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Journal articles on the topic 'ADME database'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Sun, L. Z., Z. L. Ji, X. Chen, J. F. Wang, and Y. Z. Chen. "ADME-AP: a database of ADME associated proteins." Bioinformatics 18, no. 12 (2002): 1699–700. http://dx.doi.org/10.1093/bioinformatics/18.12.1699.

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2

Deb, Subrata, Robert Hopefl, Anthony Allen Reeves, and Dena Cvetkovic. "ADME Gene-Related Pharmacogenomic Labeling of FDA-Approved Drugs: Comparison with Clinical Pharmacogenetics Implementation Consortium (CPIC) Evidence Levels." Medicines 11, no. 3 (2024): 6. http://dx.doi.org/10.3390/medicines11030006.

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Pharmacogenomics (PGx) can facilitate the transition to patient-specific drug regimens and thus improve their efficacy and reduce toxicity. The aim of this study was to evaluate the overlap of PGx classification for drug absorption, distribution, metabolism, and elimination (ADME)-related genes in the U.S. Food and Drug Administration (FDA) PGx labeling and in the Clinical Pharmacogenetics Implementation Consortium (CPIC) database. FDA-approved drugs and PGx labeling for ADME genes were identified in the CPIC database. Drugs were filtered by their association with ADME (pharmacokinetics)-relat

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3

Ravi, Kumar K. 1. *. Archana Giri 1. Rama Rao Nadendla 2. "INSILICO ADME PROFILING OF CDK9 INHIBITORS." Journal of Scientific Research in Pharmacy 7, no. 3 (2018): 30–34. https://doi.org/10.5281/zenodo.1207094.

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<strong><em>ABSTRACT</em></strong> <strong><em>S</em></strong><em>everal drug targets have been identified in fighting against cancer. Inhibition of Cell cycle is one of the strategies used in anti-cancer research.   CDKs [Cyclin Dependent Kinases] were found to be one of the promising drug targets. This work aims to find a potential molecule to inhibit CDKs that are involved in cell cycle progression. CDK 9 was chosen as potential drug target for cancer.  Virtual screening was carried out against CDK 9 protein using Molecular Docking tools with molecules from ZINC database. Mol

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4

Prasad, Bhagwat, Marc Vrana, Prachi Jha, Vivek Nautiyal, Deepak Kumar Bhatt, and Jingtian Zheng. "ADME QPrOmicstm mrm database: A repository of validated LC-MS/MS methods for ADME protein quantification." Drug Metabolism and Pharmacokinetics 32, no. 1 (2017): S42. http://dx.doi.org/10.1016/j.dmpk.2016.10.180.

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Bououden, Walid, and Yacine Benguerba. "Designing, Cytotoxic Evaluation, Molecular Docking and in Silico Pharmacokinetic Prediction of New Hydrocortisone Derivatives as Anti-Asthmatics Drugs." Journal of Drug Delivery and Therapeutics 10, no. 4 (2020): 8–16. http://dx.doi.org/10.22270/jddt.v10i4.4128.

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A series of new 20 corticosteroids were subjected to molecular property prediction. The Molecular, Physicochemical, and Biological properties were determined using Molinspiration Cheminformatics software. These compounds were further subjected to Toxicity Predictions using the Osiris Software. The calculated drug-related properties of the designed molecules were similar to those found in most marketed drugs. Amongst the proposed molecules, fourteen promising candidates can be considered as promising structures for the synthesis of new and more effective anti-asthmatic drugs. Result indicates t

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Sharma, Aastha, Nitish Banga, Rakesh Kumar Marwaha, and Balasubramanian Narasimhan. "Identification of novel potential benzimidazole derivatives by pharmacophore generation, 3D-QSAR, virtual screening, molecular docking and ADME/ TOX analysis against breast cancer as targeted estrogen alpha receptor." Journal of Applied Pharmaceutical Research 13, no. 2 (2025): 149–63. https://doi.org/10.69857/joapr.v13i2.951.

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Background: The estrogen alpha receptor (ERα) is critical in breast carcinogenesis. Although selective estrogen receptor modulators like tamoxifen are clinically used, their adverse effects highlight the need for safer alternatives. The study uses computational methods to identify potential ERα inhibitors within a benzimidazole scaffold. Methodology: This study employed computational approaches, including pharmacophore generation, 3D-QSAR, virtual screening, molecular docking, and in silico ADME/Tox analysis. The best pharmacophore model (DDRRR_1) identified two hydrogen donors and three aroma

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R, Thirumalaisamy. "Comparative Anti–Alzheimer’s Potential Evaluation of Curcumin and Curcumin Analogues obtained from ZINC Database: An in-Silico Validation." TEXILA INTERNATIONAL JOURNAL OF PUBLIC HEALTH 9, no. 4 (2021): 269–83. http://dx.doi.org/10.21522/tijph.2013.09.04.art023.

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Curcumin and its eleven analogues obtained from the ZINC database were screened for its anti-Alzheimer’s potential validated through in silico approach. Curcumin, eleven curcumin analogues from the ZINC database, and six standard anti-Alzheimer’s drugs were obtained from SWISS ADME and Pub chem database. All obtained molecules were subjected to drug-likeness, molecular docking, and ADMET analysis. Curcumin and eleven curcumin analogues show no violations against five drug-likeness rules, whereas 2 standard drugs (CID¬_11269353, CID_46883536) out of 5 screened standard drug molecules shows viol

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Aman, La Ode, Rahmana Emran Kartasasmita, and Daryono Hadi Tjahjono. "Virtual screening of curcumin analogues as DYRK2 inhibitor: Pharmacophore analysis, molecular docking and dynamics, and ADME prediction." F1000Research 10 (May 17, 2021): 394. http://dx.doi.org/10.12688/f1000research.28040.1.

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Background: Curcumin reduces the proliferation of cancer cells through inhibition of the DYRK2 enzyme, which is a positive regulator of the 26S proteasome. Methods: In the present work, curcumin analogues have been screened from the MolPort database using a pharmacophore model that comprised a ligand-based approach. The result of the screening was then evaluated by molecular docking and molecular dynamics based on binding the free energy of the interaction between each compound with the binding pocket of DYRK2. The hit compounds were then confirmed by absorption, distribution, metabolism, and

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Amaku, F. J., I. E. Otuokere, K. K. Igwe, and O. V. Ikpeazu. "Design of Potential SARS-CoV-2 Inhibitor." European Journal of Engineering Research and Science 5, no. 9 (2020): 1043–48. http://dx.doi.org/10.24018/ejers.2020.5.9.2058.

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This computational study comprises of pharmacophore-base virtual screening of the ZINC database, molecular docking of predicted ligands (pharmacophore agent) against the target protein, SARS-CoV-2 (PDB ID: 5r7y) and the prediction of ADMET descriptors using Swiss ADME and PROTOX-II online web servers. Meanwhile, remdesivir, ZINC72392503, ZINC72809903, ZINC06560017, ZINC76101700, ZINC88423098 and ZINC91600695 had a docking scores of -2.0 Kcal/mol, -6.7 Kcal/mol, -6.4 Kcal/mol, -6.0 Kcal/mol, -6.0 Kcal/mol, -6.0 Kcal/mol and-6.0 Kcal/mol respectively. Meanwhile, ZINC72392503 was selected as the

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Amaku, F. J., I. E. Otuokere, K. K. Igwe, and O. V. Ikpeazu. "Design of Potential SARS-CoV-2 Inhibitor." European Journal of Engineering and Technology Research 5, no. 9 (2020): 1043–48. http://dx.doi.org/10.24018/ejeng.2020.5.9.2058.

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This computational study comprises of pharmacophore-base virtual screening of the ZINC database, molecular docking of predicted ligands (pharmacophore agent) against the target protein, SARS-CoV-2 (PDB ID: 5r7y) and the prediction of ADMET descriptors using Swiss ADME and PROTOX-II online web servers. Meanwhile, remdesivir, ZINC72392503, ZINC72809903, ZINC06560017, ZINC76101700, ZINC88423098 and ZINC91600695 had a docking scores of -2.0 Kcal/mol, -6.7 Kcal/mol, -6.4 Kcal/mol, -6.0 Kcal/mol, -6.0 Kcal/mol, -6.0 Kcal/mol and-6.0 Kcal/mol respectively. Meanwhile, ZINC72392503 was selected as the

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Lestari, Nur Ayu, Muhammad Isrul, Dwi Syah Fitrah Ramadhan, and Fatahu. "Skrining Virtual Berbasis Farmakofor Dari Database Bahan Alam Sebagai Inhibitor Alosterik Mutan T790M/C797 EGFR Untuk Penemuan Obat Kanker Paru." Jurnal Pharmacia Mandala Waluya 3, no. 3 (2024): 168–86. http://dx.doi.org/10.54883/jpmw.v3i3.102.

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Virus korona merupakan penyakit menular berbahaya yang disebabkan oleh virus baru (SARS-CoV-2). Usaha untuk mengeksplorasi bahan-bahan alam aktif sebagai anti-virus terus dilakukan. Salah satu tanaman lokal Indonesia yang dapat menghambat SARS-CoV-2 protein spike yaitu herba sambiloto (Andrographis paniculata) secara in silico, akan tetapi aktivitasnya terhadap mutan D614G SARS-CoV-2 belum diketahui. Tujuan dari penelitian ini yaitu untuk mengkaji aktivitas metabolit andrographolide dan turunannya dalam herba sambiloto (Andrographis paniculata) terhadap mutasi D614G SARS-CoV-2 protein spike se

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12

Gupta, Shikhar, and C. Gopi Mohan. "Dual Binding Site and Selective Acetylcholinesterase Inhibitors Derived from Integrated Pharmacophore Models and Sequential Virtual Screening." BioMed Research International 2014 (2014): 1–21. http://dx.doi.org/10.1155/2014/291214.

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In this study, we have employedin silicomethodology combining double pharmacophore based screening, molecular docking, and ADME/T filtering to identify dual binding site acetylcholinesterase inhibitors that can preferentially inhibit acetylcholinesterase and simultaneously inhibit the butyrylcholinesterase also but in the lesser extent than acetylcholinesterase. 3D-pharmacophore models of AChE and BuChE enzyme inhibitors have been developed from xanthostigmine derivatives through HypoGen and validated using test set, Fischer’s randomization technique. The best acetylcholinesterase and butyrylc

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13

Moda, T. L., L. G. Torres, A. E. Carrara, and A. D. Andricopulo. "PK/DB: database for pharmacokinetic properties and predictive in silico ADME models." Bioinformatics 24, no. 19 (2008): 2270–71. http://dx.doi.org/10.1093/bioinformatics/btn415.

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14

Zheng, C. J., L. Z. Sun, L. Y. Han, Z. L. Ji, X. Chen, and Y. Z. Chen. "Drug ADME-associated protein database as a resource for facilitating pharmacogenomics research." Drug Development Research 62, no. 2 (2004): 134–42. http://dx.doi.org/10.1002/ddr.10376.

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15

Schurdak, Mark, Lawrence Vernetti, Luke Bergenthal, et al. "Applications of the microphysiology systems database for experimental ADME-Tox and disease models." Lab on a Chip 20, no. 8 (2020): 1472–92. http://dx.doi.org/10.1039/c9lc01047e.

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16

Thakre, Revati, Aarti More, Pradeep Deshmukh, et al. "Exploring Anti-inflammatory Targets of Flavonoids through Integrated Molecular Docking and Network Pharmacology." Jordan Journal of Pharmaceutical Sciences 18, no. 1 (2025): 160–79. https://doi.org/10.35516/jjps.v18i1.2713.

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Inflammation is a complex physiological response associated with numerous diseases. Flavonoids, a class of natural compounds widely distributed in plants, have demonstrated promising anti-inflammatory properties. However, their comprehensive mechanisms of action and potential molecular targets remain indefinable. In the present study, we employed a network pharmacology approach combined with molecular docking to investigate the anti-inflammatory effects of some flavonoids. Initially, we collected and curated a comprehensive database such as ADMET parameters and targets from Swiss ADME, ADMET 2

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17

Pathak, Vijay kumar. "Network pharmacology and Molecular docking-based activity of Hemidesmus indicus (L.) R.Br. in Acute myeloid leukemia : A Computational Study." International Journal of Ayurvedic Medicine 14, no. 3 (2023): 703–16. http://dx.doi.org/10.47552/ijam.v14i3.3883.

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ABSTRACT  Background  Acute myeloid leukemia (AML) is malignancy of the stem cell precursors of the myeloid lineage occurs due to variations in genetics. Incidence rate of childhood AML in Asian population is 8.4 per million. There is no exact description of AML is Ayurveda, it can be considered into Raktapitta (~bleeding disorder) disease. Hemidesmus indicus (L.) R.Br. (~H. indicus) is described for treatment of Raktapitta. The main treatment for AML is chemotherapy, and patient are searching for Ayurvedic medicines. Hence attempt is made for evaluating activity of H. indicus in A

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18

Pathak, Vijay Kumar. "Network pharmacology-based anti-obesity activity of Gavedhuka (a millet): In silico study." Journal of Drug Research in Ayurvedic Sciences 9, no. 6 (2024): 426–32. https://doi.org/10.4103/jdras.jdras_94_23.

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Abstract BACKGROUND: Millet is a small-seeded crop widely used in Ayurveda for maintaining health; it has a significant effect on the economic impacts in developing countries. In Ayurveda, Gavedhuka (Coix lacryma-jobi L.), a type of millet, is described for its anti-obesity activity. The prevalence of obesity has been increasing across the globe in past few decades. With increase in prevalence, mortality risks among obese persons have also been increasing. The objective of this study was to explore the activity of Gavedhuka (C. lacryma-jobi L.) in obesity using network pharmacology. METHODS: B

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19

Agustin, Diah, Mumtaz Nabila Ulfah, Siti Nur Aisyah, Pamuji Lestari Arumsari, Kadita Octavia Pertiwi, and Fatchiyah Fatchiyah. "In Silico Study of Vacuolin-1 as an Inhibitor of HSP27 for Precancerous Treatment of Breast Cancer." JSMARTech 2, no. 3 (2021): 107–12. http://dx.doi.org/10.21776/ub.jsmartech.2021.002.03.107.

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Breast cancer has a great chance of being cured if it is diagnosed and treated properly in its early stage. The pre-cancer stage is an early stage of cancer development characterized by the overexpression of HSP27. Therefore, HSP27 can be a therapeutic target of cancer. This study aims to analyze whether vacuolin-1, a small drug compound known for its ability to inhibit metastasis, can inhibit HSP27 to prevent precancerous development in breast cancer, as well as its ADME and biosafety aspects. Protein & ligand structures were obtained from RCSB PDB and PubChem database. Preparation was pe

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Noor, Md Ali Asif, Md Mazedul Haq, Md Arifur Rahman Chowdhury, Hilal Tayara, HyunJoo Shim, and Kil To Chong. "In Silico Exploration of Novel EGFR Kinase Mutant-Selective Inhibitors Using a Hybrid Computational Approach." Pharmaceuticals 17, no. 9 (2024): 1107. http://dx.doi.org/10.3390/ph17091107.

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Targeting epidermal growth factor receptor (EGFR) mutants is a promising strategy for treating non-small cell lung cancer (NSCLC). This study focused on the computational identification and characterization of potential EGFR mutant-selective inhibitors using pharmacophore design and validation by deep learning, virtual screening, ADMET (Absorption, distribution, metabolism, excretion and toxicity), and molecular docking-dynamics simulations. A pharmacophore model was generated using Pharmit based on the potent inhibitor JBJ-125, which targets the mutant EGFR (PDB 5D41) and is used for the virt

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Deepak, G., A. Dinakara Rao Dr., and Babu Khan Mohammad. "Identifying Potential Bace-1 Enzyme Inhibitors /Lead Small Molecules: Relevance to Alzheimer's Diseases." Identifying Potential Bace-1 Enzyme Inhibitors /Lead Small Molecules: Relevance to Alzheimer's Diseases 10, no. 10 (2022): D586—D587. https://doi.org/10.6084/m9.figshare.21436593.

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   It is unclear what causes Alzheimer's disease. However, genetic data support the amyloid hypothesis, which states that abnormal beta-amyloid protein aggregation initiates the illness process. There is a lengthy pre-clinical stage of Alzheimer's disease. The terrible consequences of amyloidogenic diseases like Alzheimer's. More than 7000 tiny molecules have been screened from ZINC subsets and exposed to 165 compounds and 16. From a research perspective, I have examined numerous databases like the ZINC Subset, PubChem compound database, and Drug bank database. For dockin

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Nabiya, Farnaz, Anchana Devi Chenniappan, and Rajamiriyam Marichamy. "Plant-derived Bioactive Compounds Targeting MMP-9 for Treatment of Endometrial Carcinoma: An In silico Study." Journal of Plant Science Research 38, no. 2 (2023): 701–15. http://dx.doi.org/10.32381/jpsr.2022.38.02.24.

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Endometrial cancer, also called uterine cancer, is the second most common and fourth leading cause of death among gynecological problems in the world. Matrix metalloproteinase-9 (MMP-9) has been found to play an important role in the formation and metastases of endometrial cancer. Thus, this study investigates the naturally anti-inflammatory compounds available from plant sources that can target the MMP-9 by various in silico approaches. The target 1L6J (Crystal structure of human matrix metalloproteinase-9) structure was retrieved from the PDB database. Five plant compounds were selected base

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Patel, Sanakousar K., Prachi Parvatikar, Supriya Bhosale, Sumangala Patil, and Kusal K. Das. "Repurposing of potential bioactive compounds from various database to study their effects on MMP-7 by virtual screening." Research Journal of Biotechnology 19, no. 2 (2023): 14–19. http://dx.doi.org/10.25303/1902rjbt014019.

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Matrix metalloproteinase-7 (MMP7), a member of the matrix metalloproteinase (MMP) family, is involved in the mediation of both agonist-induced vascular tone and cardiac remodelling. We aimed to study the effect of a few bioactive molecules on (MMP-7) by in silico analysis. Data of bioactive molecules were collected from Pubchem and NPACT databases. PDB database was used for the generation of the 3D structure of protein MMP-7. ADME/T properties showed 5 bioactive molecules obeying Lipkin’s rule. Based on molecular docking, β-Sitosetrol and calyxin B are the top two compounds possessing higher l

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Anbuselvam, Mohan, Ji Katherine C., Chitra Balasubramanian, Jeeva Anbuselvam, and Ji Hai-Feng. "Molecular docking analysis of N-myristoyl-transferase with small molecules from the ZINC database for screening potential anti-malarial drugs." Bioinformation 21, no. 06 (2025): 1397–403. https://doi.org/10.6026/973206300211397.

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Malaria is one of the major global public health problems, is primarily caused by protozoan parasites of the genus Plasmodium and transmitted through the bites of infected female Anopheles mosquitoes. N-Myristoyltransferase (NMT) is an important drug target, particularly for Plasmodium vivax. Therefore, it is of interest to describe the molecular docking analysis of N-myristoyl-transferase with small molecules from the ZINC database for screening potential anti-malarial drugs. Hence, we report four potential compounds namely ZINC37555319, ZINC41016284, ZINC41016205, and ZINC47160805 with accep

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Rajalakshmi, Manikkam. "DaiCee: A database for anti-cancer compounds with targets and side effect profiles." Bioinformation 16, no. 11 (2020): 843–48. http://dx.doi.org/10.6026/97320630016843.

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Identification of the toxicity of compounds is more crucial before entering clinical trials. Awareness of physiochemical properties, possible targets and side effects has become a major public health issue to reduce risks. Experimental determination of analyzing the physiochemical properties of a drug, their interaction with specific receptors and identifying their side-effects remain challenging is time consuming and costly. We describe a manually compiled database named DaiCee database, which contains 2100 anticancer drugs with information on their physiochemical properties, targets of actio

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Jamil, Ahmad Shobrun, and Mochammad Rehan Alghifari. "Insight into Jasminum sambac Molecular Docking Interaction with GCK related to Diabetes Mellitus." Indonesian Journal of Computational Biology (IJCB) 2, no. 1 (2023): 40. http://dx.doi.org/10.24198/ijcb.v2i1.45616.

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Diabetes mellitus is one of non comunicable disease witrh high prevalencies in Indonesia. The aim of thie study are exploring the potential of J sambac phytochemical constituen for treating DM. The potential of J sambac as a DM therapy candidate was demonstrated through in silico analysis using several databases and computer aided drug discovery tools. The bioactive compounds analyzed were obtained from pubchem data, for the protein database taken from RSCB PDB, to predict or test ADME using SWISSADME and to analyze target proteins and metabolic pathways, biological activity and related diseas

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AKKAYA, Hatice, and Engin SÜMER. "IN SILICO APPROACHES ON PHENYLALANINE HYDROXYLASE INHIBITOR-RELATED COMPOUNDS USED IN PARKINSON’S DISEASE TREATMENT." Ankara Universitesi Eczacilik Fakultesi Dergisi 48, no. 2 (2024): 11. http://dx.doi.org/10.33483/jfpau.1380350.

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Objective: In Parkinson’s disease, Levodopa with Carbidopa addresses dopamine deficiency. Phenylalanine hydroxylase catalyzes phenylalanine to tyrosine conversion crucial for dopamine synthesis. Inhibiting phenylalanine hydroxylase may enhance Carbidopa's effects, preventing peripheral dopamine synthesis. The study used virtual scanning, molecular docking, and dynamics simulation to explore phenylalanine hydroxylase interactions with Carbidopa and similar ligands. ADME/T assessments and drug similarity tests were conducted to evaluate therapeutic potential in biological systems. Material and M

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Liu, Jun-feng, An-na Hu, Jun-feng Zan, Ping Wang, Qiu-yun You, and Ai-hua Tan. "Network Pharmacology Deciphering Mechanisms of Volatiles of Wendan Granule for the Treatment of Alzheimer’s Disease." Evidence-Based Complementary and Alternative Medicine 2019 (February 12, 2019): 1–12. http://dx.doi.org/10.1155/2019/7826769.

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Objective. To explore the mechanisms of the volatiles of Wendan granule (WDG) for the treatment of Alzheimer’s disease, network pharmacology method integrating absorption, distribution, metabolism, and excretion (ADME) screening, target fishing, network constructing, pathway analysing, and correlated diseases prediction was applied. Methods. Twelve small molecular compounds of WDG were selected as the objects from 74 volatiles with the relative abundances above 2 %, and their ADME parameters were collected from Traditional Chinese Medicine Systems Pharmacology platform (TCMSP), and the corresp

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Alkaff, Ahmad Husein, Mutiara Saragih, Shabrina Noor Imana, Mochammad Arfin Fardiansyah Nasution, and Usman Sumo Friend Tambunan. "Identification of DNA Methyltransferase-1 Inhibitor for Breast Cancer Therapy through Computational Fragment-Based Drug Design." Molecules 26, no. 2 (2021): 375. http://dx.doi.org/10.3390/molecules26020375.

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Epimutation by DNA Methyltransferase 1 (DNMT1), an epigenetic regulator enzyme, may lead to the proliferation of breast cancer. In this report, 168,686 natural products from the PubChem database were screened and modified by in silico method to acquire the potential inhibitor of DNMT1. The initial screening of PubChem natural products using Lipinski’s and Veber’s rules of three and toxic properties have resulted in 2601 fragment candidates. Four fragments from pharmacophore-based molecular docking simulation were modified by utilizing FragFP and the Lipinski’s and Veber’s rules of five, and re

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Priyadharshni, K., and P. Shanthi. "Bio-Efficacy of Flavonoid Phytocompound Isolated From Acmella Calva (Dc.) R.K. Jansen." Journal of Plant Science Research 39, no. 2 (2023): 235–43. http://dx.doi.org/10.32381/jpsr.2023.39.02.25.

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The phytocompound 5,7,3’,4’–Flavon-3-ol isolated and characterized through spectral studies was analyzed for its anticariogenic activity through disc diffusion method and In-silico analysis. It was carried against dental caries causing microbes such as Streptococcus mutans at different concentration (20, 40, 60, 80, 100, 120, 140 and 160 μg/ml) of which the maximum zone of inhibition was noticed at 160 μg/ml. In in-silico analysis, the molecular docking of phytocompound was analyzed against 4 proteins of the pathogen which were retrieved from PDB database. The phytocompound 5,7,3’,4’ – Flavon-

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Sanches, Vitor H. da S., Cleison C. Lobato, Luciane B. Silva, et al. "Rational Approach to New Chemical Entities with Antiproliferative Activity on Ab1 Tyrosine Kinase Encoded by the BCR-ABL Gene: An Hierarchical Biochemoinformatics Analysis." Pharmaceuticals 17, no. 11 (2024): 1491. http://dx.doi.org/10.3390/ph17111491.

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Background: This study began with a search in three databases, totaling six libraries (ChemBridge-DIVERSet, ChemBridge-DIVERSet-EXP, Zinc_Drug Database, Zinc_Natural_Stock, Zinc_FDA_BindingDB, Maybridge) with approximately 2.5 million compounds with the aim of selecting potential inhibitors with antiproliferative activity on the chimeric tyrosine kinase encoded by the BCR-ABL gene. Methods: Through hierarchical biochemoinformatics, ADME/Tox analyses, biological activity prediction, molecular docking simulations, synthetic accessibility and theoretical synthetic routes of promising compounds an

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Alam, Mudassir, Kashif Abbas, Faiza Iram, Mohd Tanjeem Raza, Mohd Mustafa, and Zerafshan Zehra. "Molecular Docking and Dynamics Studies of Withania somnifera Derived Compounds as GABA-A Receptor Modulators for Insomnia." Chronobiology in Medicine 6, no. 2 (2024): 77–86. http://dx.doi.org/10.33069/cim.2024.0010.

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Objective: This study aimed to identify potential phytochemicals from <i>Withania somnifera</i> (ashwagandha) that can act as gamma-aminobutyric acid A (GABA-A) receptor agonists or stimulant, and evaluate their suitability as potential insomnia treatments. Methods: Various computational approaches were employed, including virtual screening, biological activity prediction, physicochemical and drug-likeness analysis, absorption, distribution, metabolism, excretion, and toxicity (ADME/T) analysis, and molecular dynamics simulations. The Diseases Plants Eliminate (DISPEL) server was u

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James, Nivya, V. Shanthi, and K. Ramanathan. "Discovery of novel anaplastic lymphoma kinase inhibitors: Structure and energy-based pharmacophore strategy." Journal of Theoretical and Computational Chemistry 18, no. 03 (2019): 1950014. http://dx.doi.org/10.1142/s0219633619500147.

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The clinical outcomes in patients with non-small cell lung cancer have improved, as a result of anaplastic lymphoma kinase (ALK) inhibition. Therefore in the current study, substantial effort has been made to identify ALK inhibitors through systematic virtual screening experiment consisting of e-pharmacophore and pharmacophore perception techniques. Initially, a pharmacophore model (AAAHP.193) and an e-pharmacophore model (DDRRR) encompassing the whole dataset of 12 known ALK inhibitors were developed. The hypotheses could retrieve effective compounds from DrugBank database (8621 molecules), w

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Maretha, Tri Luthfiana, Ahmad Shobrun Jamil, Siti Rofida, and M. Artabah Muchlisin. "Network Pharmacology Analysis of Cananga odorata as a Treatment for Anxiety Disorders." Proceedings of International Pharmacy Ulul Albab Conference and Seminar (PLANAR) 3 (November 13, 2023): 137. http://dx.doi.org/10.18860/planar.v3i0.2479.

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Anxiety disorder is a psychological disorder associated with the existence of mental disorders and experiencing constant anxiety. In C. odorata, part of the flower has the potential as a sedative for the nervous system and for dealing with anxiety. The study aims to analyze the potential compound content in Cananga odorata for treating anxiety disorders with In silico-based pharmacological network analysis. CO compound data from the KNApSAck database, Absorption, Distribution, Metabolism, and Excretion (ADME) screening using SwissADME, predicted target proteins using Swiss Target Prediction, G

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Petitet, François, Olivier Barberan, Elodie Dubus, et al. "Development of an ADME and drug–drug interactions knowledge database for the acceleration of drug discovery and development." Expert Opinion on Drug Discovery 1, no. 7 (2006): 737–51. http://dx.doi.org/10.1517/17460441.1.7.737.

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Shami, Ashwag, Nada K. Alharbi, Fatimah A. Al-Saeed, et al. "In Silico Subtractive Proteomics and Molecular Docking Approaches for the Identification of Novel Inhibitors against Streptococcus pneumoniae Strain D39." Life 13, no. 5 (2023): 1128. http://dx.doi.org/10.3390/life13051128.

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Streptococcus pneumoniae is a notorious Gram-positive pathogen present asymptomatically in the nasophayrnx of humans. According to the World Health Organization (W.H.O), pneumococcus causes approximately one million deaths yearly. Antibiotic resistance in S. pneumoniae is raising considerable concern around the world. There is an immediate need to address the major issues that have arisen as a result of persistent infections caused by S. pneumoniae. In the present study, subtractive proteomics was used in which the entire proteome of the pathogen consisting of 1947 proteins is effectively decr

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Abilasha, D., and P. Palanisamy. "Phytochemical Evaluation, Molecular Docking, ADMET Properties and Anticancer Activity of Ethanolic Extract of Solanum trilobatum Leaf Extract." Asian Journal of Chemistry 36, no. 7 (2024): 1489–96. http://dx.doi.org/10.14233/ajchem.2024.31413.

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In this study, the anticancer potential of ethanolic extract of Solanum trilobatum leaf, which contained high quantities of alkaloids, terpenoids, steroids and flavonoids, was investigated. The GC-MS analysis detected 30 phytocompounds in the ethanolic extract and according to the Pubchem database, 10 of these phytocompounds have significant biological activity. When using AutoDock Vina, docking investigations were conducted using the cancer cell line proteins from the colon (5FGK) and cervical (4J96), respectively. ADMET predictions were made via SwissADME and the pkCSM online webserver. Acco

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Wang, Dongmei, Chuanjian Lu, Jingjie Yu, Miaomiao Zhang, Wei Zhu, and Jiangyong Gu. "Chinese Medicine for Psoriasis Vulgaris Based on Syndrome Pattern: A Network Pharmacological Study." Evidence-Based Complementary and Alternative Medicine 2020 (April 28, 2020): 1–16. http://dx.doi.org/10.1155/2020/5239854.

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Background. The long-term use of conventional therapy for psoriasis vulgaris remains a challenge due to limited or no patient response and severe side effects. Complementary and alternative treatments such as traditional Chinese medicine (TCM) are widely used in East Asia. TCM treatment is based on individual syndrome types. Three TCM formulae, Compound Qingdai Pills (F1), Yujin Yinxie Tablets (F2), and Xiaoyin Tablets (F3), are used for blood heat, blood stasis, and blood dryness type of psoriasis vulgaris, respectively. Objectives. To explore the mechanism of three TCM formulae for three syn

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Akinsulure, Simbo T., Oluwadamilola P. Alao, and Damilola S. Bodun. "Computational Screening of Phytochemicals from Trigonella foenum-graecum as Potential Inhibitor of Alpha-Amylase and Maltase-Glucoamylase in Treatment of Type 2 Diabetes." International Journal of Biochemistry Research & Review 33, no. 6 (2024): 196–206. http://dx.doi.org/10.9734/ijbcrr/2024/v33i6902.

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Introduction: Diabetes mellitus is a major illness suffered by several individuals, a metabolic dysfunction of glucose that leads to life-threatening complications. Type 2 diabetes is a combination of insulin action resistance, insufficient insulin production, and excessive glucagon secretion. Aim: Numerous medications have been developed to manage diabetes mellitus by inhibiting various glucose metabolism enzymes and transporter proteins. However, the several adverse effects and high cost of treatment cannot be ignored. Thus, discovering and designing a small-molecule inhibitor with minimal s

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Lanka, Goverdhan, Revanth Bathula, Manan Bhargavi, and Sarita Rajender Potlapally. "Homology modeling and molecular docking studies for the identification of novel potential therapeutics against human PHD3 as a drug target for type 2 diabetes mellitus." Journal of Drug Delivery and Therapeutics 9, no. 4 (2019): 265–73. http://dx.doi.org/10.22270/jddt.v9i4.3039.

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PHD3 (Prolyl Hydroxylating Domain) 3 protein contains the HRE (Hypoxia Response Element) and plays an important role in regulating HIF subunits. The hydroxylating ability of PHD3 of HIF subunits makes PHD3 is a prominent therapeutic target to control type 2 diabetes mellitus. The structure based approach is used to design novel molecular entities against PHD3 protein. In this present work, a 3D homology model of PHD3 was generated by MODELLER9.9 as the experimental structure of PHD3 is not reported in the protein database. The 3d structural model of PHD3 refined through energy minimization in

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Awwaluddin, Faiznanda, Ahmad Shobrun Jamil, Siti Rofida, and M. Artabah Muchlisin. "The Therapeutic Role of Olea europaea in Alcohol Dependence Base in Network Pharmacology Analysis." Proceedings of International Pharmacy Ulul Albab Conference and Seminar (PLANAR) 3 (November 13, 2023): 201. http://dx.doi.org/10.18860/planar.v3i0.2486.

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Alcohol dependence is a state of alcohol becoming a vital part of the life of a person who consumes it; when discontinued, it can lead to a wide range of physical and mental health disorders as well as a decrease in life productivity in people with alcohol dependence. Olea Europaea (OE) is a plant capable of treating alcohol dependence. The method used in silico-based pharmacological grid analysis to determine the ability of the OE compound to treat alcohol dependence. EO compound data is obtained from the KnapSack database, absorption, distribution, metabolism, and excretion (ADME) screening

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Debnath, Abhijit, Rupa Mazumder, Anil Kumar Singh, and Rajesh Kumar Singh. "Identification of novel cyclin-dependent kinase 4/6 inhibitors from marine natural products." PLOS ONE 20, no. 1 (2025): e0313830. https://doi.org/10.1371/journal.pone.0313830.

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Cyclin-dependent kinases 4 and 6 (CDK4/6) are crucial regulators of cell cycle progression and represent important therapeutic targets in breast cancer. This study employs a comprehensive computational approach to identify novel CDK4/6 inhibitors from marine natural products. We utilized structure-based virtual screening of the CMNPD database and MNP library, followed by rigorous filtering based on drug-likeness criteria, PAINS filter, ADME properties, and toxicity profiles. From an initial hit of 9,497 compounds, 2,344 passed drug-likeness and PAINS filters. Further ADME filtering yielded 50

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Sierra-Hernandez, Olimpo, Oscar Saurith-Coronell, Juan Rodríguez-Macías, et al. "In Silico Identification of Potential Clovibactin-like Antibiotics Binding to Unique Cell Wall Precursors in Diverse Gram-Positive Bacterial Strains." International Journal of Molecular Sciences 26, no. 4 (2025): 1724. https://doi.org/10.3390/ijms26041724.

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The rise in multidrug-resistant bacteria highlights the critical need for novel antibiotics. This study explores clovibactin-like compounds as potential therapeutic agents targeting lipid II, a crucial component in bacterial cell wall synthesis, using in silico techniques. A total of 2624 clovibactin analogs were sourced from the PubChem database and screened using ProTox 3.0 software based on their ADME-Tox properties, prioritizing candidates with favorable pharmacokinetic profiles and minimal toxicity. Molecular docking protocols were then employed to assess the binding interactions of the s

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Shehadi, Ihsan A., Huda R. M. Rashdan, and Aboubakr H. Abdelmonsef. "Homology Modeling and Virtual Screening Studies of Antigen MLAA-42 Protein: Identification of Novel Drug Candidates against Leukemia—An In Silico Approach." Computational and Mathematical Methods in Medicine 2020 (March 16, 2020): 1–12. http://dx.doi.org/10.1155/2020/8196147.

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Monocytic leukemia-associated antigen-42 (MLAA-42) is associated with excessive cell division and progression of leukemia. Thus, human MLAA-42 is considered as a promising target for designing of new lead molecules for leukemia treatment. Herein, the 3D model of the target was generated by homology modeling technique. The model was then evaluated using various cheminformatics servers. Moreover, the virtual screening studies were performed to explore the possible binding patterns of ligand molecules to MLAA’s active site pocket. Thirteen ligand molecules from the ChemBank™ database were identif

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Xu, Bo, Yu Zhou, Qing Wang, et al. "Use of Network Pharmacology and Molecular Docking Methods to Elucidate the Curative Effect of Epimedium–Anemarrhen on Osteoporosis." Natural Product Communications 17, no. 3 (2022): 1934578X2210869. http://dx.doi.org/10.1177/1934578x221086904.

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Objective: Using network pharmacology and molecular docking methods, this study aimed to elucidate the key targets and molecular mechanisms of the Epimedium–Anemarrhen (EA) combination as a therapeutic approach for osteoporosis (OP). Methods: The TCMSP database was used to identify effective active ingredients and information on targets of EA according to the ADME threshold. An OP target database was established using the GeneCards, OMIM, DrugBank, and DisGeNET databases. The intersection of drug targets and disease targets was used to identify common genes, and protein interaction network, GO

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Ferreira, Letícia Tiburcio, Joyce V. B. Borba, José Teófilo Moreira-Filho, Aline Rimoldi, Carolina Horta Andrade, and Fabio Trindade Maranhão Costa. "QSAR-Based Virtual Screening of Natural Products Database for Identification of Potent Antimalarial Hits." Biomolecules 11, no. 3 (2021): 459. http://dx.doi.org/10.3390/biom11030459.

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With about 400,000 annual deaths worldwide, malaria remains a public health burden in tropical and subtropical areas, especially in low-income countries. Selection of drug-resistant Plasmodium strains has driven the need to explore novel antimalarial compounds with diverse modes of action. In this context, biodiversity has been widely exploited as a resourceful channel of biologically active compounds, as exemplified by antimalarial drugs such as quinine and artemisinin, derived from natural products. Thus, combining a natural product library and quantitative structure–activity relationship (Q

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Reeves, Anthony Allen, Robert Hopefl, and Subrata Deb. "Evaluation of pharmacogenomic evidence for drugs related to ADME genes in CPIC database." Drug Metabolism and Personalized Therapy, October 19, 2022. http://dx.doi.org/10.1515/dmpt-2022-0123.

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Abstract Objectives Clinical Pharmacogenetics Implementation Consortium (CPIC) is a platform that advances the pharmacogenomics (PGx) practice by developing evidence-based guidelines. The purpose of this study was to analyze the CPIC database for ADME related genes and their corresponding drugs, and evidence level for drug-gene pairs; and to determine the presence of these drug-gene pairs in the highest mortality diseases in the United States. Methods CPIC database was evaluated for drug-gene pairs related to absorption, distribution, metabolism, and excretion (ADME) properties. National Vital

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CHAVAN, SHIVAM, SHUBHAM WANARASE, and SAMEER SHARMA. "IN SILICO ANALYSIS AND DOCKING STUDY OF THE ACTIVE PHYTO COMPOUNDS OF MORINGA OLEIFERA AGAINST MARBURG VIRUS VP35 PROTEIN." Innovare Journal of Sciences, September 30, 2022, 5–12. http://dx.doi.org/10.22159/ijs.2022.v10i1.46218.

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Objective: Marburg is a transmissible disease of the Filoviridae family. It infected a million people worldwide. Hence, an attempt was made to identify natural compounds from Moringa oleifera, having multiple medicinal values in Indian Ayurveda, to prevent the disease, using molecular docking, drug likeness prediction, absorption, distribution, metabolism, and excretion (ADME) analysis, and toxicity prediction. Methods: Marburg main protein was retrieved from the protein data bank database. The ligands with poor binding and molecules that can affect docking were removed and docking is done wit

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Debnath, Abhijit, Hema Chaudhary, Parul Sharma, Rajesh Singh, and Shikha Srivastava. "A Deep Dive into PDE5 Inhibition: Innovative Discoveries via Virtual Screening." Letters in Drug Design & Discovery 21 (April 3, 2024). http://dx.doi.org/10.2174/0115701808279586231221043744.

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Background: PDE5 inhibitors have had a surge in popularity over the last decade owing to their efficacy in the treatment of erectile dysfunction, coronary vasculopathy, and pulmonary arterial hypertension. These inhibitors exhibit competitive binding with phosphodiesterase type 5 and inhibit the hydrolysis of cyclic guanosine monophosphate, hence elevating the levels of cGMP in smooth muscle cells and prolonging the duration of an erection. However, due to production costs and side effects, further research is needed to discover new PDE5 inhibitors. background: The field of PDE5 inhibitors has

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MANDAL, SAJAL, and SHUBHAM WANARASE. "IN SILICO APPROACH TO IDENTIFY POTENTIAL ANTI-PSORIATIC COMPOUNDS FROM CURCUMA LONGA." Innovare Journal of Medical Sciences, July 6, 2023, 1–6. http://dx.doi.org/10.22159/ijms.2023.v11i4.47979.

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Objectives: Psoriasis is a type of skin disease which is accompanied with over production of keratinocytes, itchiness, and scaly skin. In this study, an attempt was made to recognize naturally occurring phytocompounds from the plant Curcuma longa which can be helpful in treating psoriasis using molecular docking techniques. Methods: The protein associated to the mechanism of psoriasis was obtained from the protein data bank database, along with retrieving the phytocompounds from C. longa. The phytocompounds were docked with the protein using PyRx docking. Further, analysis was done using Swiss

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