG) -10.37 kcal/mol and an inhibition constant (Ki) of 26.06 nM. Conclusion: Probability {\textquotedblleft}to be active{\textquotedblright} (Pa) 5-O-2- phenylacetylpinostrobin of 0.595 for kinase inhibitors and 0.666 for apoptosis agonists, thus becoming candidates for breast cancer drugs. The QSPR model can be used to predict the properties of molecules such as CLtot, this will be useful in the drug design process. The best QSPR regression equation for pinostrobin and its derivatives is Log (1/CLtot) = 0.705 Log S + 0.035 MR + 0.375. This equation can be used as a reference in predicting CLtot.

}, keywords = {5-O-acylpinostrobin, Molecular docking, PASS, Pharmacokinetic, Physicochemical properties}, doi = {10.5530/pj.2021.13.147}, author = {Ersanda Nurma Praditapuspa and Siswandono and Tri Widiandani} } @article {1647, title = {The Potential Interaction of Ethionamide-Thyroid Hormone Receptor Induces Hypothyroidism}, journal = {Pharmacognosy Journal}, volume = {13}, year = {2021}, month = {September 2021}, pages = {1174-1179}, type = {Research Article}, chapter = {1174}, abstract = {

Background: Hypothyroidism is a common side effect found in patients with multidrug-resistant tuberculosis taking ethionamide. The mechanism of ethionamide-induced hypothyroidism is potentially caused by the structure of ethionamide compounds chemically similar to thioamide, such as propylthiouracil (C7H8N2S), which inhibits thyroid hormone synthesis. However, hypothyroidism is caused not only by a lack of production but also by signaling alteration. Thyroid hormone action is mediated by thyroid hormone receptors (TRs), members of the nuclear receptor superfamily that regulate their target genes. Unfortunately, there are limited studies on the potential interaction of ethionamide with TRs. Objective: In the present study, we want to elaborate on the potential interaction of ethionamide with TRs which might alter the thyroid hormone genomic regulation. Methods: Molecular docking studies were used to evaluate the potential interaction between ethionamide with TRα and TRβ. Results: The molecular docking results on TRα showed more than one hydrogen bond{\textendash}steric interaction formed from the ethionamide{\textendash}amino acid residue interaction. Ethionamide{\textendash}TRβ interaction showed more than one steric interaction, but the hydrogen bonds are not visualized. The docking score between ethionamide and TRα is -7.373 kcal/ mol and higher than its interaction with TRβ. Conclusion: These findings indicate that ethionamide can interact with TRα and TRβ. However, the ethionamide{\textendash}TRα interaction is stronger than ethionamide{\textendash}TRβ interaction. Our study reports a novel mechanism of action of ethionamide-induced hypothyroidism.

}, keywords = {Ethionamide, Hypothyroidism, Molecular docking, TRα, TRβ}, doi = {10.5530/pj.2021.13.150}, author = {Ronny Lesmana and Firyali Rahmani Shidqi and Hanna Goenawan and Iwan Setiawan and Marisca Evalina Gondokesumo and Farida Suhud and Nasrul Wathoni} } @article {1644, title = {Xanthine Oxidase Inhibition Activity and ADMET Properties of Terap (Artocarpus odoratissimus Blanco) Leaves Metabolites: Phytochemical Screening and in silico Studies}, journal = {Pharmacognosy Journal}, volume = {13}, year = {2021}, month = {September 2021}, pages = {1150-1160}, type = {Research Article}, chapter = {1150}, abstract = {

Indonesia, with its biodiversity, is overgrown by various kinds of plants that have medicinal potential, including Terap (Artocarpus odoratissimus Blanco). The leaves of A. odoratissimus are empirically used by local people of Borneo Island to treat gout. The purpose of this study was to determine the antigout activity of the active compound from A. odoratissimus leaves through xanthine oxidase inhibition using the molecular docking method and to determine the ADMET properties of these compounds. Phytochemical screening showed that A. odoratissimus leaf extract contained alkaloids, flavonoids, steroids/triterpenoids, and phenolics. The results of TLC showed that A. odoratissimus leaf extract contained steroid and flavonoid compounds in the form of stigmasterol and rutin. The results of molecular docking showed that flavan-3-ol provided the lowest bond-free energy against xanthine oxidase with a ΔG value of -8.3 kcal/mol, lower than allopurinol and hypoxanthine as reference ligands. Flavan-3-ol interacts with xanthine oxidase through hydrogen bonding with amino acid residues in the form of Arginine 912 and Lysine 1045. The prediction of ADMET properties from flavan-3-ol shows that the compound can be absorbed and has good permeability. Overall, the flavan-3-ol found in A. odoratissimus leaves shows the potential to be developed as a xanthine oxidase inhibitor for use in gout therapy.

}, keywords = {Artocarpus odoratissimus, Molecular docking, Xanthin Oxidase}, doi = {10.5530/pj.2021.13.148}, author = {Nisa Naspiah and Mohammad Rizki Fadhil Pratama and Sukardiman} } @article {1239, title = {In vitro Assay and Study Interaction of Uncaria gambir (Hunter) Roxb. as Anti-fibrotic Activity Against A549 Cell Line}, journal = {Pharmacognosy Journal}, volume = {12}, year = {2020}, month = {September 2020}, pages = {1232-1240}, type = {Original Article}, chapter = {1232}, abstract = {

Aim: The aim of this study is to finding inhibitor potential from several compounds in gambir plant by using in vitro MTT assay and study interaction with molecular docking. The interaction of amino acids on the binding site with substances in the gambir plant was analyzed to determine its potential as a herbal-based therapy candidate for pulmonary fibrosis. Material and Methods: Protein target using TGFβ1 and NF-κB and compounds from gambir plant ((+)-Catechin. Epigallocatechin gallate, (+)-Epicatechin, Gambiriin A1, Gambiriin A2, Gambiriin B1, Gambiriin B2, Gambiriin C, Procyanidin B1, Procyanidin B3). Result: The results from docking analysis observed that compounds from gambir fruit contain anti-fibrotic activity which act by inhibiting DNA transcription of NF-κB and TGF-β1receptors. The compound Procyanidin B3, an essential amino acid, contains a hydrogen bond with the greatest NF-κB inhibitory activity on Gly214 and Lys337. Compounds from Uncaria gambir (Hunter) Roxb. can be an inhibitor to TGFβ1, all the compounds are on the active site of TGFβ1, and use native ligand which is an inhibitor of TGFβ1 (Naphtyridine). The positive compound catechin has the highest inhibitory activity. Gambiriin B1 and Gambiriin A2 are the most identical compounds with similar affinity binding value. Uncaria gambir (Hunter) Roxb. is already a proven antifibrotic which is further confirmed by (IC50: 19,255 {\textpm} 1.08 μg/ml, p \< 0.05) in A549 cell line. Conclusion: The results demonstrated that Gambiriin have cytotoxic effects and was found potentially as anti-fibrotic by MTT assay and in silico evaluation.

}, keywords = {Gambiriin compounds, Inhibitor of p50 NF-κB, Molecular docking, Pulmonary fibrosis, TGF-β1 receptors}, doi = {10.5530/pj.2020.12.172}, author = {Desdiani Desdiani and Iris Rengganis and Samsuridjal Djauzi and Agus Setiyono and Mohamad Sadikin and Sri Widia A Jusman and Nuryati Chairani Siregar and Suradi and Putri C Eyanoer and Fadilah Fadilah} } @article {953, title = {Co-Chemotherapeutic Effect of Ageratum conyzoides L. Chloroform Fraction and 5-Fluorouracil on Hela Cell Line}, journal = {Pharmacognosy Journal}, volume = {11}, year = {2019}, month = {September 2019}, pages = {913-918}, type = {Original Article}, chapter = {913}, abstract = {

Objective: This study was to determine the co-chemotherapeutic effect of the chloroform fraction of bandotan (Ageratum conyzoides L.) (CFB) and its combination with 5-Fluorouracil (5-FU) by in vitro and in silico assay. Methods: Ethanolic extract of bandotan were fractionated with chloroform. Thin Layer Chromatography (TLC) used to identify active compound and in vitro study with MTT Assay to determine the viability of HeLa cells after extract treatment. Molecular docking used Autodock Vina for in silico study to visualize molecular interaction and affinity between nobiletin and 5-FU with Bcl-XL protein. Results: The result of TLC for CFB showed the Rf value of 0.75, it has the similar value with quersetin standard and indicated that CFB contains flavonoid compound. The Molecular docking had ΔG for nobiletin and 5-FU were -8.0 and -4.7 kcal/mol, respectively. This result showed that the affinity of nobiletin with Bcl-XL protein higher than 5-FU. Single cytotoxic assay of CFB and 5-FU showed the IC50 value of 30 μg/ml and 45 μg/ml, respectively. Combination assay of CFB and 5-FU showed the CI value of 0.36, meaning the presence of synergistic effects. Conclusion: CFB has a positive effect to inhibit viability of HeLa cervical cancer cells and potential to develop as co-chemotherapy agent with 5-FU.

}, keywords = {Ageratum conyzoides L., Bcl-XL protein, Cytotoxic assay, Molecular docking, Nobiletin}, doi = {10.5530/pj.2019.11.146}, author = {Rifki Febriansah and Titi Komalasari} } @article {996, title = {In silico Analysis of Flavonoid Glycosides and its Aglycones as Reverse Transcriptase Inhibitor}, journal = {Pharmacognosy Journal}, volume = {11}, year = {2019}, month = {October 2019}, pages = {1252-1255}, type = {Original Article}, chapter = {1252}, abstract = {

Background: HIV continues to be a major global public health issue, having claimed more than 35 million lives so far. In 2016, 1 million people died from HIV-related causes globally. HIV-1 reverse transcriptase is one of HIV{\textquoteright}s vital enzymes for virus reproduction. If the enzyme is inhibited, the virus multiplication could be significantly decreased. There are currently many treatments for HIV, but more effective treatment is always needed because of the possibility of drug resistance and side effects for long-term use. Based on the previous study, there are some natural compounds with high affinity to the HIV-1 reverse transcriptase enzyme. Some of these compounds are flavonoid glycosides. Aims and Method: This study was aimed to learn more about in silico HIV-1 reverse transcriptase inhibitory activities of flavonoid glycosides using docking method. Results: The results showed that the most recommended flavonoid glycosides are those with the lowest binding energy, which were kaempferol-3-O-rhamnoside, myricetin-3-O-rhamnoside and quercetin-3-O-rhamnoside. This was due to the interactions of all three flavonoid rings and sugar moiety with key amino acid residues, which were Leu100, Lys101, Glu138, Tyr181, His235 and Tyr318. Conclusion: Flavonoid glycosides with rhamnose as glycone showed lower binding energy on HIV-1 reverse transcriptase.

}, keywords = {Flavonoid, Glycosides, HIV, Molecular docking, Reverse transcriptase}, doi = {10.5530/pj.2019.11.194}, author = {Stefandi J Wijaya and Arry Yanuar and Rosita Handayani and Rezi Riadhi Syahdi} } @article {1032, title = {Isolation and Structural Elucidation of Allantoin a Bioactive Compound from Cleome viscosa L.: A Combined Experimental and Computational Investigation}, journal = {Pharmacognosy Journal}, volume = {11}, year = {2019}, month = {November 2019}, pages = {1391-1400}, type = {Original Article}, chapter = {1391}, abstract = {

Allantoin, a crystalline compound was isolated from the methanolic extract of Cleome viscosa and it was reported for first time from this plant. The structure of Allantoin was elucidated by single crystal XRD and it was further confirmed through FTIR and ESI-MS spectroscopy techniques. It was crystallized in monoclinic crystal system with the space group P2i/c. Electronic structure characterization of the isolated Allantoin was done through density functional theory calculation. The atomic charges, dipole moment, frontier molecular orbital and the electrostatic potential map of the molecule in the gaseous phase and in the active site have also been analyzed. The optimized geometry was used for molecular docking to identify the possible binding mode. Furthermore, the in vitro antibacterial activity of the isolated Allantoin against Gram-positive and Gram-negative bacteria was evaluated. Maximum Inhibitory Concentrations (MIC) of isolated Allantoin results showed 4 μg/mL for B. subtilis and 8 μg/mL for S. aureus, E. coli and K. pneumoniae.

}, keywords = {Allantoin, Antibacterial activity, Cleome viscosa, Molecular docking, XRD}, doi = {10.5530/pj.2019.11.215}, author = {Lakshmanan G and Sivaraj C and Ammar A and Anantha Krishnan D and Gopinath S and Saravanan K and Gunasekaran K and Murugesan K} } @article {1052, title = {Study of Molecular Docking of Vitexin in Binahong (Anredera cordifolia (Ten.) Steenis) Leaves Extract on Glibenclamide-CYP3A4 Interaction}, journal = {Pharmacognosy Journal}, volume = {11}, year = {2019}, month = {November 2019}, pages = {1471-1476}, type = {Original Article}, chapter = {1471}, abstract = {

Introduction: Diabetes Mellitus is a disease that has a high prevalence in Indonesia. About 90-95\% of all diabetes cases were caused by the failure or incapability of insulin target cells to respond to the insulin in normal state. The use of glibenclamide antidiabetic drugs with herbs has been occurred frequently in the community. Vitexin, one of active compounds in binahong (Anredera cordifolia (Ten.) Steenis) leaves, has been known to have an antidiabetic effects. This study aimed to determine the molecular docking interaction of glibenclamide and vitexin in binahong leaves against CYP3A4 as antidiabetic drug. Method: Molecular docking methods were carried out using Autodock Vina software and interaction was visualized using discovery studio. Results: The study indicated that the value of glibenclamide complex free energy with CYP3A4 was -3.2 kcal/mol and the stability has increasing to -4.4 kcal/mol after docked with vitexin. The glibenclamide and vitexin complexes had 7 Pi alkyl hydrophobic bonds, 1 hydrocarbon hydrogen bond 1 Pi-cation electrostatic interactions, other interactions between Pi bond and sulfur atoms in cysteine amino acid residues, Pi bond interactions in phenylalamin aromatic groups with electron pairs oxygen atom. Conclusion: This study concluded that vitexin could improve glibenclamide stability.

}, keywords = {Diabetes mellitus, Glibenclamide, Molecular docking, Vitexin}, doi = {10.5530/pj.2019.11.227}, author = {Dwitiyanti and Yahdiana Harahap and Berna Elya and Anton Bahtiar} } @article {745, title = {Antibacterial Property and Molecular Docking Studies of Leaf Calli Phytochemicals of Bridelia scandens Wild.}, journal = {Pharmacognosy Journal}, volume = {10}, year = {2018}, month = {August 2018}, pages = {1221-1229}, type = {Original Article}, chapter = {1221}, abstract = {

Background: Bridelia scandens Wild. (Euphorbiaceae) leaves are widely used to cure asthma, bronchitis pleurisy, exudation, sores in mouth and genital cancers. Objective: To evaluate antibacterial activity of the leaf calli methanol extract (LCME). Materials and Methods: Mass production of leaf calli was established on MS medium supplemented with 0.5 mg/L BAP and 0.5 mg/L 2, 4-D. Methanol extract of the dried calli was subjected to HR-LCMS analysis, antibacterial screening of the extract was carried out against human pathogenic clinical isolates. Molecular docking study of HR-LCMS identified compounds was performed by docking with bacterial enzyme DNA gyrase. Results: HR-LCMS analysis of LCME shows that the compounds azaperone bifonazole, fusidic acid, lasalocid and quinine as the major constituents. The antibacterial screening of LCME against clinical pathogens showed significant bactericidal activity against the strains Staphylococcus aureus (17.67\±0.88 mm.d.), Streptococcus pneumonia (13.67\±0.33), Pseudomonas aeruginosa (16.33\±0.67), Salmonella typhi (17.67\±0.33), and Vibrio cholera (15.33\±0.33) as compared to the standard drug ciprofloxacin. The molecular docking of lasalocid against the bacterial enzyme DNA gyrase exhibited good binding affinity of -4.9 kcal/mol, good drug likeness (2.5589), 2 hydrogen bonds and hydrophobic interaction with 7 amino acid residues, so that lasalocid processes good inhibitor as compared to other 4 compounds. Conclusion: LCME of Bridelia scandens showed significant antibacterial activity against Staphylococcus aureus and Salmonella typhi. Lasalocid is the major phytocomponent of LCME which exhibited good inhibitory activity against bacterial enzyme DNA gyrase. This investigation supported traditional claim of LCME as potential antibacterial drug.\ 

}, keywords = {ADMET, Antibacterial, Bridelia scandens, DNA Gyrase, Molecular docking}, doi = {10.5530/pj.2018.6.209}, author = {Ravikumar Shivakumar and Krishna Venkatarangaiah and Sudhesh Shastri and Ravishankara Burladinni Nagaraja and Ajith Sheshagiri} } @article {615, title = {Immunoinformatics Study of Procyanidins as Mast Cell Stabilizers}, journal = {Pharmacognosy Journal}, volume = {10}, year = {2018}, month = {May 2018}, pages = {814-817}, type = {Original Article}, chapter = {814}, abstract = {

Background: Allergens are foreign proteins that stimulate the production of immunoglobulin E (IgE), when they come in contact with human body. These allergens after binding with IgE through Fc\εRI receptor, triggers the signal transduction reaction in mast cell and basophil cells, leading to allergic reactions by releasing some mediators. Four correctly written as surface-exposed tryptpphans Trp 87, Trp 110, Trp 113 and Trp 156 of Fc\εRI receptor protein,play significant role in IgE and Fc\εRI receptor binding interaction. Polyphenols in apple are proven effective for allergic rhinitis treatment by preventing degranulation of granulocytes. Objective:To prevent release of mediators like histamine etc., a therapeutic strategy can be designed by inhibiting IgE and Fc\εRI receptor interactions.This strategy may provide a symptomatic treatment for allergic reactions due to exposure to pollen allergens. Materials and methods: Molecular docking studies are used to analyse the IgE with Fc\εRI receptor binding in presence and absence of procyanidin molecules, present in apple. Results: For procyanidin molecules, binding affinity of IgE molecule with its high affinity receptor (Fc\εRI receptor)decreases markedly. Thepositions of Trp 87, Trp 110, Trp 113 and Trp 156 are changed for the presence of procyanidin C1 molecule. Since IgE and Fc\εRI receptor binding is highly affected in presence of procyanidin C1, so this compound can inhibit mast cell degranulation by altering the binding affinity of IgE with its its high affinity receptor (Fc\εRI receptor). Conclusion: Procyanidin C1 can be used as natural anti-allergic drug by stabilizing mast cells during pollen allergic reaction after experimental verification.

}, keywords = {Allergy, IgE, IgE receptor FcεRI, Mast cell stabilizer, Molecular docking, Procyanidins, Tryptophan residues}, doi = {10.5530/pj.2018.4.138}, url = {http://fulltxt.org/article/676}, author = {Anamika Basu and Anasua Sarkar and Piyali Basak} } @article {601, title = {In silico and in vitro Studies on Lyngbya majuscula using against Lung Cancer Cell Line (A549)}, journal = {Pharmacognosy Journal}, volume = {10}, year = {2018}, month = {March 2018}, pages = {421-428}, type = {Original Article}, chapter = {421}, abstract = {

Objective: To predict an anticancer drug from the members of cyanobacteria, in silico molecular docking was carried out between the cyanobacterial bioactive compounds and lung cancer causing receptor. The highest docking score was produced by Lyngbyastatin (Lyngbya majuscula). In the present study anticancer potential of L. majuscula was evaluated on human lung cancer cell line (A549) using its methanolic extract. Methods: Molecular docking was carried out between the Epidermal Growth Factor Receptor tyrosine kinase and cyanobacterial compounds. Based on the docking results, Lyngbyastatin was found to be the most effective compound. As this compound is present in the L. majuscula, the cytotoxicity of this organism was assessed by standard cell viability assays like MTT method. Algal methanolic extract treated with A 549 cell line morphology was studied by DAPI staining. DNA fragmentation assay was also conducted to study the presence of DNA laddering. Results: Totally 75 bioactive compounds were docked with Epidermal Growth Factor Receptor tyrosine kinase . Of them, 12 compounds were selected based on the docking score. Among the 12 bioactive compounds, Lyngbyastatin found to be most effective compound. L. majuscula showed potential anticancer activity against A549 cell line with IC50 value of 14.82\± 0.62 \μg/ml in MTT method. Most of the treated cells lost their characteristic stretched appearance with shrinkage of nucleus. DNA profile revealed the presence of sheared DNA in treated ones but no fragmentation was observed. Conclusion: The results indicated potent anticancer of algal methanolic extract on A549 cell line, which may be good candidates for further investigation to isolate bioactive anticancer compounds.

}, keywords = {Cytotoxic, Lyngbya majuscula, Lyngbyastatin, Molecular docking, MTT assay DAPI staining}, doi = {10.5530/pj.2018.3.69}, url = {http://fulltxt.org/article/502}, author = {Sangeetha Muniaraj and Vijayakumar Subramanian and Prabhu Srinivasan and Manogar Palani} } @article {620, title = {Pharmacophore Modelling of Brassicaceae Members as Potent HIF (Hypoxia Inducible Factor) Inhibitors Involved in Cancer Angiogenesis}, journal = {Pharmacognosy Journal}, volume = {10}, year = {2018}, month = {May 2018}, pages = {798-802}, type = {Original Article}, chapter = {798}, abstract = {

Angiogenesis is considered as an essential pathological feature of cancer due to its interplay between cancer and other diseases. Natural products found to act as antiangiogenic agents that mediate the angiogenic switch between pro and anti angiogenic factors. Among the different targets, HIF is an important and critical factor that stands as a key mediator between angiogenesis, inflammation and cancer. In our study different phytochemicals of Brassicaceae were analysed for their drug like properties and mapped for pharmacophore development. The developed pharmacophore was virtually screened and further subjected to Lipinski and ADMET filters. The molecular interaction studies of the 10 retrieved compounds were studied by binding with HIF. Among the compounds 1stdrug like molecule HTS 0115 (C15H21BrN2O3) was found to have best docked score and its interaction was further validated using dynamics simulation. The compound found to share the pharmacophoric features with progoitrin a biochemical form of glucosinolate with reported anticancer and anti thyroid activities. Thus the drug like compound HTS 0115 can be further optimised as a putative HIF inhibitor in tumor angiogenesis.

}, keywords = {Angiogenesis, Brassicaceae, HIF, Molecular docking, Pharmacophore, Simulation}, doi = {10.5530/pj.2018.4.135}, url = {http://fulltxt.org/article/673}, author = {Jeyavel Renukadevi and Ganesan Nandhinidevi and Muthiah Bavanilatha and Hemanath Tharani and Rajarajan Sathiyabama and Subramani Vasumathi} } @article {442, title = {Molecular Docking, ADMET Analysis and Dynamics Approach to Potent Natural Inhibitors against Sex Hormone Binding Globulin in Male Infertility}, journal = {Pharmacognosy Journal}, volume = {9}, year = {2017}, month = {November 2017}, pages = {s35-s43}, type = {Original Article}, chapter = {s35}, abstract = {

Objectives: The Sex Hormone Binding Globulin (SHBG) plays an important role in male infertility. Methods: The present research computationally emphases to SHBG protein with 47 natural phytocompounds using docking studies. Results: From the results showed the interactions between 1KDM protein with 47 phytocompounds, a natural compound chlorogenic acid showed the best glide docking XP score -7.255 kcal/mol and the binding energy value of -47.869 kcal/ mol. Based on the result, the chlorogenic acid and target were run on MD simulations stable at 10 ns. Conclusion: Finally, this study concludes the chlorogenic acid is a suitable drug candidate for infertility.

}, keywords = {ADMET property, Male infertility, MD simulations, Molecular docking, Phytocompounds, SHBG}, doi = {10.5530/pj.2017.6s.155}, url = {http://fulltxt.org/article/379}, author = {Morvin Yabesh Jobu Esther and Vijayakumar Subramaniyan and Arulmozhi Praveen Kumar and Mahadevan Subramanian and Manogar Palani} }