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1
Kurian, Thomas, and Rani Sebastian. "Computational Screening of Heterocyclic L-Type Calcium Channel Blockers for Potential Anti-Parkinson’s Activity." Journal of Pharmaceutical Research 24, no. 1 (2025): 45–48. https://doi.org/10.18579/jopcr/v24.i1.23.
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Treating cardiovascular disorders like hypertension, arrhythmias, angina pectoris, and congestive heart failure involves using calcium channel blockers that bind allosterically to Cave L-type channels in myocytes in cardiac muscle. The heterocyclic compounds like 1, 4 dihydropyridines, phenyl alkyl amines, and benzodiazepines are calcium antagonists for cardiac diseases. The receptor protein CavAb in complex with Br- Verapamil was selected as a target for studying the interaction and prediction of calcium channel blocking activity of five heterocyclic compounds based on chemical structural features. using two popular software’s, Auto Dock and PyRx. The results predicted the activity of "2-(3, 4-methoxyphenyl)-5-(2, 2-phenylethylamine)-2-propan-2-ylpentanenitrile" and was chosen as the best score -6.9 – (strong) by auto dock and -9.8 by PyRX compared to the standard verapamil. Verapamil: - PyRX: -6.5, - Auto Dock: -5.22, Higher anticipated activity compounds (strong): 1. [(3R, 4S)-1-[2-ethyl (dimethylamine)]-4 (four-methoxyphenyl)5-dihydro-3H-1-benzazepin-3-yl, -7-methylsulfanyl-2-oxo-4] Acetate: - PyRX: -7.9, 2. 2-(3,4-ethoxyphenyl) - Auto Dock: -5.37(2) Phenyl ethylamine -5-2-propane-2-ylpentanenitrile:- PyRX: -9.8 molecules with weak estimated activity - Auto Dock: -6.251. 5-dicarboxylate, 4-dihydropyridine-3, 6-dimethyl-4-(3-nitrophenyl)-1, diethyl 2, PyRX: -7.2, 2. 4'- hydroxy-3'-methoxy acetophenone, Auto Dock: -3.81 PyRX: -5.6, Auto Dock: -4.31, 3. 1,4-dihydropyridine-3,5-dicarboxylate is diethyl 2,6-dimethyl-4-(4-nitrophenyl):PyRX: -6.8, Auto Dock: -4.52.Calcium channel blockers antiparkinson's effect is under recent global investigations. The ADME parameters studied for the compound were Inhibition of CYP1A2, BBB permeability, distribution, total clearance, oral rat acute toxicity (LD50), and toxicity with Swiss-ADME software. Lead optimization by identifying a molecule's salient characteristics will contribute to toxicity and building safer analogs. Keywords: Docking, Parkinson's, Heterocyclic, Auto dock Vina, PyRX
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Tharrun Daniel Paul L, Roshan Kumar Sah, and Thirunavukkarasu Palaniyandi. "Molecular docking studies of pancreatic cancer expressed proteins with Psidium guajava (guava) derived bioactive compounds." International Journal of Research in Pharmaceutical Sciences 11, SPL4 (2020): 3176–83. http://dx.doi.org/10.26452/ijrps.v11ispl4.4664.
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The current study evaluates the binding affinities (kcal/mol) of different proteins expressed in pancreatic cancer with Psidium guajava derived bioactive compounds by performing molecular docking through auto dock vina. Auto dock vina was used to perform molecular docking between the proteins expressed in pancreatic cancer and P. guajava derived bioactive compounds. Nine proteins and nine ligands were chosen for molecular docking. Among the nine ligands, gemcitabine which is a commercial first-line drug used to treat pancreatic cancer, was selected. The docking output was visualized using the Biovia Discovery Studio visualizer. From the docking results, we found that, out of the nine ligands, quercetin had a better binding affinity than the other ligands and the commercial drug (gemcitabine). SNAI1 docked with quercetin had a binding affinity of -9.6 kcal/mol, which was found to be the highest. In conclusion, it can be said that the compound quercetin derived from the ethanolic extract of the P. guajava has the highest binding affinity, so it can be used for the treatment of pancreatic cancer after modification to its properties so that it has good efficacy and pharmacokinetic properties. Further studies will be based on the in-vitro testing of the extract and gene and protein expression analysis using RT-PCR and MALDI-TOF, respectively.
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Muhammad, Imran Qadir, Fatima Kiran, Munir Ayesha, and Bilal Hussain Syed. "Docking Study of Altered Nelfinavir & Indinavir with Protease of Human Immunodeficiency Virus." Mediterranean Journal of Basic and Applied Sciences (MJBAS) 6, no. 3 (2022): 48–54. https://doi.org/10.46382/MJBAS.2022.6306.
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Nelfinavir and Indinavir are protease inhibitors that function against HIV-1 (HIV-1). Protease inhibitors act by preventing HIV's protease enzyme from functioning. Infectious HIV-1 protease enzyme is proteolytic enzyme in nature that transforms virus causing polyprotein precursors into particular functional proteins. Nelfinavir and Indinavir bind to the protease's active site and prevent it from working. This inhibitor prevents the breaking of virus causing polyproteins, preventing the growth of immature and the non-infectious virus causing particles. However, protease inhibitors are always utilized with at least two further drugs which are anti-HIV drugs. Using the pubchem database from NCBI, we used docking techniques to find the structures of Indinavir and nelfinavir. Then used ds4.1 to modify it then open in auto dock or pay mole to see their attachment after docking with protein.
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Kola, Mamatha, Mukalla Uha, Sabavat Anjali, et al. "Revolutionizing Pharma: How AI is Shaping Pharmaceutical Sector." Journal of International Research in Medical and Pharmaceutical Sciences 20, no. 1 (2025): 1–7. https://doi.org/10.56557/jirmeps/2025/v20i19061.
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The pharmaceutical sector has been playing a crucial role in the innovation, development, discovery and delivery of novel drugs. This article explains about the role of Artificial intelligence (AI), which has nowadays become an integral part of the pharmaceutical sector in drug discovery. It also includes different AI models like Deep Chem, RDKit, ChemBERTa, Auto Dock Vina and some other that has been used at different stages of drug discovery. The article gives us an insight about the contributions of AI in drug delivery, drug design, in biological product development and in medical devices.
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Krishna K S, Gowri, Bhagath K. L. Bhagath K L, Gokul Raj R. S. Gokul Raj R S, Savitha Mol G. M. Savitha Mol G M, Divya S. Nair Divya S Nair, and Prasobh G. R. Prasobh G R. "In Silico Evaluation of the Anti-Diabetic Potential of Rhamnetin from Macaranga peltata." International Journal of Pharmaceutical Research and Applications 10, no. 1 (2025): 1426–28. https://doi.org/10.35629/4494-100114261428.
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Molecular docking studies have become an essential tool in drug discovery, facilitating the identification of potential drug candidates through computational methods. This study focuses on insilico molecular docking of phyto constituents from Macarangapeltata, particularly Rhamnetin, for their potential anti-diabetic activity. Using Auto Dock Vina within PyRx software, the binding interactions of these compounds with diabetesrelated receptors 1 HIT and 1 HIQ were analyzed. The docking results suggest a strong binding affinity, indicating their potential as the rapeutic agents. These findings high light the significance of computational approaches in natural product-based drug discovery, reducing the reliance on animal models and enhancing the rational design of novel drugs.
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Kumar, Tushar. "Molecular Docking Studies of Possible Treatment of Diabetes using Vasicine against Islet Amyloid Polypeptide." International Journal for Research in Applied Science and Engineering Technology 9, no. VI (2021): 4202–9. http://dx.doi.org/10.22214/ijraset.2021.35984.
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Diabetes is the becoming one of the most common problem all over the world. About 1 in 10 persons are suffering from diabetes and most from type 2 diabetes. It occurs due to problem in pancreas which further results defect in the insulin secretion, as insulin maintains blood glucose level. The effect of Alpha-Amyrin Acetate, Myrcene and Vasicine compounds against Islet Amyloid polypeptide (IAPP) protein was seen through molecular docking studies. IAPP acts as complementary to insulin in regulating the sugar level for the treatment of diabetes disease by virtual screening. Different tools and software used in this research were Uniprot, Pubchem, Swiss ADMS, PyRx, Auto dock Vina/MGL tool and PyMOL.
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Perike, Nagaraju, Praveen Kumar Edigi, Nirmala Gurrapu, Sridhara Devi Nagulapally, Sushmitha Bujji, and N. J. P. Subhashini. "Synthesis and Characterization of Novel Indole Containing 1,2,3-Triazole Linked 1,3,4-Thiadiazole Hybrids: Evaluation of Anticancer Activity and Molecular Docking Studies." Asian Journal of Chemistry 36, no. 8 (2024): 1946–52. http://dx.doi.org/10.14233/ajchem.2024.32258.
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Novel scaffolds containing indole, 1,2,3-triazole linked thiadiazole derivatives (9a-l) were synthesized and confirmed with analytical techniques like 1H NMR, 13C NMR and LC-MS. All the compounds were further screened for their anticancer activity against two cancer cell lines A-549 and MCF-7 by making use of MTT assay and doxorubicin as standard drug. Among the compounds 9c, 9d and 9e demonstrated prominent activity against the tested cancer cell lines A-549 and MCF-7 cell lines compared to doxorubicin. Auto dock Vina of PyRx tool was employed in order to perform molecular docking studies on ERK2. Interestingly, the binding energies and interactions acquired from docking results of compounds are in accordance with the investigatory data.
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Maity, Surajit, Gopal Krishna Padhy, Lakshmi Kanta Kanthal, and Suman Pattanayak. "Evaluation of Phytochemicals Constituents of Gyrocarpus asiaticus Willd. and Lactuca runcinata DC for Antioxidant Activity by Molecular Docking Study." Asian Journal of Chemistry 36, no. 1 (2023): 49–58. http://dx.doi.org/10.14233/ajchem.2024.28337.
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In this study, based on the molecular docking study, the antioxidant activity of phytochemicals constituents of hydroalcoholic extract of Gyrocarpus asiaticus Willd. and Lactuca runcinata DC were evaluated. For molecular docking study, ligand generation of phytochemicals constituents of Lactuca runcinata DC and Gyrocarpus asiaticus Willd. were performed by visualizing software Biovia Discovery Studio. The docking study of two proteins viz. NADPH oxidase (PDB ID 2CDU) and human carbonyl reductase–I (PDB ID 3BHI) with the identified phytochemicals constituents was done by Auto Dock Vina. Depending on the docking score, the best three compounds were selected from each plant. For physico-chemical properties prediction and toxicity of these compounds were predicted by the Swiss ADME and Orisis properties explorer.
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Nasimah Rahim, Siti Zalita Talib, Nur Ainun Mokhtar, Nurulbahiyah Ahmad Khairudin, and Ragheed Hussam Yousif. "In-Silico Search Analysis of Potential Inhibitors for 3-Chymotrypsin-Like Protease Of Sars-Cov-2 (Covid-19)." Journal of Research in Nanoscience and Nanotechnology 4, no. 1 (2021): 49–56. http://dx.doi.org/10.37934/jrnn.4.1.4956.
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In this study, three commercial drugs, Imatinib, Nilotinib and Dexamethasone were docked against 3 Chymotrypsin-like Protease or the 3CLPRO of the Severe Acute Respiratory Syndrome (SARS-CoV-2) of coronavirus COVID-19 using the program Auto dock Vina. The protein and the ligands were downloaded from the Protein Data Bank and Pub Chem, respectively. The docked conformations were analysed in terms of the molecular interactions such as hydrogen bonds and hydrophobic interactions. The best drug with the lowest binding energy was Nilotinib with -9.5 kcal/mol followed by Imatinib -9.1 kcal/mol. The objective of this study is to investigate the effectiveness of the three commercial drugs against the protein 3CLPRO.
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Verma, Arvind Kumar, Arun Kumar, and Kunwar Abhishek Singh. "Synthesis and molecular docking for anticonvulsant activity of some new benzoxazole derivatives." INDIAN JOURNAL OF HETEROCYCLIC CHEMISTRY 35, no. 02 (2025): 551. https://doi.org/10.59467/ijhc.2025.35.551.
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To explore the anticonvulsant action related to the benzoxazole framework, a series of benzoxazole-piperazine derivatives, namely N-(4-(benzo[d]oxazol-2-yl)phenyl)-2-(piperazin-1-yl) acetamides (3a-e) (3), was synthesized by reacting N-(4-(benzo[d]oxazol-2-yl)phenyl)-2-chloroacetamide (2) with various substituted piperazines. Molecular docking studies were conducted using Auto Dock Vina 1.5.7 to evaluate the compounds' binding affinities with anticonvulsant-related targets protein data bank ID: 3PO7, 7WLJ, using zonisamide as a standard drug to ensure their potential. Several compounds exhibited notable and effective docking scores, indicating promising potential for anticonvulsant activity. Overall, all synthesized compounds demonstrated significant docking interactions, supporting further investigation into their therapeutic relevance.. KEYWORDS :Benzoxazole, Anticonvulsant activity, Human health, Docking.
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Dikmen, Gökhan, and Özgür Alver. "NMR, FT-IR spectroscopic studies and molecular docking study of 4-acetoxyphenethyl acrylate." Journal of Theoretical and Computational Chemistry 16, no. 03 (2017): 1750025. http://dx.doi.org/10.1142/s0219633617500250.
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Conformational, structural, vibrational spectroscopic properties and nuclear magnetic chemical shift values of 4-acetoxyphenethyl acrylate (4APA) were investigated using spectroscopic and theoretical approaches including FT-IR and NMR spectroscopes and quantum chemical calculations. FT-IR spectroscopic measurement was carried out between 3500[Formula: see text]cm[Formula: see text]–400[Formula: see text]cm[Formula: see text]. Geometric parameters, vibrational wavenumbers and nuclear magnetic chemical shift values were estimated using B3LYP hybrid density functional theory method with 6-311[Formula: see text]G(d, p) basis set. 1H, [Formula: see text]C, APT and HETCOR NMR experiments of 4APA were obtained in DMSO solution. For a quantitative description of vibrational wavenumbers, total energy distribution (TED) values with scaled quantum mechanical (SQM) method were calculated. Moreover, molecular docking study of title molecule was theoretically carried out using Auto Dock Vina Program.
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FATHI-AL-BURGUS, Abdallah, Omar THANOON-ALI, and Omar YOUNIS AL-ABBASY. "Design, synthesis and molecular docking of new spiro heterocyclic coumarin as antibacterial agents." Revue Roumaine de Chimie 69, no. 7-8 (2024): 399–404. http://dx.doi.org/10.33224/rrch.2024.69.7-8.07.
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In this study, coumarin derivatives were synthesized from coumarin 3-carbohydrazide (1) and 4-(pyrimidin-2-yl diazenyl)-antipyrine (2), leading to the intermediate compound (3). The final compounds were synthesized through the cyclocondensation of compound (3) with mercaptoacetic acid, acetic anhydride, sodium azide, 2-aminobenzoic acid, and maleic anhydride. This process resulted in the formation of five spiro heterocyclic coumarins (4a-e) respectively. The novel compounds were purified by column chromatography, and were identified by FT-IR,1H, and 13C-NMR. The antibacterial activity of the prepared compounds was evaluated in vitro using the disk diffusion method against Escherichia coli and Staphylococcus aureus bacteria. Compound (4b) showed significant antibacterial activity, among others. Furthermore, the docking study of (4b) with DNA gyrase for both bacterial strains was investigated using (Auto Dock Vina), and (Discovery Studio software), which revealed vital interactions and binding conformations.
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Alamshany, Zahra M., Reham R. Khattab, Nasser A. Hassan, et al. "Synthesis and Molecular Docking Study of Novel Pyrimidine Derivatives against COVID-19." Molecules 28, no. 2 (2023): 739. http://dx.doi.org/10.3390/molecules28020739.
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A novel series of pyrido[2,3-d]pyrimidines; pyrido[3,2-e][1,3,4]triazolo; and tetrazolo[1,5-c]pyrimidines were synthesized via different chemical transformations starting from pyrazolo[3,4-b]pyridin-6-yl)-N,N-dimethylcarbamimidic chloride 3b (prepared from the reaction of o-aminonitrile 1b and phosogen iminiumchloride). The structures of the newly synthesized compounds were elucidated based on spectroscopic data and elemental analyses. Designated compounds are subjected for molecular docking by using Auto Dock Vina software in order to evaluate the antiviral potency for the synthesized compounds against SARS-CoV-2 (2019-nCoV) main protease M pro. The antiviral activity against SARS-CoV-2 showed that tested compounds 7c, 7d, and 7e had the most promising antiviral activity with lower IC50 values compared to Lopinavir, “the commonly used protease inhibitor”. Both in silico and in vitro results are in agreement.
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Rachel, Mathew* V. S. Anjana S. Nakshathra R. S. Shahana A. P. Sona Nair A. Vaheeda. "Computational Design and Anti-Inflammatory Assessment of Novel 1,3,4-Oxadiazole Derivatives." International Journal of Pharmaceutical Sciences 3, no. 3 (2025): 2055–67. https://doi.org/10.5281/zenodo.15063808.
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Inflammatory diseases are widespread and affect millions of people worldwide. Current treatments of inflammatory diseases have limited efficacy and significant side effects. So an attempt is to be made to explore the anti-inflammatory activity of 1,3,4-oxadiazole. A novel series of 1,3,4-oxadiazole derivatives bearing imidazole moiety were designed using ACD Lab/ Chemsketch 12.0 and their properties were predicted using the Molinspiration software and they obeyed the Lipinski rule of five. The designed derivatives showing optimal physicochemical properties were selected for docking studies Docking studies of these compounds were performed on cox-2 (5IKQ) using Auto Dock Vina. The result obtained from the docking study revealed that compounds a35, a36, a26 showed good activities on cox-2. Overall, the study concluded that 1,3,4-oxadiazole derivatives bearing imidazole moiety could be considered as promising for the development of novel anti-inflammatory agents.
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Dr. Dharshini Priya G, Dr. Suguna M, Dr. Dhineshraman G, et al. "Bioinformatics Based: in Silico Docking Analysis of Polyherbal Formulation for The Management of Parkinson’s Disease (Nadukku Vatham)." Journal of Advanced Zoology 44, S6 (2023): 1372–80. http://dx.doi.org/10.17762/jaz.v44is6.2484.
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Background: The discipline of Siddha medicine, particularly herbal formulations, can benefit greatly from the use of molecular docking because it enables the molecular interactions of the formulation’s lead molecules with receptors to be understood, as well as the inference of the formulation's basic biochemical targets. Aim: The goal of this study is to carry out an In-silico computational analysis of the phytochemicals found in Kuruver Kudineer (KK), a traditional Siddha remedy that is used for managing behavioral deficit in Parkinsons disease. Methodology: The ligand structures were developed and optimized using Auto Dock Tools (Morris, Goodsell et al., 1998). Using Auto dock Vina, the compounds were all docked. The function of the target protein Monoamine Oxidase -A (PDB 2Z5X), which is involved in the breakdown of the neurotransmitters by MAO-A, will be inhibited by the creation of a hydrogen bond between phytocomponents and the target's core amino acids (Tyr 69, Ile 335, Tyr 407, and Tyr 444). In order to control the dopamine level, phytocomponents that inhibit the target enzyme MAO-A may be used as potential targets. Results: The compounds present in Kuruver Kudineer (KK) like Gingerenone-A, Betulinic acid, Zingiberene, Rutin, Geniposide and β-sitosterol showed maximum interactions with MAO –A when compared to that of Clorgyline. According to the outcomes of the computational investigation, the bio-active substances present in the Siddha formulation Kuruver Kudineer (KK) have significant affinity to the target MAO-A (PDB 2Z5X). Conclusions: From the results of the present study, it was concluded that the MAO – A reveal significant effect to managing the behavioral deficit and thereby considered an excellent drug choice for the clinical management of Parkinson’s disease (Nadukku vatham)
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Veeraswamy, Sharmila Devi, Ilavarasan Raju, and Sumithra Mohan. "An Approach to Antifungal Efficacy through Well Diffusion Analysis and Molecular Interaction Profile of Polyherbal Formulation." Biomedical and Pharmacology Journal 15, no. 4 (2022): 2069–84. http://dx.doi.org/10.13005/bpj/2544.
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In the current scenario, there is a thirst for research against emerging microorganisms, and it becomes challenging to introduce new drugs against organism virulence are pretty interesting. Herbal medicines are now gaining popularity as a treatment option for various diseases worldwide. The present study analyzes the antifungal effect of a polyherbal formulation through in vitro well diffusion method using fungal strains such as Candida albicans, Aspergillus niger, Aspergillus fumigatus, Cryptococcus neoformans, and Sporothrix schenckii. Molecular docking is done using the Auto dock vina tool to predict the mechanism of action of the phytomolecules present in the polyherbal formulation. The molecular interactions are visualized using molecular modelling (PyMOL) software. The antifungal effect was observed in a concentration-dependent manner with a significant zone of inhibition. Also, phytomolecules in polyherbal formulation showed potential inhibition on CYP450 Lanosterol 14 α-demethylase 1, 3 β-Glucan synthase, and Thymidylate synthase from docking analysis.
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Kamalarajan, P., J. Irshad Ahamed, S. Ramesh, and M. F. Valan. "Molecular Docking, Computational DFT, Biological Activity, Phytochemical Analysis and Spectrum Analysis Investigations of Neoandrographolide." Asian Journal of Chemistry 37, no. 3 (2025): 543–51. https://doi.org/10.14233/ajchem.2025.33120.
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In this work, neoandrographolide (C26H40O8) was isolated first time from the ethanolic extract of Nilavembu Kudineer Chooranam (NKC), traditional Siddha medicine powder. Thin-layer chromatographic (TLC), GC-MS and mass spectrometry techniques were employed to extract after the preliminary phytochemical screening. Neoandrographolide has a significant level of α-amylase inhibition activity. The ab initio DFT theory of DFT-B3LYP/6-311++ G(d,p) basis set technique was used for theoretical studies and comparison with the three experimental spectral studies such as 1H, 13C NMR, FTIR and UV-visible methods. When compared to the theoretical computational density functional theory (DFT) using Gaussian 9.0, the results have shown that the investigated compounds are potential therapeutic leads for in vitro biological and in silico molecular docking utilizing auto dock vina 4.2. Based on the results, it is confirmed that compound neoandrographolide would be most effective against α-amylase inhibitor activities.
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Bandi, Jyothi, and Navaneetha Nambigari. "Identification of Novel Anticancer Agent by in silico Methods for Inhibition of KLK-12 Protein." Asian Journal of Organic & Medicinal Chemistry 6, no. 1 (2021): 13–23. http://dx.doi.org/10.14233/ajomc.2021.ajomc-p304.
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A critical route for cancer metastases is pathological angiogenesis. The protein Kallikrein-12 (KLK-12) is a serine protease reported to be involved in a variety of biochemical processes that have a functional role in angiogenesis. The KLK-12 protein hydrolyzes the cysteine rich angiogenic inducer 61 (CYR61) protein and controls the bioavailability of angiogenesis-inducing growth factors. The work proposed involves the homology modeling of the KLK-12 protein, identify essential residues to be putatively linked to the natural substrate. Protein-protein docking is done to characterize Trp35, Gln36, Gly38, Trp82 and His107 residues of the active site, in addition to active site servers (active site prediction server and CASTp). Using Auto Dock Vina software, virtual screening studies were carried out to identify the substituted carboxamide scaffolds as a pharmacophore binding at the active site. Based on binding energy, ADME and visual inspection, an isochromene carboxamide moiety is identified as antiangiogenic and cancer antagonists.
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Kurian, Thomas, and Rani Sebastian. "Molecular Docking Study of Heterocyclic Compounds for Antifungal Activity Against Granulomatous Amoebic Encephalitis." Journal of Pharmaceutical Research 23, no. 3 (2024): 174–77. http://dx.doi.org/10.18579/jopcr/v23.3.101.
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Our study identified seven unique heterocyclic compounds: 2-(m Tolylthio) Chalcone, chitosan oligosaccharide, and 2-hydroxy chalcone. Six-chloropyridine, 4-naphthoquinone, Thiobenzimidazole, 2-thiobenzoxazole, 6-carboxylic acid ethyl ester, and Anthrimide are probable choices that may be found in a chemical database. Posaconazole and Isuvuconazole are reference compounds found in a literature study. The isuvuconazole-bound complex of Acanthamoeba castellanii CYP51 of PDBID 6UX0 is the focus of our investigation. Docking simulations were carried out to evaluate these drugs' binding affinity to the Acanthamoeba castellanii CYP51 complex, using Isuvuconazole as the reference compound. Vina Wizard and PyRX software were used to carry out the docking simulations. Anthrimide, the ligand, demonstrated a binding energy of -10.3 kcal/mol in our data, indicating great promise for treating antifungal diseases in the future. Auto dock further validated this value to be -10.2. Further in vivo testing will confirm the findings of this study. Keywords: Docking, Amoebic, Encephalitis, Heterocyclic, Antifungal, PyRX
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Mustarichie, Resmi, та Danni Ramdhani. "In-silico study of compounds of Curcuma xanthorriza against enzyme tyrosinase sac and α-MSH". Asian Journal of Pharmaceutical Research and Development 10, № 3 (2022): 1–5. http://dx.doi.org/10.22270/ajprd.v10i3.1135.
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Previous report determined that curcumin, demetoxycurcumin and xanthorrhizol are an active compounds contained in Curcuma xanthorrhiza which have activity in inhibiting the tyrosinase enzyme and α-melanocyte stimulating hormone (α-MSH ) in vitro. This study aimed to determine and visualize the interaction of the three compounds with the tyrosinase enzyme and α-MSH in order to find their possibility for skin whitening. The experiment carried out using Auto Dock Vina program .The results of docking simulations showed that the three compounds can interact spontaneously with the tyrosinase enzyme and α-MSH. On the tyrosinase enzyme, xanthorrhizol interact most easily through the formation of hydrogen bonds with Asn205. On the α-MSH, demethoxycurcumin interact most easily through the formation of two hydrogen bonds with His3 and Arg5. With the inhibitory effect on the enzyme tyrosinase and α-melanocyte stimulating hormone (α-MSH) means preventing the formation of skin coloring pigment melanin, indicating that the three compounds studied can be applied as skin whitening agents.
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Shubham, Khandare* Dinesh Kawade Dhananjay Tidke Nikita Gaikwad Ritik Jamgade. "Design, Docking and ADME-T Prediction of Novel Pyrimidine-Based Antimicrobials via the Biginelli Reaction." International Journal of Pharmaceutical Sciences 3, no. 3 (2025): 993–1007. https://doi.org/10.5281/zenodo.15012873.
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Pyrimidines are a crucial group of heterocycles in pharmaceutical research due to their antiviral, anticancer, antibacterial, and antioxidant properties. The heterocyclic compound 1,2,3,4-tetrahydropyrimidine (THPM) exhibits various therapeutic applications and is recognized as a significant pharmacologically active component. Our study assessed the antimicrobial efficacy of the designed compounds against various microorganisms, including Gram-positive and Gram-negative bacteria, as well as pathogenic fungi. These compounds were synthesized using either microwave or conventional methods, or through a multi-component reaction like the Biginelli reaction. The SDF file was transformed into a PDB file using UCSF Chimera 1.18 software for molecular docking, Avagadro for energy optimization, and Autodock vina. Physicochemical characteristics and ADME-T predictions were conducted using the pkCSM web server, revealing that the most potent compound demonstrated effective binding modes with microbial targets and promising pharmacokinetic safety profiles. The research provides valuable insights into the potential use of these compounds as antibacterial and antifungal agents.
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Sudha, T., D. Mahalakshmi, and P. Kumar Nallasivan. "Design, Synthesis, Characterization, Molecular Docking Studies, In vitro and In vivo Cervical Cancer Activity of Novel N-Substituted Pyrazole Derivatives." Asian Journal of Chemistry 36, no. 10 (2024): 2260–68. http://dx.doi.org/10.14233/ajchem.2024.32021.
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The aim of this study is to design, synthesize, characterize few novel N-substituted pyrazole derivatives and evaluated for their anticancer capabilities; these compounds were selected based on their ability to inhibit the HPV E6 protein. The IR, 1H & 13C NMR, mass spectral and elemental analysis were used to determine the structural details of the newly synthesized substances. The molecular docking was performed using Auto Dock Vina, and the protein-ligand interaction was analyzed using Discovery Studio. The sulforhodamine B (SRB) assay was used to determine the in vitro anticancer activity against the HeLa cell line. Body weight analysis, mean survival time and % increase in life span approaches were used to assess in vivo anticancer effectiveness in Swiss albino mice bearing Dalton’s Lymphoma Ascites (DAL) tumor model. Synthesized compounds have excellent docking energies, according to docking experiments. Compounds I, II and III were selected for anticancer activity in vivo DAL-bearing mice based on the findings of their in vitro and SRB assays exhibiting the antiproliferative activity. Pyrazole derivatives, compounds I and III, demonstrated significant potential as anticancer agents.
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Gulia, Rajrani, Vikas Sangwan, Anshul Singh, Sonaxi Kharb, and Ritu Solanki. "Synthesis, Characterization, Biological Activity and Molecular Docking Studies of Phthalic Acid based Macrocyclic Transition Metal Complexes." Asian Journal of Chemistry 35, no. 7 (2023): 1632–44. http://dx.doi.org/10.14233/ajchem.2023.27926.
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A novel series of macrocyclic complexes of [M(L)Cl2] (M = Co(II), Ni(II) and Cu(II), L = macrocyclic ligand) were synthesized by template condensation method using 3,4-diaminotoluene and phthalic acid in the presence of divalent transition metal ions e.g., Co(II), Ni(II) and Cu(II) in their chloride form. These synthesized metal complexes were fully characterized by spectroscopic techniques, namely UV-Visible, IR, ESR and ESI-MS. Their thermal behaviour was determined by TGA and DTA. Further these macrocyclic complexes were screened for antimicrobial activity against bacterial species (Staphylococcus aureus, Bacillus subtilis, Pseudomonas aeruginosa and Escherichia coli) and fungi (Aspergillus niger and Candida albicans) and then compared against standard drug streptomycin and itraconazole, respectively. In addition to these the antioxidant activity of the macrocyclic complexes were also investigated through scavenging effect on the DPPH radicals. Finally, the biological potency of synthesized compounds was evaluated using Auto Dock Vina. All the synthesized macrocyclic complexes were found to be potent against bacterial and fungal species, which suggest their potential application as antibacterial and antifungal agents.
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Oyebamiji, Abel Kolawole, Jonathan Oyebamiji Babalola, Kehinde Abraham Odelade, et al. "Potential inhibiting activities of phytochemicals in Scilla natalensis bulbs against schistosomiasis." Ecletica Quimica 48, no. 3 (2023): 54–80. http://dx.doi.org/10.26850/1678-4618eqj.v48.3.2023.p54-80.
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Schistosomiasis remains one of the severe ailments that affect both man and woman in South Africa. It is caused by blood fluke, and the rate at which it causes death is alarming in some areas of America, Asia as well as in African countries. It is a neglected tropical disease (NTD) with grave impact on social and economic situation of countries with low sanitation awareness. Thus, the search for lasting solution to this menace, has drawn the attention of many global researchers using phytochemicals from Scilla natalensis via in silico approach. The studied compounds were optimized using Spartan 14. Docking study was executed via Pymol, Autodock tool, Auto dock vina and discovery studio. Compound 9 with –8.2 kcal mol–1 and –9.4 kcal mol–1 as binding affinity proved to possess highest ability to inhibit glutathione S-transferase and thioredoxin-glutathione reductase than other compounds. Also, ADMET properties for compound 9 and praziquantel were explored and reported. Our findings may open the door for the design of novel drug-like molecules with better efficiency.
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Jadhav, Sagar Ashok, Payal Chavan, Supriya Suresh Shete, et al. "In Silico ADMET and Docking Study of Selected Drug Used in Therapy of COVID-19." Journal of Pharmaceutical Technology, Research and Management 10, no. 1 (2022): 47–73. http://dx.doi.org/10.15415/jptrm.2022.101006.
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Docking is one of the most widely utilized technique used method in structure -based drug design because of its capability to predict the binding conformation of ligands to appropriate target. Ability of binding/ affinity towards the target i.e., bioactive peptides or specific receptor provides strong evidence of binding conformation pattern and affinity for further investigation. Aim- The present study was conducted for evaluation of current API’s potential used in COVID-19. Methods: In-silico molecular docking was performed using softwares such as SWISS ADME, MOLSOFT, MOLINSPIRATION, PYMOL, AUTO-DOCK VINA AND BIOVIA DS VISUALIZER. Results: The current research comprehend the drug likeliness character of selected API’s and their binding affinity with various targets selected by SWISS TARGET PREDICTION. Conclusion: The present investigation suggests that all the targets follow Lipinski rule of five except Remdesivir and Anakinra besides which it possesses enhanced binding affinity toward targets, the binding energy of the protein ligand interaction additionally confirms that the ligand fits into the dynamite pockets which proves to be evident for further in- vivo and in-vitro evaluations.
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Nada, Alaa H., Hoda Mahrous, and Ahmed I. Abd Elmaksoud. "Molecular Insights into the Anticancer Mechanism of Glycyrrhetinic Acid in Hepatocellular Carcinoma." Scholars International Journal of Biochemistry 7, no. 02 (2024): 16–24. http://dx.doi.org/10.36348/sijb.2024.v07i02.001.
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The study aimed to predict the binding affinity and interaction patterns between DNMT1, DNMT2, DNMT3A, DNMT3B, TET-1, c-Myc, TET-2, NF-kB and methionine synthase in complex with Glycyrrhetinic acid (GA) using molecular docking simulations. In this study, A crystal structure of proteins (DNA methyltransferase 1, DNA methyltransferase 2, DNA methyltransferase 3A, DNA methyltransferase 3B, NF-kB, TET-1, c-Myc, TET-2 and methionine synthetase) was downloaded from the Protein Data Bank (PDB). the Auto Dock Vina and visualization by Discovery Studio and Chimera program were utilized for molecular docking study. The docking findings are examined to determine the docking pose based on binding affinity, hydrogen bonding, and other beneficial interactions (hydrophobic bond). In addition, it is used to visualise the proteins ligand interactions and analyze the binding pose of GA. Comparing the various binding energies and torsions of the test compound and the control revealed that the test GA had a perfect docking score, and it was predicted to possess comparable anti-tumour and anticancer activity.
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Gupta, Saloni, Prashant Beniwal, Sanjay Khanna, and Ganesh N. Sharma. "Investigating Anti-Diabetic Potential of Magniferin via Alpha Amylase Inhibitory Activity; In Silico Studies and In Vitro Validation." Indian Journal Of Science And Technology 18, no. 11 (2025): 839–47. https://doi.org/10.17485/ijst/v18i11.290.
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Objectives: To determine the affinity of magniferin with alpha amylase enzyme plays a central role in diabetes and diabetes-driven complications. Methods: The data for magniferin (mol2) and alpha amylase (pdb) enzyme was retrieved from Pub Chem and the protein data Bank. Molecular docking studies were carried out using Auto Dock Vina. In silico findings were evaluated by alpha Amylase Inhibitory assay and alpha amylase mRNA expression profile. Findings: Binding energies (-50.9012 kcal/mol) of the docked structure showed significant affinity that clearly showed alpha amylase inhibitory properties of magniferin. The magniferin affinity with alpha amylase was due to interaction with amino acids (Asp, Glu, and Asp). Further, in vitro studies showed magniferin significantly inhibits alpha amylase enzyme activity (247.63 µg/ml). Novelty: The magniferin showed affinity with the amino acid residues present in the enzyme active site. The expression profile of alpha amylase gene was examined using Intestinal epithelial cells treated with magniferin with a control. These findings clearly showed the potential of magniferin as anti-diabetic activity via inhibiting alpha amylase. Keywords: Magniferin, Natural Products, Docking, Affinity, Anti-Diabetic, Binding Energy and Gene Expression
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Kolawole, Oyebamiji Abel, Akintelu Sunday Adewale, Simon N. Odoemene, Oyeneyin Oluwatoba Emmanuel, and Semire Banjo. "Theoretical Bioevaluation of 1,2,4-Thiadiazole-1,2,4-triazole Derivatives via Molecular Modelling Approach." Asian Journal of Organic & Medicinal Chemistry 6, no. 1 (2021): 40–46. http://dx.doi.org/10.14233/ajomc.2021.ajomc-p307.
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Breast cancer still remains one of the precarious ailments among humans globally. The vulnerability of this ailment in homeopathic world remains colossal and this has drawn the attention of seasoned researchers to find lasting solution to this hazard. Therefore, 10 novel 1,2,4-thiadiazole-1,2,4-triazole derivatives were studied so as to explore their anti-breast cancer activities. The studied compounds were optimized using Spartan 14 and the QSAR study was executed by using Gretl and MATLAB. Also, docking study was observed using Pymol (for treating downloaded protein), Autodock Tool (for locating binding site in the downloaded protein and for converting ligand and receptor to .pdbqt format from .pdb format), Auto dock vina (for docking calculation) and discovery studio (for viewing the nonbonding interaction between the docked complexes). The selected descriptors were used to developed effective QSAR model and it was observed that the developed QSAR model using artificial neural network (ANN) predicted better than the prediction made by multiple linear regression (MLR). More so, the calculated binding affinity revealed that compound g (-11.4 kcal/mol) possess ability to inhibit 3α-hydroxysteroid dehydrogenase type 3 (PDB ID: 4xo6) than other studied compounds as well as etoposide (Standard).
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G A Miana, G. A. Miana, M. Kanwal M Kanwal, S. Maqsood S Maqsood, et al. "In-silico, Antioxidant and Antiepileptic Effect of N(2,3-methylenedioxy-4benzoyloxy-phenthylamine)-3,4-dimethyl-1, propanoamide Derivatives." Journal of the chemical society of pakistan 44, no. 4 (2022): 374. http://dx.doi.org/10.52568/001073/jcsp/44.04.2022.
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Epilepsy is a severe neurological illness that affects millions of people the globally and is characterized by unpredicted and intermittent seizures.This research aimed to investigate the antiepileptic and antioxidant properties of papaverine derivatives using in-silico, in-vitro, and in-vivo methods.Epileptic seizure was induced in Swiss albino mice of either gender by administering PTZ (pentylenetetrazol). The antioxidant potential of test compounds was computed using previously published DPPH assay methods with minor modifications, while In-silico experiments were conducted using Auto-dock Vina (1.5.6) software and post dock analysis was completed using Discovery Studio Visualizer. The results showed that both compounds have strong antioxidant potential, with a noticeable change in color when compared to ascorbic acid as a control, and very low mortality when anti-epileptic potential was observed. The development of seizures was greatly delayed at first, but after 30 minutes of PTZ, they were completely gone. Both synthesized derivatives also comply the andquot;Lipinskiand#39;s rule of 5andquot;, which states that after structural alterations, extensive investigations, and trials, the chemical products would be evaluated for epilepsy management in the future In-silico investigations demonstrated that ligands with sufficient hydrogen bonds, pi-pi bonds, and Vander-Waals forces have a suitable propensity to engage with the binding pocket of selected protein targets. The current investigation of papaverine derivatives and their binding affinities against gamma aminobutyric acid (GABA) protein may have a vital function in epilepsy aetiology, according to the results of the studies. H1 and H2 were further verified in vivo for their anticonvulsant and antioxidant therapeutic potential. This could lead to more research into neurological problems.
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Priya, R. Hari, and P. Thirumalai Vasan. "In Silico and Pharmacokinetic Activity of Bioactive Components from Annona muricata Leaves Against Breast Cancer." Indian Journal Of Science And Technology 17, no. 13 (2024): 1283–91. http://dx.doi.org/10.17485/ijst/v17i13.1949.
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Objectives: To identify the potential inhibitors isolated from Annona muricata leaves against the epidermal growth factor of tyrosine kinase receptor, a crucial factor involved in the development of breast cancer. Methods: In this study, the ethanolic extract of Annona muricata leaves was studied by GC-MS analysis. The functional compounds derived from the GC-MS spectrum were docked with a target molecule, the Epidermal Growth Factor of Tyrosine Kinase Receptor [PDB Id: 1M17], for breast cancer using Auto dock vina. The Bioactivities of compounds against the key role enzymes like GPCR ligand, nuclear, and enzyme inhibitor in Breast Cancer was analyzed using Molinspiration. The pharmacokinetic and pharmacodynamic attributes of the chemical compounds were studied by the Swiss ADME tool. Findings: The outcomes from Molecular docking proved that the bioactive compounds such as 9,19-Cyclolanost-24-en-3-ol, (3.beta.), Octadec - 9 - enoic acid, Cycloeucalenol, and Phytol could act as potentially active inhibitors against the Epidermal Growth Factor of Tyrosine Kinase Receptor in Breast Cancer. Novelty: The inhibitory effect of the bioactive components from the ethanolic extract of Annona muricata leaves against the Epidermal Growth Factor of Tyrosine Kinase Receptor through the in silico approach has not been explored. This research work will be the first to attempt the in silico mode to determine the potential inhibitors of the Epidermal Growth Factor of Tyrosine Kinase Receptor and successfully identified four bioactive compounds that down-regulate the expression of EGFR and control the proliferation of breast cancer cells. Keywords: Drug Development, Breast Cancer, Inhibitor, Pharmacokinetics, Pharmacodynamics, Auto Docking, Bioactive Compounds
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Suhadi, Andrio, Rizarullah Rizarullah, and Feriyani Feriyani. "Simulasi Docking Senyawa Aktif Daun Binahong Sebagai Inhibitor Enzyme Aldose Reductase." Sel Jurnal Penelitian Kesehatan 6, no. 2 (2019): 55–65. http://dx.doi.org/10.22435/sel.v6i2.1651.
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The metabolic syndrome is the cause of death around the world caused by diabetic mellitus. Binahong leaf is a kind of plant that is widely used to treat various diseases. This study aims to investigate the inhibitory activity of binahong leaves compound in inhibiting the aldose reductase which has role of converting glucose into sorbitol by docking simulation. The compound of binahong leaves consists of ursolic acid, vitexin, and oleonolic acid (ligand testing). These compound were taken from PubChem site, while aldose reductase enzyme (receptor) was obtained from the world protein bank with PDB 2HV5 code. This study incorporated in silica technique by using Auto dock vina software, Discovery Studio and Ligplot as visualization. The result of grid box optimization by redocking comparative ligand was 0.7Å RMSD. The docking result showed that the free Gibbs energy (∆G) of aldose reductase was (-11.7), Vitexin (-8.3), Ursolic acid (-7.7) and Oleonolic acid (-8.6). These value suggested that there was a stable inhibition reaction from the binahong leaves compound and the comparative ligand. Based on the Lipinski Rule, the composition of binahong leaves compound meets the Lipinski Rule criteria which means this medicine can be used orally except for vitexin and comparative ligands of zopolrestate which exceed the number of the atom.
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Ogunyemi, Babatunde Temitope, and Ogunyemi Olajide Oderinlo. "In-silico investigation of oxoaporphine alkaloids of Xylopia aethiopica against SARS-COV-2 main protease." AROC in Natural Products Research 02, no. 01 (2022): 01–12. http://dx.doi.org/10.53858/arocnpr02010112.
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Background: The ongoing coronavirus pandemic poses a significant social, economic, and health threat worldwide. The situation is exacerbated further by vaccine hesitancy and the ongoing development of mutant strains that could lead to drug resistance. It is therefore critical to find new anti-viral chemotherapeutic agents to reduce or end the epidemic. This study aimed to investigate the antiprotease activity of the oxoaporphine alkaloids in Xylopia aethiopica. Methods: Computational techniques such as molecular docking were used to probe the oxoaporphine alkaloids in the plant for their ability to inhibit the main protease of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The docking score calculations which quantifies the predictive binding affinity of both ligand and target was carried out using Auto-Dock Vina software. Results: The results showed that oxoaporphine alkaloids had a better binding affinity than hydroxychloroquine sulfate (standard). Similarly, the values of the chemical descriptors obtained for these alkaloids revealed notable profiles, and these alkaloids also have good oral bioavailability according to rule of five. Conclusion: These findings imply that these plant-based alkaloids could be investigated further as prospective leads against SARS-CoV-2 main protease. Furthermore, structural-activity relationships on these compounds could be an effective way to mitigate the predicted side effects
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Lianingsih, Fitri. "In silico analysis of Trisindoline 1 compound against Mpro SARS-CoV-2 as novel potential drugs candidate." Sasambo Journal of Pharmacy 2, no. 2 (2021): 42–50. http://dx.doi.org/10.29303/sjp.v2i2.87.
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The novel coronavirus 2019 (SARS-CoV-2) is one of the viruses that can infect humans and cause high mortality worldwide. The protease (Mpro) is key SARS-CoV-2 an enzyme mediates the viral replication and the transcription. Mpro is currently used as the candidate for the SARS-CoV-2 vaccine because Mpro is one of the key enzymes in the viral life cycle that essential for interactions between the virus and host cell receptor during viral entry. The Mpro can be a target protein to design the novel drug of SARS-CoV-2. The drug design from natural products that are considered to have low toxicity is needed against the virus. The study aims to determines the potential pharmacology of Trisindoline 1 compound from the sponge Hyrtios altum against SARS-CoV-2 and to find the amino acid residues between interaction ligand-protein receptors. The methods of this study use the virtual screening of Auto Dock Vina and visualization the amino acid residue using Bio via Discovery Studio. The result of this study was the selected marine compound from Trisindoline 1 may have potential to developed as inhibitor of SARS-CoV-2.Keywords: In Silico, Mpro, Sars Cov 2, Trisindoline 1, Sponges
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Shehu, M. M., P. A. Vantsawa, J. Appah, V. M. Y, Dan, and M. M. Hamza. "Molecular Docking Modeling Using In-silico Inhibitory Potentials of Parkia biglobosa Compounds against a Resistant Trypanosoma brucei brucei strain." International Journal of Science for Global Sustainability 10, no. 2 (2024): 41–49. http://dx.doi.org/10.57233/ijsgs.v10i2.641.
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In this study, the molecular docking model was used to investigate the antitrypanosomal inhibitory potential of Parkia biglobosa. Twenty-eight different compounds were identified as potential candidates; however, the returned binding energy (kcal/mol) suggested four suitable candidates (beta-sitosterol, epi-gallocatechin, epi-catechin-3-O-gallate, catechin and taraxerone). The antitrypanosomal activity of these compounds was investigated using a molecular docking assay against two proteins from T. brucei brucei, namely arginine kinase 3 (Accession No. EAN76668.1) and trans-sialidase (AlphaFold ID: AF-Q57YTZ-F1). Using the SwissAdme server (SwissADME), all herbal substances were screened in silico for drug-likeness according to the guidelines of Lipinsk, Egan and Veber. Molecular docking was performed to identify putative binding orientations and binding energies (BE) of drugs at the selected binding domains of trans-sialidase and arginine kinase 3 using Auto Dock Vina in the open-source Python Prescription 0.8 program. The returning binding energy (kcal/mol) of P. biglobosa's druglike compounds indicates that they bind well to the active sites of both proteins. However, additional investigation is needed to test P. biglobosa in vitro or in vivo to see if it may be used as an effective and less expensive drug because it is a more accessible plant.
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Nogara, Pablo Andrei, Rogério de Aquino Saraiva, Diones Caeran Bueno, et al. "Virtual Screening of Acetylcholinesterase Inhibitors Using the Lipinski’s Rule of Five and ZINC Databank." BioMed Research International 2015 (2015): 1–8. http://dx.doi.org/10.1155/2015/870389.
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Alzheimer’s disease (AD) is a progressive and neurodegenerative pathology that can affect people over 65 years of age. It causes several complications, such as behavioral changes, language deficits, depression, and memory impairments. One of the methods used to treat AD is the increase of acetylcholine (ACh) in the brain by using acetylcholinesterase inhibitors (AChEIs). In this study, we used the ZINC databank and the Lipinski’s rule of five to perform a virtual screening and a molecular docking (using Auto Dock Vina 1.1.1) aiming to select possible compounds that have quaternary ammonium atom able to inhibit acetylcholinesterase (AChE) activity. The molecules were obtained by screening and furtherin vitroassays were performed to analyze the most potent inhibitors through the IC50value and also to describe the interaction models between inhibitors and enzyme by molecular docking. The results showed that compound D inhibited AChE activity from different vertebrate sources and butyrylcholinesterase (BChE) fromEquus ferus(EfBChE), with IC50ranging from 1.69 ± 0.46 to 5.64 ± 2.47 µM. Compound D interacted with the peripheral anionic subsite in both enzymes, blocking substrate entrance to the active site. In contrast, compound C had higher specificity as inhibitor ofEfBChE. In conclusion, the screening was effective in finding inhibitors of AChE and BuChE from different organisms.
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Patle, Deepshikha, Paranjeet Kaur, and Navneet Khurana. "Identification of Novel Coixol-Based Derivatives as the Potential Anti-diabetic Agents Through Molecular Docking Studies." Asian Pacific Journal of Health Sciences 9, no. 4 (2022): 127–34. http://dx.doi.org/10.21276/apjhs.2022.9.4s1.22.
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Objective: The objective of this study was to design and identify the novel promising anti-diabetic agents based on the naturally existing potent insulin secretagogue coixol that can improve the potency overcome the adverse effects of existing medicines. Methods: The Auto Dock Vina (ADT) 1.5.6 and PyMOL software were used for molecular docking and visualization purposes. The molecular structures were drawn in Chem Draw 16.0 and by the help of Chem Bio draw three dimensions, all structures were energy minimized by MM2 method and converted to PDB extension file which is readable at the ADT interface. Result: Total 254 designed molecules from each series 1–4 were checked for binding score with the receptor 5yw7. Out of that total 12 molecules from each series were selected on the basis of their binding affinity in each series. Among these coixol (Natural product), DP322, DP330, and DP422 were studied in-depth. Conclusion: Coixol-based derivatives which scored best binding affinity such as DP332, DP330, and DP422 were shown promising result on the interaction with the K+ ATP sensitive Potassium channel protein (5yw7). The entire study suggests that these novel coixol-based derived molecules could be a promising lead for the further discovery and investigation of insulin sensitizing agents for the treatment of diabetes.
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Qian, Qian, and Wen Lan Luo. "A network pharmacology method explores the molecular mechanism of Coptis chinensis for the treatment of Alzheimer’s disease." Medicine 103, no. 5 (2024): e37103. http://dx.doi.org/10.1097/md.0000000000037103.
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To predict the molecular mechanisms of action of Coptis chinensis in the treatment of Alzheimer’s disease using network pharmacology. The active ingredients and targets of Coptis chinensis were obtained from the Traditional Chinese Medicine System Pharmacology Database. Target information for Alzheimer’s disease was screened using the GeneCard and OMIM databases. The Venn diagram tool was used to identify the intersecting targets of Coptis chinensis and Alzheimer’s disease. The obtained target information was entered into the STRING database to construct a protein-protein interaction network. The R language was used to perform Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses of significant targets. Auto Dock Vina software was used for molecular docking. Fourteen effective active ingredients and 158 key targets associated with Coptis chinensis were identified. There were 1113 targets related to Alzheimer’s disease genes. A drug-component-disease-target network was constructed and 84 key targets were identified for the treatment of Alzheimer’s disease by Coptis chinensis. The main signaling pathways were the PI3K-Akt, AGE-RAGE, MAPK, HIF-1, TNF, and relaxin signaling pathways. The molecular docking results showed that berberine has a high affinity for Alzheimer’s Disease. Coptis chinensis could play a multi-target and multi-pathway role against Alzheimer’s disease, which has guiding significance for clinical research.
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Saloni, Gupta, Beniwal Prashant, Khanna Sanjay, and N. Sharma Ganesh. "Investigating Anti-Diabetic Potential of Magniferin via Alpha Amylase Inhibitory Activity; In Silico Studies and In Vitro Validation." Indian Journal of Science and Technology 18, no. 11 (2025): 839–47. https://doi.org/10.17485/IJST/v18i11.290.
Full textAbstract:
Abstract <strong>Objectives:</strong> To determine the affinity of magniferin with alpha amylase enzyme plays a central role in diabetes and diabetes-driven complications. <strong>Methods:</strong> The data for magniferin (mol2) and alpha amylase (pdb) enzyme was retrieved from Pub Chem and the protein data Bank. Molecular docking studies were carried out using Auto Dock Vina. In silico findings were evaluated by alpha Amylase Inhibitory assay and alpha amylase mRNA expression profile. <strong>Findings:</strong> Binding energies (-50.9012 kcal/mol) of the docked structure showed significant affinity that clearly showed alpha amylase inhibitory properties of magniferin. The magniferin affinity with alpha amylase was due to interaction with amino acids (Asp, Glu, and Asp). Further, in vitro studies showed magniferin significantly inhibits alpha amylase enzyme activity (247.63 µg/ml). <strong>Novelty:</strong> The magniferin showed affinity with the amino acid residues present in the enzyme active site. The expression profile of alpha amylase gene was examined using Intestinal epithelial cells treated with magniferin with a control. These findings clearly showed the potential of magniferin as anti-diabetic activity via inhibiting alpha amylase. <strong>Keywords:</strong> Magniferin, Natural Products, Docking, Affinity, Anti-Diabetic, Binding Energy and Gene Expression
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R, Hari Priya, and Thirumalai Vasan P. "In Silico and Pharmacokinetic Activity of Bioactive Components from Annona muricata Leaves Against Breast Cancer." Indian Journal of Science and Technology 17, no. 13 (2024): 1283–91. https://doi.org/10.17485/IJST/v17i13.1949.
Full textAbstract:
Abstract <strong>Objectives:</strong> To identify the potential inhibitors isolated from Annona muricata leaves against the epidermal growth factor of tyrosine kinase receptor, a crucial factor involved in the development of breast cancer. <strong>Methods:</strong> In this study, the ethanolic extract of Annona muricata leaves was studied by GC-MS analysis. The functional compounds derived from the GC-MS spectrum were docked with a target molecule, the Epidermal Growth Factor of Tyrosine Kinase Receptor [PDB Id: 1M17], for breast cancer using Auto dock vina. The Bioactivities of compounds against the key role enzymes like GPCR ligand, nuclear, and enzyme inhibitor in Breast Cancer was analyzed using Molinspiration. The pharmacokinetic and pharmacodynamic attributes of the chemical compounds were studied by the Swiss ADME tool. <strong>Findings:</strong> The outcomes from Molecular docking proved that the bioactive compounds such as 9,19-Cyclolanost-24-en-3-ol, (3.beta.), Octadec - 9 - enoic acid, Cycloeucalenol, and Phytol could act as potentially active inhibitors against the Epidermal Growth Factor of Tyrosine Kinase Receptor in Breast Cancer. <strong>Novelty:</strong> The inhibitory effect of the bioactive components from the ethanolic extract of Annona muricata leaves against the Epidermal Growth Factor of Tyrosine Kinase Receptor through the in silico approach has not been explored. This research work will be the first to attempt the in silico mode to determine the potential inhibitors of the Epidermal Growth Factor of Tyrosine Kinase Receptor and successfully identified four bioactive compounds that down-regulate the expression of EGFR and control the proliferation of breast cancer cells. <strong>Keywords:</strong> Drug Development, Breast Cancer, Inhibitor, Pharmacokinetics, Pharmacodynamics, Auto Docking, Bioactive Compounds
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Geeta Mounika, Netala Silvia, Gondu Eswara Rao, et al. "In-silico Analysis of Terpenes From Mentha rotundifolia (L) As Human Angiotensin Converting Enzyme-Related Carboxypeptidase (ACE2) Inhibitors." International Journal of Research in Pharmaceutical Sciences 12, no. 2 (2021): 1158–61. http://dx.doi.org/10.26452/ijrps.v12i2.4648.
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The Mentha genus includes several species such as Mentha rotundifolia L., which is widely distributed around the Mediterranean basin, America and in western Asia. The plant is recommended in folk medicine for the treatment of various diseases. It has also been used to discover biomolecules that have significant beneficial effects with fewer side effects. Mentha rotundifolia (L) leaves are potential as an antihypertensive cause of terpenes which contain in them. 36 different terpenes and terpenoids have been identified and selected from this plant. This study evaluated the mechanism of phytoconstituents from the above plant in the inhibition of angiotensin-converting enzyme-related carboxypeptidase (ACE2) with molecular docking. Selected ligands were docked on the receptor (PDB ID: 1R4L) using Auto Dock Vina and analysed by PyMol. 2D and 3D structures of compounds were drawn by the Chem Draw program. The standard drug that has been taken for the study, lisinopril, has shown a binding affinity of -7.8 Kcal/mol. Calacorene, one of the terpenes present in the plant, has interacted with Phe274, Asp367, Glu406, Thr445, Thr371 residues of protein and produced a docking score similar to that of the standard drug Lisinopril. In the light of the results obtained, the plant studied is promising as a source of natural hypotensive agent that can be further developed as a lead molecule.
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O. Eberendu, K., C. I. Nwankwo, O. M. Mac-kalunta, et al. "New (2Z)-1-(2,4-dinitrophenyl)-2-[(2E)-3-(2-nitrophenyl)prop-2-en-1-ylidene]hydrazine and its V(II) and Ni(II) complexes: synthesis, characterization and in silico sars-CoV-2 inhibition studies." Bulletin of the Chemical Society of Ethiopia 39, no. 4 (2025): 673–86. https://doi.org/10.4314/bcse.v39i4.6.
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Hydrazones are an important family of compounds with an azomethine proton (-NHN=CH-), which have been reported to possess high biological activity such as antioxidants, anti-consultants, analgesics, antimicrobial, anti-protozoals, anti-parasitic, anti-platelets, cardio-protective, anti-diabetic, anti-HIV and anti-helminthic. This research was aimed at synthesizing a new aniline hydrazone and its V(II) and Ni(II) complexes, and in silico SARS-CoV-2 inhibition studies. The (2Z)-1-(2,4-dinitrophenyl)-2-[(2E)-3-(2-nitrophenyl)prop-2-en-1-ylidene]hydrazine (DNEAA) was synthesized by the reaction of 2,4-dinitrophenylhydrazine and 3-(2-nitrophenyl)prop-2-enal. DNEAA and its V(II) and Ni(II) complexes were synthesized and characterized by UV-visible, FTIR, and NMR spectroscopy. Molecular docking was performed using Auto Dock Vina software. Spectroscopic analysis suggested that DNEAA coordinated with the metal ions through azomethine nitrogen, NH, two NO2 and two Cl-. An octahedral geometry was proposed for the metal complexes. The ability of DNEAA to chelate V(II) and Ni(II) is hereby assured. Molecular docking results gave binding energies >9.5 kcal/mol. Following these findings, it is recommended that biological studies and preclinical and clinical trials against SARS-CoV-2 protease be carried out. Bull. Chem. Soc. Ethiop. 2025, 39(4), 673-686. DOI: https://dx.doi.org/10.4314/bcse.v39i4.6
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Umar, Haruna Isiyaku, Ijeoma Akunna Duru, Uchechi Emmanuela Enenebeaku, Lynda Chioma Ngozi Olehi, Christian Ebere Enyoh, and Chidi Edbert Duru. "Inhibitory potentials of ivermectin, nafamostat, and camostat on spike protein and some nonstructural proteins of SARS-CoV-2: Virtual screening approach." Jurnal Teknologi Laboratorium 11, no. 1 (2022): 33–42. http://dx.doi.org/10.29238/teknolabjournal.v11i1.344.
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The search for potent oral drugs either through synthetic routes or by drug repurposing for combating the dreaded covid-19 virus is still ongoing. The coronavirus spike glycoprotein and several other non-structural proteins play crucial roles in the replication and transmission of this virus. Recent research have identified ivermectin, nafamostat, and camostat as promising drug inhibitors of SARS-CoV-2 target proteins. The broad-spectrum inhibitory action of ivermectin, nafamostat, and camostat on the spike glycoprotein and some non-structural proteins of this virus was studied in silico. The spike glycoprotein, nsp3, nsp5, nsp9, nsp10, nsp13, and nsp16 were selected for this study and were downloaded from the protein data bank. Flexible docking procedure implemented in Auto Dock Vina module was deployed for the docking procedure of the drugs with the protein receptors. Although ivermectin had the best inhibitory action on the viral spike protein and nsp10, nafamostat was identified as the compound with the best broad-spectrum activity on this virus, having the highest binding affinity values of – 9.4kcal/mol, – 7.9 Kcal/mol, – 6.1 Kcal/mol, – 8.0 Kcal/mol, and – 8.7 Kcal/mol for nsp3, nsp5, nsp9, nsp13, and nsp16 respectively. This drug, in combination with ivermectin could therefore be explored further as potential compounds that could be modified to curb the menace of the covid-19 pandemic.
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Pawar, Prajakta Arun, Vivek Ranjan Sinha, and Ashok Kumar Yadav. "Compatibility Study and Solid Dose Formulation of Rosuvastatin Calcium." Journal of Modern Pharmacology and Pathology 2 (June 6, 2024): 5. http://dx.doi.org/10.53964/jmpp.2024005.
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Objective: The goal of present study is to recognize acceptable excipients to increase performance and stability of oral solid formulations of rosuvastatin calcium by estimating compatibility study of rosuvastatin calcium and used excipients. Methods: Analytical instruments like fourier transform infrared spectroscopy Spectrum RX 1, [differential scanning calorimetry-Q20, TA], Bruker Advance Neo 500MHz NMR spectrometer, thin layer chromatography] were utilized. Excipients and rosuvastatin calcium were got from Loba chemie and Biocon, respectively. USP1-type dissolution apparatus, and Auto Dock VINA 1.2.0 software were applied. Results: Numerous analytical methods established that rosuvastatin calcium was compatible with used excipients. Docking score was found -2.1, and minimal interactions were demonstrated by complexes of rosuvastatin calcium with microcrystalline cellulose (MCC) and lactose. Further, an immediate release of rosuvastatin calcium tablet was studied using a combination of various excipients. Tablets of rosuvastatin calcium were formulated with appropriate excipients. Tablets from batches 1, 2, 3, and 4 were observed to disintegrate in 3.0, 4.0, and 5.0min, respectively. Conclusion: Lactose, talc, starch, dicalcium phosphate, MCC, and carbopol were found to be compatible with rosuvastatin calcium using analytical procedures. At 90min, the percentage of drug release for batches 1, 2, 3, and 4 were 89%, 85%, 82%, and 79%, respectively. The above study showed that batch 1 had the greatest drug release and the shortest disintegration time. Docking studies presented possible interactions between rosuvastatin calcium and excipients.
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Venkatesh G, Maharaja D, and Sowmiyadevi S. "A novel in-silico based drug discovery of neuroprotective targets for." Indian Journal of Pharmacy and Pharmacology 11, no. 2 (2024): 80–84. https://doi.org/10.18231/j.ijpp.2024.014.
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(MSG) is a frequently used food additive that enhances flavour and is well-liked worldwide and has a significant interaction on nervous system. It is a ligand based docking study. By using Chem Sketch or Chem Draw, Swiss target prediction tool, Auto Dock Vina 4.2.6, BIOVIA Discovery Studio Visualizer, and neuroprotective targets of MSG with promising interactions with particular brain targets, we harness the computational power of molecular docking. The aim of this study is to identify and evaluate the neuroprotective targets for using method. In silico experiments had been used to screen for monosodium glutamate. Based on the docking interaction score and conventional hydrogen bond interactions, monosodium glutamate demonstrated maximal affinity towards a number of neuroprotective targets, including ionotropic NMDA 2A, metabotropic 4(R), and metabotropic 1(B). These three proteins interact powerfully with MSG. Despite the fact that the US FDA, FSSAI, WHO, and a number of other organizations advise an estimated safe dose of MSG, Certain adverse effects still have an impact on people. In future the dose reduction study can conduct to reduce the dose range to the particular dose for beneficial and neuroprotective effects by targeting these three proteins based on their docking interactions. For research on neuroprotection, these three targets are better choices. The identification of neuroprotective targets opens the door to more in-vivo and in-vitro research on neuroprotective treatments.
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Sneha, Nandeshwar* Sapan Shah Rida Saiyad Nikita Gaikwad Pooja Wankhade. "In-Silico Evaluation of Flavone Derivatives for Cardioprotective Effects: A Comparative Molecular Docking Approach." International Journal of Pharmaceutical Sciences 3, no. 3 (2025): 2543–56. https://doi.org/10.5281/zenodo.15087478.
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Background: In this study, we used molecular docking to explore the binding affinity, ADME, and toxicity of flavone derivatives on several receptors associated with cardioprotective action. The binding affinity of several flavone derivatives to various receptors involved in cardioprotective action was determined. Auto Dock Vina, PyMol, Discovery Studio, AutoDock Tools, ChemSketch, Swiss ADME, and PROTOX 3.0. Methods: Molecular docking. Results: The binding results of the selected plant compounds and target proteins, namely 1o86, 7Q29, 5JMY, 4DLI, 2YCW, and 1CX2, showed that the good binding affinity and good receptor binding mode selected target. However, among all protein β 1 adrenergic receptor (ID:- 2YCW) showed lowest binding affinity with compound D10 (2-(4-tert-butylphenyl)-4H-1-benzopyran-4-one) (binding energy – 11.0 Kcal/mol), D44 (binding energy – 10.6 Kcal/mol). D39 (binding energy – 10.4 Kcal/mol), D32, D35 & D42 (binding energy – 10.2 Kcal/mol). Conclusions: The current study attempted to computationally find chemicals that can bind to the numerous targets of cardiovascular disease. The docking scores and interaction analysis indicate that most drugs have the ability to bind to many targets involved in cardiovascular illness. However, the β 1 adrenergic receptor has a high binding affinity. Absorption, distribution, metabolism, excretion, and toxicity, as well as toxicity prediction, revealed several chemicals that could be employed as possible candidates against cardiovascular disease.
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NA’ABBA, Zaharaddeen Umar, Iliyasu Gwarzo DATTI, Pankaj Teli KUMAR, Hassan Muhammad SABO, and Muhammad Abdullahi AUWAL. "Molecular Docking Analysis of Azadirachta Indica Phytocompounds against Androgen Receptor Protein for the Treatment of Prostate Cancer." Journal of Biotechnology 1, no. 1 (2022): 9–36. http://dx.doi.org/10.36108/jbt/2202.10.0120.
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In affluent countries, prostate cancer (PCa), one of the leading causes of male death, continues to be a serious medical burden. Androgen stimulates growth and advancement primarily through the androgen receptor. PCa is thought to include some molecular pathways in its growth and progression. In this work, several bioactive components of the neem plant (Azadirachta indica) were studied using the molecular docking analysis to identify and create novel medicines or inhibitors that can target androgen receptors for the treatment of prostate cancer. Azadirachta indica has been demonstrated to have therapeutic potential in the treatment of cancer. We investigated the molecular interactions of 30 bioactive chemicals in Azadirachta indica leaves against prostate cancer in this work. Androgen receptor protein is implicated in the genesis and progression of prostate cancer. A screening technique was used to perform molecular docking. PyMOL v 1.1r1 and Discovery studio 2020 were used to execute auto dock vina of the PyRx v 0.8 docking software and visualization, respectively. The SwissADME online software was used to assess the hit compounds’ physicochemical attributes. The selected ligands demonstrated good inhibitory action in docking tests with the target proteins. The binding affinities range from -6.0 to -8.5 (kcal/mol) in the docking results of the selected hits, which is greater than the typical medicines employed. Among the identified ligands, Etofenprox had the greatest binding score with the target protein, whereas 4-hydroxystyrene, 3-Methylbenzaldehyde, and Limonene had the lowest binding energy with the target protein.
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Kanagaraj, Jyothi, Ramesh Ghurupreya, Derina J. Pearlin, and K. Ponmozhi. "Phytocompounds from Withania somnifera against breast cancer: An in-silico study." Biomedicine 42, no. 4 (2022): 720–25. http://dx.doi.org/10.51248/.v42i4.1244.
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Introduction and Aim: Withania somnifera, called as Indian Ginseng is a very important plant in traditional medicinal practices. The plant possesses a wide range of activity and has been used to treat multiple diseases. Ginseng possesses anti-inflammatory, neuroprotective, hypoglycemic, antiarthritic, hepatoprotective, antioxidant, anti-stress, immunostimulatory and anti-cancer therapeutic activities. Cancer is a health burden prevalent worldwide and, breast cancer is the top major cause of death among women and people in the low and middle-income countries are affected in higher number because they have low treatment access. This is an in-silico study and focused on studying the interaction between five phytocompounds namely, anaferine, isopelletierin, sitoindoside IX, somniferine, withanone present in W.somnifera and the 3 proteins involved in breast cancer pathway viz., C-Raf, AKt 2 and GSK 3? through molecular docking. Methodology: We retrieved the above three proteins from PDB, retrieved five ligands from PubChem, and docking was done. Docking of the phytocompounds against the target proteins were carried out using Auto dock vina. Results: From the docking results, we found that the phytocompounds; sitoindoside IX, somniferine, withanone from Withania somnifera are effective in inhibiting the proteins causing breast cancer whereas anaferine and isopelletierin are less effective in inhibiting the breast cancer. Conclusion: This study concludes that the phytocompounds sitoindoside IX, somniferine, withanone from W. somnifera have the potential ability to treat breast cancer. These findings will aid in the development of natural based therapy against breast cancer.
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Beshah Tessema, Fekade, Aweke Mulu Belachew, Yilma Hunde Gonfa, et al. "Efficacy of fumigant compounds from essential oil of feverfew (Chrysanthemum parthenium L.) against maize weevil (Sitophilus zeamais Mots.): Fumigant toxicity test and in-silico study." Bulletin of the Chemical Society of Ethiopia 38, no. 2 (2024): 457–72. http://dx.doi.org/10.4314/bcse.v38i2.13.
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Post-harvest insects are among the significant problems in the agricultural sector. The most accessible tools available for managing post-harvest arthropod-pests are fumigants because of the convenience of their applications and fast action in disinfecting. This study aimed to examine the fumigant toxicity of essential oil (EO) against maize weevil and identify the specific fumigants among the major components. The EO was extracted from aerial part of Chrysanthemum parthenium L. using Clevenger apparatus and was tested for fumigant toxicity. GC-MS was used to determine the chemical composition of EO. The major components were identified and screened virtually using Auto dock vina 1.2. in PyRx 0.8 platform. Dm AChE PDB ID: 6XYY was used as a target for molecular docking and malathion and pirimiphusmethyl were used as a reference for comparison. From the results of binding affinities, most of the major EO components showed better fumigant activity than the reference fumigants. More specifically 1,6-dioxaspiro[4,4]non-ene, b-farensen, bornyl-tiglate, g-terpinene, p-cymene, bornyl-acetate, bornyl-isovalerate, terpinen-4-ol, trans-chrysanthenyl-acetate and a-phellandrene were found to be effective fumigants against maize weevil. The above findings suggest that the EO of the aerial part of C. parthenium can be a potential candidate for the development of novel natural fumigants for stored products.
 KEY WORDS: Essential oil, Fumigants, Insecticides, Binding affinity, Maize weevil
 Bull. Chem. Soc. Ethiop. 2024, 38(2), 457-472. 
 DOI: https://dx.doi.org/10.4314/bcse.v38i2.13
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Shraddha, P. Hegde, B.V Suma, R. Jawale Nayana, and Laxmi C.H Jhansi. "Molecular Docking and Admet Studies of Cholesta-22, 24-Dien-5-Ol, 4, 4-Dimethyl Compound for the Antibacterial Property." Journal of Research and Development in Pharmacological Practices 1, no. 1 (2025): 21–26. https://doi.org/10.5281/zenodo.15331413.
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<strong><em>Objective:</em></strong><em> Bacterial infections are posing a serious threat to the human health because of their high frequency and rapid transmission. Staphylococcus aureus is a Gram-positive bacterium responsible for a wide range of clinical infections. Treating these infections presents a significant challenge in modern medicine, primarily due to the rise of drug-resistant strains. Cholesta-22,24-dien-5-ol, 4,4-dimethyl, a steroidal compound found in various plant, fungal, and animal species, has shown notable biological activities, including antibacterial and trypanocidal effects. The primary goal of this study is to evaluate the binding affinity of Cholesta-22,24-dien-5-ol, 4,4-dimethyl against seven distinct target proteins of Staphylococcus aureus, using norfloxacin as a reference drug, and to assess the ADMET properties of the compound.</em> <strong><em>Methods And Materials: </em></strong><em>The binding affinity between the ligand and protein was determined using rigid docking with AutoDock Vina 1.5.6. The 3D structures of seven antibacterial target proteins were obtained from the Protein Data Bank. The ligand molecules were generated using ChemDraw Professional. Rigid docking was applied to calculate the binding affinities between the ligand and the proteins.</em> <strong><em>Results:</em></strong><em> The binding affinity of Cholesta-22,24-dien-5-ol, 4,4-dimethyl compound with seven different target proteins of staphylococcus aureus that is dihydrofolate reductase (PDB ID:2W9S), DNA gyrase (PDB ID: 3U2D), dehydrosqualene synthase (PDB ID:2ZCO), clumping factor A(PDB ID:1N67),fibrinogen binding protein (PDB ID:3DOA), pantothenate synthase (PDB ID: 2X3F),Staphylococcus aureus sortase A (PDB ID:1T2P) were studied using molecular docking tool Auto dock vina 1.5.6 and the docking scores were -9.0,-8.1,-8.6, -9.1,-7.8,-7.3,and -7.3 respectively. 2D interactions were visualized using Biovia discovery studio 2021. ADMET properties were studied using the web tool Swiss ADME.</em> <strong><em>Conclusion: </em></strong><em>In summary, Cholesta-22,24-dien-5-ol, 4,4-dimethyl compound exhibits promising results based on the in-silico studies in comparison with the reference drug norfloxacin. The docking studies of the compound with the protein dihydrofolate reductase (PDB ID:2W9S) and clumping factor A (PDB ID:1N67) have shown the highest docking score of -9.0 and -9.1 respectively. ADMET studies of the compound were also reported.</em>
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Kumar, Om, G. Keerthana, Ashitha B Arun, Ananya Joliholi, and Lokesh Ravi. "Construction of 3D Model of Protein Drug Targets for Renibacterium Salmoninarum - A Bacterial Pathogen Causing Bacterial Kidney Disease in Young Salmonid Fish." Biosciences Biotechnology Research Asia 18, no. 3 (2021): 591–601. http://dx.doi.org/10.13005/bbra/2943.
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The aim of this study is to construct 3D models of potential drug targets for the Bacterial Kidney Disease (BKD) causing pathogen Renibacterium salmoninarum. The bacterial pathogen Renibacterium salmoninarum was selected for homology modeling studies since there were no known protein structures of the organism reported in the NCBI database. The reported protein sequences were run through DrugBank to pick out drug-targets. Online databases and web tools such as PMDB, UniProt, Drug Bank, and SwissModel were employed in this analysis. An aggregate of 412 protein sequences were identified as potential drug targets and were retrieved from the UniProt. Homology models of the protein sequences were constructed using the SwissModel database for all 412 proteins. These were then refined through a protein blast and Ramachandran plot analysis. Out of the 412 constructed models, 143 models were of reliable quality. These were then submitted to the PMDB database for further reference. To demonstrate the application of these constructed models, protein-ligand docking analysis using Auto Dock Vina was performed. Among the antibiotics that were tested against their known drug targets, trimethoprim demonstrated significant potential for the inhibition of R. salmoninarum’s dihydrofolate reductase protein, with a binding energy of -9.06 Kcal/mol and with the formation of 3 hydrogen bonds. Therefore through protein-ligand docking studies and the construction of 3D models of protein drug targets, Trimethoprim is proposed as a solution to the Bacterial Kidney Disease (BKD) problem in salmonid fishes. Further in-vitro evidences are in demand to prove this hypothesis.