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Journal articles on the topic 'Molecular Docking Simulation Druglikeness Screening'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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1

Thuy, Bui Thi Phuong, Vo Duy Nhan, Nguyen Minh Quang, Nguyen Thanh Duoc, and Pham Van Tat. "Evaluation of SARS‐CoV‐2 inhibition of some compounds inCYMBOPOGON CITRATUS oil combining docking and molecular dynamics simulations." Vietnam Journal of Chemistry 59, no. 6 (2021): 790–99. http://dx.doi.org/10.1002/vjch.202100022.

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AbstractThe visual screening and simulation methods were used to evaluate the inhibitory ability of 34 compounds in Cymbopogon citratus oil against SARS‐CoV‐2. We chose the best compound, SC22, with a DS of ‐12.80 Kcal. mol‐1 with a distance RMSD of 0.23. This was the most effective compound at inhibiting the viral protein 6LU7. For the protein ACE2 or an endemic host receptor, the docking ability of SC22 showed DS = ‐13.13 Kcal.mol‐1 and RMSD = 1.32 Å; SC10 docked in DS = ‐12.79 Kcal.mol‐1 and RMSD = 0.91 Å; SC11 gave the docking values DS = ‐12.77 Kcal.mol‐1 and RMSD = 1.15 Å. SC26 showed DS

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Ajala, Olusegun Samson, Moshood Olusola Akinleye, Mbang Owolabi, and Grace Ukpo. "In Silico Evaluation of Aromatase Inhibitory Anti-benign Prostatic Hyperplasia Potentials of Spirostan Sapogenins." Malaysian Journal of Pharmaceutical Sciences 21, no. 1 (2023): 63–89. http://dx.doi.org/10.21315/mjps2023.21.1.5.

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Inherent oestrogen receptor alpha (ERα) and other nuclear receptor signaling activities of typical aromatase inhibitors (AIs) preclude their clinical use as anti-oestrogenic anti-benign prostatic hyperplasia (anti-BPH) agents. Spirostan sapogenins (SS) constitute a chemical space from which AIs without such deterrents could be sought. This work was aimed at in silico discovery of clinical aromatase inhibitory anti-oestrogenic anti-BPH drug leads. Fortysix SS were docked against an inhibitor conformation of the human placenta aromatase. Nuclear receptor signaling activation tendencies of seven

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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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Ariavianti, Elsafira, Filia Stephanie, and Usman Sumo Friend Tambunan. "Virtual Screening Based on Pharmacophore to Discover Host ER Alpha-Glucosidase II Inhibitor for Dengue Therapy." Key Engineering Materials 840 (April 2020): 221–29. http://dx.doi.org/10.4028/www.scientific.net/kem.840.221.

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Dengue is one of the crucial diseases in human-caused by dengue virus (DENV) infection. However, the development of DENV antiviral is often facing a problem because no effective drug to treat infection caused by all DENV serotypes. The inhibition of host protein involved in DENV life cycle can be a potential approach in dengue drug discovery, and also avoiding antiviral resistance. Endoplasmic Reticulum (ER) α-glucosidase II is one of the target host protein in DENV endoplasmic reticulum that plays an important role in the maturation process of DENV envelope glycoprotein. Natural products have

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Kharisma, Viol Dhea, Santika Lusia Utami, Wahyu Choirur Rizky, et al. "Molecular docking study of Zingiber officinale Roscoe compounds as a mumps virus nucleoprotein inhibitor." Dental Journal (Majalah Kedokteran Gigi) 56, no. 1 (2023): 23–29. http://dx.doi.org/10.20473/j.djmkg.v56.i1.p23-29.

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Background: Mumps virus (MuV) can trigger severe infections, such as parotitis, epididymo-orchitis, and meningitis. The effectiveness of MuV vaccine administration has been proven, but current outbreaks warrant the development of antivirals against MuV. Zingiber officinale var. Roscoe or ginger is often used as an alternative remedy. Currently, there are no known in vitro or in vivo studies that investigate ginger as an MuV antiviral. Purpose: This study aims to evaluate the antiviral potency of the bioactive compounds in Zingiber officinale var. Roscoe against MuV. Methods: Antiviral activity

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Ibrahim, Mutiat B., Adeola T. Kola-Mustapha, Niyi S. Adelakun, and Neil A. Koorbanally. "Phytoconstituents from Markhamia tomentosa Bind To HPV Oncoprotein with Apoptogenic Potential: A Molecular Modeling Approach." Annals of Science and Technology 6, no. 2 (2021): 28–46. http://dx.doi.org/10.2478/ast-2021-0008.

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Abstract Markhamia tomentosa crude extract and fractions exhibited potent growth inhibitory effects capable to induce apoptosis in cervical (HeLa) cancer cell line via in vitro model. Presently, interaction of M. tomentosa phytoconstituents with molecular drug targets to exert its anticancer property is evaluated via in silico study. Identified phytoconstituents from M. tomentosa were retrieved from PubChem database and docked in active sites of HPV 16 E6, caspase -3 and caspase -8 targets using AutoDockVina from PyRx software. Screening for druglikeness; and absorption, distribution, metaboli

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Azmi, Muhammad Bilal, Simran Kumari, Sakina Aquil, et al. "KIFC1 inhibition: Exploring the potential of propolis-derived small molecules for targeting cancer progression through in silico analysis." PLOS One 20, no. 6 (2025): e0324678. https://doi.org/10.1371/journal.pone.0324678.

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Propolis, a resinous compound produced by bees, possesses diverse medicinal properties and has gained significant attention for its potential in cancer therapy. This study investigated the therapeutic significance of propolis-derived compounds targeting the kinesin-like protein KIFC1, a motor protein overexpressed in various cancers, using a multistep computational methodology. Therefore, it is essential to utilize different in silico methods to predict their therapeutic potential. A 3D library of propolis-derived compounds sourced from previously published literature was compiled and screened

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Nasution, Rani Sakila, Indang Dewata, Nofri Yuhelman, Neny Sandrawati та Arif Juliari Kusnanda. "Molecular Docking and Pharmacoinformatics Study of Bioactive Compounds in Sweet Flag (Acorus calamus L.) as Antidiabetic Agents Targeting α-Glucosidase". Jurnal Pijar Mipa 20, № 4 (2025): 598–604. https://doi.org/10.29303/jpm.v20i4.8994.

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Diabetes mellitus (DM) is a chronic metabolic disorder whose prevalence continues to rise, necessitating safer and more effective therapeutic alternatives. This study aims to explore the potential of active compounds from the calamus plant (Acorus calamus L.) as candidates for α-glucosidase enzyme inhibitors using an in silico approach. Pharmacokinetic screening, toxicity prediction, and Lipinski's Rule of Five screening were conducted to assess the pharmacological suitability of the compounds, followed by molecular docking using MOE 2022 software. The results of the study showed that several

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Bepari, Asim Kumar, and Hasan Mahmud Reza. "Identification of a novel inhibitor of SARS-CoV-2 3CL-PRO through virtual screening and molecular dynamics simulation." PeerJ 9 (April 13, 2021): e11261. http://dx.doi.org/10.7717/peerj.11261.

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Background The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has ravaged lives across the globe since December 2019, and new cases are still on the rise. Peoples’ ongoing sufferings trigger scientists to develop safe and effective remedies to treat this deadly viral disease. While repurposing the existing FDA-approved drugs remains in the front line, exploring drug candidates from synthetic and natural compounds is also a viable alternative. This study employed a comprehensive computational approach to screen inhibitors for SARS-CoV-2 3CL-PRO (also known as the main protease), a prime mol

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Ogunyemi, Oludare M., Gideon A. Gyebi, Abdo A. Elfiky, et al. "Alkaloids and flavonoids from African phytochemicals as potential inhibitors of SARS-Cov-2 RNA-dependent RNA polymerase: an in silico perspective." Antiviral Chemistry and Chemotherapy 28 (January 2020): 204020662098407. http://dx.doi.org/10.1177/2040206620984076.

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Corona Virus Disease 2019 (COVID-19) is a pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Exploiting the potentials of phytocompounds is an integral component of the international response to this pandemic. In this study, a virtual screening through molecular docking analysis was used to screen a total of 226 bioactive compounds from African herbs and medicinal plants for direct interactions with SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). From these, 36 phytocompounds with binding affinities higher than the approved reference drugs (remdesivir and sobosivi

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Kudaravalli, Sreedevi 1. *. G. Suryanarayana Murthy2 Jangala Venkateswara Rao 3. Mangamoori Lakshmi Narasu 4. "Insilico Studies of Cardiospermum canescens derived compounds towards Anti inflammatory activity." Journal of Pharma Research 8, no. 12 (2019): 11. https://doi.org/10.5281/zenodo.4018765.

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ABSTRACT The objective was to predict the binding affinity and energy of phytochemicals of Cardiospermum canescens to synthesis a drug against Inflammation. The medicinal plant derived phytocompounds and the human 15-lipoxygenase-2 were undergone Molecular docking and interaction along with druggability assessment. The software, GOLD for the structure-based virtual screening to know receptor-ligand binding affinity and energy. The human 15-lipoxygenase-2 as receptor was obtained (PDB ID: 4NRE) from the Protein Data Bank (PDB). The prediction of pharmacokinetics, bioavailability and druglikenes

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Sayantan, Pradhan, Mondal Sudipa, and Sinha Chittaranjan. "In search of Tuberculosis drug design : An in silico approach to azoimidazolyl derivatives as antagonist for Cytochrome P450." Journal of Indian Chemical Society Vol. 93, Sep 2016 (2016): 1067–84. https://doi.org/10.5281/zenodo.5639353.

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Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata-700 032, India <em>E-mail </em>: c_r_sinha@yahoo.com<em> Fax</em> : 91-33-2414658 <em>Manuscript received online 04 January 2016, accepted 29 February 2016</em> Tuberculosis is a deadly disease and is caused by <em>Mycobacterium tuberculosis</em> (Mtb). Cytochrome P450s (CYPs) in the Mtb genome is playing important physiological role for its growth and survivability. Azole drugs have potent anti-mycobacterial activity and molecular docking studies indicate that CYP inhibition is the major target of the drugs. Ou

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Martiz, Reshma Mary, Shashank M. Patil, Mohammed Abdulaziz, et al. "Defining the Role of Isoeugenol from Ocimum tenuiflorum against Diabetes Mellitus-Linked Alzheimer’s Disease through Network Pharmacology and Computational Methods." Molecules 27, no. 8 (2022): 2398. http://dx.doi.org/10.3390/molecules27082398.

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The present study involves the integrated network pharmacology and phytoinformatics-based investigation of phytocompounds from Ocimum tenuiflorum against diabetes mellitus-linked Alzheimer’s disease. It aims to investigate the mechanism of the Ocimum tenuiflorum phytocompounds in the amelioration of diabetes mellitus-linked Alzheimer’s disease through network pharmacology, druglikeness and pharmacokinetics, molecular docking simulations, GO analysis, molecular dynamics simulations, and binding free energy analyses. A total of 14 predicted genes of the 26 orally bioactive compounds were identif

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Frimayanti, Neni, Abdi Wira Septama, Hilwan Yuda Teruna, and Eldiza Puji Rahmi. "In silico investigation of artocarpin, cycloarotcarpin, artocarpanone, and cyanomaclurin for Dengue virus inhibitor DEN2 NS2B/NS3 serine protease." Journal of Pharmacy & Pharmacognosy Research 13, no. 1 (2025): 193–202. http://dx.doi.org/10.56499/jppres24.2052_13.1.193.

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Context: Dengue virus (DENV) infection remains a significant global public health challenge that necessitates the development of novel therapeutic strategies. Aims: To investigate compounds isolated from Artocarpus heterophyllus for their potential as inhibitors of the DENV NS2B/NS3 serine protease. Methods: Initially, molecular docking was performed to predict the binding orientation of these flavonoid compounds with the serine protease enzyme. It was followed with pharmacophore, density functional theory (DFT), and ADMET-druglikeness. Results: Results reveal promising interactions between cy

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Cahyaningrum, Lydia, Retno Rubianti, Tsania Mahira, Kevin Gabriel, Agus Rusdin, and Dhania Novitasari. "STUDI IN SILICO METABOLIT SEKUNDER DALAM TANAMAN TAHONGAI (Kleinhovia hospita L.) SEBAGAI KANDIDAT AGEN TERAPI KARSINOMA HEPATOSELULER TERTARGET RESEPTOR c-MET (IN SILICO STUDY OF SECONDARY METABOLITES IN TAHONGAI PLANT(Kleinhovia hospita L.) AS A CANDIDATEFOR HEPATOCELLULER CARCINOMA THERAPEUTIC AGENT TARGETING c-MET RECEPTOR)." Indonesian Journal of Pure and Applied Chemistry 7, no. 2 (2024): 83. http://dx.doi.org/10.26418/indonesian.v7i2.82567.

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Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-related mortality in the world, mainly caused by chronic disease or virus. Prior studies have documented that the upregulation of c-MET can trigger the cancer progression, hence c-MET has been widely explored as target therapy for HCC. Tahongai plant (Kleinhovia hospita L.) has known to possess several biological effects, including anticancer activity. However, the molecular mechanism in this plant has not been studied yet. In this study, the bioactive constituents from Tahongai were evaluated based on the physicochemical fea

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Utami, Wiji, Apriyanto Apriyanto, Laila Antari, Herlina Rasyid, and Ika Nur Fitriani. "Inhibition of Human Acetylcholinesterase (4EY7) using Bioactive Compound from Moringa oleifera: Molecular Docking and Dynamic Studies." Jurnal Kimia Valensi 10, no. 2 (2024): 290–303. https://doi.org/10.15408/jkv.v10i2.39840.

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Alzheimer's disease is a neurodegenerative disorder caused by acetylcholine hydrolysis that impairs cognitive brain function. This research aims to determine the interaction and dynamic of ligands from Moringa oleifera on AChE through Lipinski's Rule, ADMET properties, molecular docking calculations, and molecular dynamic simulations. Lipinski's Rule calculation provided ligand limits that adhere to druglikeness properties. ADMET results also showed that several ligands satisfy ADMET properties. Pterygospermine has lower binding energy than the ligand control (-10.28 kcal mol-1) with amino aci

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Adedeji, Eunice O., Gbolahan O. Oduselu, Olubanke O. Ogunlana, Segun Fatumo, Rainer Koenig, and Ezekiel Adebiyi. "Anopheles gambiae Trehalase Inhibitors for Malaria Vector Control: A Molecular Docking and Molecular Dynamics Study." Insects 13, no. 11 (2022): 1070. http://dx.doi.org/10.3390/insects13111070.

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Trehalase inhibitors are considered safe alternatives for insecticides and fungicides. However, there are no studies testing these compounds on Anopheles gambiae, a major vector of human malaria. This study predicted the three-dimensional structure of Anopheles gambiae trehalase (AgTre) and identified potential inhibitors using molecular docking and molecular dynamics methods. Robetta server, C-I-TASSER, and I-TASSER were used to predict the protein structure, while the structural assessment was carried out using SWISS-MODEL, ERRAT, and VERIFY3D. Molecular docking and screening of 3022 compoun

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Tran, Linh Thuy Thi, Trong Nhan Le, Duc Viet Ho, et al. "Virtual Screening and in Vitro Evaluation to Identify a Potential Xanthine Oxidase Inhibitor Isolated from Vietnamese Uvaria cordata." Natural Product Communications 17, no. 2 (2022): 1934578X2210803. http://dx.doi.org/10.1177/1934578x221080339.

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Xanthine oxidase (XO) is a potential target for gout disease experiments on animals and humans. Using a molecular docking technique to search for anti-XO compounds from Vietnamese medicinal plants, we discovered that numerous compounds from Uvaria cordata (Dunal) Alston (Annonaceae family) showed this activity. Among these, cordauvarin A exhibited the strongest binding affinity (−8.8 kcal/mol) to XO through a binding interaction with 5 amino acids (eg Gln-1194, Ala-1079, Ser-1080, Met-1038, and Arg-912) of XO protein. Lipinski's rule of five was used to predict the druglikeness of this compoun

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Maradesha, Tejaswini, Reshma Mary Martiz, Shashank M. Patil, et al. "Integrated network pharmacology and molecular modeling approach for the discovery of novel potential MAPK3 inhibitors from whole green jackfruit flour targeting obesity-linked diabetes mellitus." PLOS ONE 18, no. 1 (2023): e0280847. http://dx.doi.org/10.1371/journal.pone.0280847.

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The current study investigates the effectiveness of phytocompounds from the whole green jackfruit flour methanol extract (JME) against obesity-linked diabetes mellitus using integrated network pharmacology and molecular modeling approach. Through network pharmacology, druglikeness and pharmacokinetics, molecular docking simulations, GO analysis, molecular dynamics simulations, and binding free energy analyses, it aims to look into the mechanism of the JME phytocompounds in the amelioration of obesity-linked diabetes mellitus. There are 15 predicted genes corresponding to the 11 oral bioactive

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Keshavarz, Fatemeh, and Bernardo Barbiellini. "Application of molecular docking simulation to screening of metal–organic frameworks." Computational Materials Science 226 (June 2023): 112257. http://dx.doi.org/10.1016/j.commatsci.2023.112257.

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Murtadlo, Ahmad Affan Ali, Sin War Naw, Md Emdad Ullah, Muhammad Badrut Tamam, and Dora Dayu Rahma Turista. "ADMET Screening of Sambucus nigra as Antiviral Agent Through Computational Simulation." SAINSTEK International Journal on Applied Science, Advanced Technology and Informatics 2, no. 01 (2023): 1–6. http://dx.doi.org/10.24036/sainstek/vol2-iss01/17.

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Sambucus nigra L. (Elderberry) can be used as a source of antiviral compounds. Previously this medicinal plant was commonly used to fight influenza virus infections that cause flu and cough. Some preliminary research studies showed antiviral activity in Sambucus nigra L. extracts. Sambucus nigra L are used as antiviral agents that work effectively, it is important to do absorption, distribution, metabolism, excretion, and toxicity (ADMET) screening, the analysis aims to evaluate and predict the pharmacokinetic and toxicological properties of query compounds. ADMET screening method refers to a

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Alam, Aftab, Muhammad Junaid, Muhammad Fawad Ali, et al. "Computational Development of New Inhibitors for Apoptosis Stimulating Protein of p53 (iASPP) Using Pharmacophore Modeling, Docking, and MD Simulation Approaches." Journal of Cancer Biomoleculars and Therapeutics 1, no. 2 (2024): 1–9. http://dx.doi.org/10.62382/jcbt.v1i2.27.

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Inhibitor of apoptosis-stimulating protein of p53 (iASPP) overexpression is associated with diverse human tumors, including lung cancer, colorectal cancer, prostate cancer, acute leukemia, hepatocellular carcinoma, cervical cancer, and ovarian cancer. This study aims to find new and potent inhibitors for the iASPP drug target. Using pharmacophore-based virtual screening, molecular docking, and molecular dynamics simulation an integrated strategy was developed to find highly effective iASPP inhibitors. Subsequently, the pharmacophore model was employed as a screening query to find promising inh

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Pandi, Sangavi, Langeswaran Kulanthaivel, Gowtham Kumar Subbaraj, Sangeetha Rajaram, and Senthilkumar Subramanian. "Screening of Potential Breast Cancer Inhibitors through Molecular Docking and Molecular Dynamics Simulation." BioMed Research International 2022 (June 28, 2022): 1–9. http://dx.doi.org/10.1155/2022/3338549.

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Cyclooxygenase-2 (COX-2) is a key enzyme involved in overexpression in several human cancerous diseases including breast cancer. By performing efficient virtual screening in a series of active molecules or compounds from the Maybridge, NCI (National Cancer Institute), and Enamine databases, potential identification of COX-2 inhibitors could lead to new prognostic strategies in the treatment of breast cancer. Based on a 50% structural similitude, compounds were chosen as the inductive model of COX-2 inhibitions from these databases. Selected compounds were filtered and tested with Lipinski’s ru

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Tondar, Abtin, Sergio Sánchez-Herrero, Asim Kumar Bepari, Amir Bahmani, Laura Calvet Liñán, and David Hervás-Marín. "Virtual Screening of Small Molecules Targeting BCL-2 with Machine Learning, Molecular Docking, and MD Simulation." Biomolecules 14, no. 5 (2024): 544. http://dx.doi.org/10.3390/biom14050544.

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This study aimed to identify potential BCL-2 small molecule inhibitors using deep neural networks (DNN) and random forest (RF) algorithms as well as molecular docking and molecular dynamics (MD) simulations to screen a library of small molecules. The RF model classified 61% (2355/3867) of molecules as ‘Active’. Further analysis through molecular docking with Vina identified CHEMBL3940231, CHEMBL3938023, and CHEMBL3947358 as top-scored small molecules with docking scores of −11, −10.9, and 10.8 kcal/mol, respectively. MD simulations validated these compounds’ stability and binding affinity to t

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Berishvili, Vladimir P., Alexander N. Kuimov, Andrew E. Voronkov, et al. "Discovery of Novel Tankyrase Inhibitors through Molecular Docking-Based Virtual Screening and Molecular Dynamics Simulation Studies." Molecules 25, no. 14 (2020): 3171. http://dx.doi.org/10.3390/molecules25143171.

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Tankyrase enzymes (TNKS), a core part of the canonical Wnt pathway, are a promising target in the search for potential anti-cancer agents. Although several hundreds of the TNKS inhibitors are currently known, identification of their novel chemotypes attracts considerable interest. In this study, the molecular docking and machine learning-based virtual screening techniques combined with the physico-chemical and ADMET (absorption, distribution, metabolism, excretion, toxicity) profile prediction and molecular dynamics simulations were applied to a subset of the ZINC database containing about 1.7

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Krüger, Jens, Richard Grunzke, Sonja Herres-Pawlis, et al. "Performance Studies on Distributed Virtual Screening." BioMed Research International 2014 (2014): 1–7. http://dx.doi.org/10.1155/2014/624024.

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Virtual high-throughput screening (vHTS) is an invaluable method in modern drug discovery. It permits screening large datasets or databases of chemical structures for those structures binding possibly to a drug target. Virtual screening is typically performed by docking code, which often runs sequentially. Processing of huge vHTS datasets can be parallelized by chunking the data because individual docking runs are independent of each other. The goal of this work is to find an optimal splitting maximizing the speedup while considering overhead and available cores on Distributed Computing Infras

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MA, RUIXIN, XIUJUAN XU, LEI ZHAO, REN CAO, and QIANG FANG. "MUTUAL ARTIFICIAL BEE COLONY ALGORITHM FOR MOLECULAR DOCKING." International Journal of Biomathematics 06, no. 06 (2013): 1350038. http://dx.doi.org/10.1142/s1793524513500381.

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Molecular docking method plays an important role on the quest of potential drug candidates, which has been proven to be a valuable tool for virtual screening. Molecular docking is commonly referred to as a parameter optimization problem. During the last decade, some optimization algorithms have been introduced, such as Lamarckian genetic algorithm (LGA) and SODOCK embedded in the AutoDock program. On the basis of the latest docking software AutoDock4.2, we present a novel docking program ABCDock, which incorporates mutual artificial bee colony (MutualABC) into AutoDock. Computer simulation res

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Tang, Min, Yang Fu, Ying Fan, Ming-Shui Fu, Zhi Zheng, and Xun Xu. "In-silico design of novel myocilin inhibitors for glaucoma therapy." Tropical Journal of Pharmaceutical Research 16, no. 10 (2017): 2527–33. http://dx.doi.org/10.4314/tjpr.v16i10.29.

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Purpose: To explore newer computational approaches in the design of novel myocilin inhibitors for the treatment of glaucoma.Methods: An in-silico virtual screening technique based on simulation of molecular docking was utilised to design a novel myocilin inhibitors for the treatment of glaucoma. The designed novel molecules were theoretically evaluated to predict their pharmacokinetic properties and toxic effects. Lead molecules were screened out in virtual screening technique on the basis of low binding energies obtained in AutoDock based molecular docking simulation.Results: Out of ten top l

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Mateev, Emilio, Iva Valkova, Diana Tzankova, Maya Georgieva, and Alexander Zlatkov. "OPTIMIZING MOLECULAR DOCKING PROTOCOLS OF PYRROLE CONTAINING MAO-B INHIBITORS THROUGH CORRELATION COEFFICIENTS." Proceedings of CBU in Medicine and Pharmacy 2 (October 24, 2021): 92–98. http://dx.doi.org/10.12955/pmp.v2.179.

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Virtual screening is emerging as a highly applied technique for the search of hits since it significantly reduces the time required for the establishment of novel, effective compounds compared to high-throughput screening. Implementing correlation coefficients to determine if a molecular docking study is robust and reliable has been established as common practice in recent years. The aim of this work was to determine if a relevant pairwise correlation between the scoring functions (ChemPLP, GoldScore, Chemscore and ASP) of the docking software GOLD 5.2 and previously determined experimental da

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Aloufi, Bandar Hamad. "Screening of Phytochemicals against Osteoporosis: Molecular Docking and Simulation-Based Computational Approaches." International Journal Of Pharmaceutical Research And Allied Sciences 11, no. 1 (2022): 87–98. http://dx.doi.org/10.51847/o8p74spequ.

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Narender, Boggula, Katta Mahaboobi Sruthi, Megavath Subhash, Mukherjee Jayanti, and Rao Tadikonda Rama. "Molecular Docking - An Overview." Chemistry Research Journal 8, no. 5 (2023): 24–34. https://doi.org/10.5281/zenodo.11382179.

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<strong>Abstract </strong> Molecular docking has become an increasingly important tool for drug discovery. In this review, we present a brief introduction of the available molecular docking methods, and their development and applications in drug discovery. Molecular docking has been widely employed as a fast and inexpensive technique in the past decades, both in academic and industrial settings. Although this discipline has now had enough time to consolidate, many aspects remain challenging and there is still not a straightforward and accurate route to readily pinpoint true ligands among a set

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Mostefaoui, L., F. Mesli, M. Merad та S. Ghalem. "Virtual screening of triazoles inhibitors of 11β-hydroxysteroid dehydrogenaseenzymes using -ADME-moleculardocking, and molecular dynamics simulation studies". Journal of Fundamental and Applied Sciences 12, № 2 (2023): 712–27. http://dx.doi.org/10.4314/jfas.v12i2.13.

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Hypertension, or elevated arterial blood pressure, is a substantial public health problem. The two 11β hydroxysteroid dehydrogenase (11β HSD) isozymes catalyze the interconversion of cortisol and cortisone. Our research consists in studying the inhibition of the enzymes with some derivatives of 1,2,4 triazoles by means of molecular docking and dynamics approaches. The interactions between the studied inhibitors and our target were further explored through molecular docking and molecular dynamics simulations, in the presence of water molecules. The molecular dynamics study was done for the best

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Rosy P., Jacquline, Jebastin Sonia Jas M., Santhanalakshmi K, Venkat Kumar Shanmugam, and Prabhakaran A. "Identification of Potential Inhibitor Targeting InhA, Molecular Docking, ADMET, Molecular Dynamic Simulation and Antibacterial Activity of Thiazolidinone Derivatives: A Computational Approach." International Journal of Zoological Investigations 08, special issue (2022): 191–202. http://dx.doi.org/10.33745/ijzi.2022.v08i0s.024.

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This study was performed to examine molecular docking of newly synthesised thiazolidinone compounds and discover potential InhA inhibitors. MIC screening produced thiazolidinone derivatives for Staphylococcus aureus illness. KBr pellet FT-IR spectra were collected on a Thermo Nicolet AVATAR-330 spectrometer. Bruker obtained 400 MHz 1H spectra of all chemicals in DMSO-d6. Five 4 thiazolidinone derivatives:4-(4-oxo-2-phenylthiazolidin-3yl)amino)benzyl)oxazolidin-2-one(8), ((2-(4 chlorophenyl)-4oxothiazolidin-3yl)amino)benzyl)- oxazolidin-2-one(9), ((2-(4-fluorophenyl)-4-oxothiazolidin-3 yl)amino

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Chen, Kuan-Chung, Wen-Yuan Lee, Hsin-Yi Chen, and Calvin Yu-Chian Chen. "In SilicoInvestigation of Potential mTOR Inhibitors from Traditional Chinese Medicine for Treatment of Leigh Syndrome." BioMed Research International 2014 (2014): 1–9. http://dx.doi.org/10.1155/2014/139492.

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A recent research demonstrates that the inhibition of mammalian target of rapamycin (mTOR) improves survival and health for patients with Leigh syndrome. mTOR proteins can be treated as drug target proteins against Leigh syndrome and other mitochondrial disorders. In this study, we aim to identify potent TCM compounds from the TCM Database@Taiwan as lead compounds of mTOR inhibitors. PONDR-Fit protocol was employed to predict the disordered disposition in mTOR protein before virtual screening. After virtual screening, the MD simulation was employed to validate the stability of interactions bet

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Jia, Wenchao, Zecheng Wang, Zhongyi Lu, Baiwen Ding, Zhoumin Li, and Danke Xu. "The discovery of lactoferrin dual aptamers through surface plasmon resonance imaging combined with a bioinformation analysis." Analyst 145, no. 19 (2020): 6298–306. http://dx.doi.org/10.1039/d0an01513j.

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An analytical method for screening multi-site recognition aptamers in lactoferrin molecules has been developed based on Surface Plasmon Resonance imaging, combined with the cluster classification calculation and molecular docking simulation.

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Yang, Zhirui, Mingquan Wu, Xin Zhou, Jin Luo, Yi Liu, and Lin Li. "Network pharmacology study on the mechanism of Curcumae Rhizoma in the treatment of non-small cell lung cancer." Medicine 104, no. 19 (2025): e42366. https://doi.org/10.1097/md.0000000000042366.

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Non-small cell lung cancer (NSCLC) poses a significant threat to public health worldwide. Curcumae Rhizoma (CR) has potent therapeutic potential in different cancers. However, the mechanism of CR treating NSCLC remains unclear. In this study, a network pharmacology-based strategy is followed to address the issue. The targets related to CR or NSCLC were obtained from multiple online public databases. Compound-target network was constructed using Cytoscape. Protein–protein interaction (PPI) was analyzed by STRING. Key transcription factors were explored in TRRUST. Gene ontology (GO) function and

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Luo, Lianxiang, Ai Zhong, Qu Wang, and Tongyu Zheng. "Structure-Based Pharmacophore Modeling, Virtual Screening, Molecular Docking, ADMET, and Molecular Dynamics (MD) Simulation of Potential Inhibitors of PD-L1 from the Library of Marine Natural Products." Marine Drugs 20, no. 1 (2021): 29. http://dx.doi.org/10.3390/md20010029.

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Background: In the past decade, several antibodies directed against the PD-1/PD-L1 interaction have been approved. However, therapeutic antibodies also exhibit some shortcomings. Using small molecules to regulate the PD-1/PD-L1 pathway may be another way to mobilize the immune system to fight cancer. Method: 52,765 marine natural products were screened against PD-L1(PDBID: 6R3K). To identify natural compounds, a structure-based pharmacophore model was generated, following by virtual screening and molecular docking. Then, the absorption, distribution, metabolism, and excretion (ADME) test was c

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LIU, YU, WENTAO LI, and RUIXIN MA. "PARTICLE SWARM OPTIMIZATION ON FLEXIBLE DOCKING." International Journal of Biomathematics 05, no. 05 (2012): 1250044. http://dx.doi.org/10.1142/s1793524511001866.

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Molecular docking is an important tool in screening large libraries of compounds to determine the interactions between potential drugs and the target proteins. The molecular docking problem is how to locate a good conformation to dock a ligand to the large molecule. It can be formulated as a parameter optimization problem consisting of a scoring function and a global optimization method. Many docking methods have been developed with primarily these two parts varying. In this paper, a variety of particle swarm optimization (PSO) variants were introduced to cooperate with the semiempirical free

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Sumathy, A., R. Suresh, and N. L. Gowrishankar. "In-silico DESIGN SCREENING OF SOME PYRAZOLONE FUSED HETEROCYCLIC ANALOGUES AS HER2 INHIBITORS TARGETING BREAST CANCER." Rasayan Journal of Chemistry 15, no. 01 (2022): 497–503. http://dx.doi.org/10.31788/rjc.2022.1516738.

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In human breast cancers, the human epidermal development factor receptor-2 is a membrane tyrosine kinase that is overexpressed, and gene amplified. Pyrazolone fused heterocyclic moieties- thiazolidinone, carboxymethyl thiazolidinone, azetidinone are significant DNA-intercalating agents here human epidermal development factor receptor-2 amplification and over expression are linked to tumour cell proliferation and the pathway of instances in breast cancer. Few novel pyrazolone fused heterocyclic analogues are designed by in-silico-technique for their human epidermal development factor receptor-2

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Santoso, Broto. "3D-MOLECULAR SCREENING OF DIKETOPIPERAZINE DERIVATES ON Staphylococcus aureus DEHYDROSQUALENE SYNTHASE USING VINA." Pharmacon: Jurnal Farmasi Indonesia 13, no. 1 (2015): 24–29. http://dx.doi.org/10.23917/pharmacon.v13i1.23.

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Dehydrosqualene synthase enzyme has been used as protein target model for exploring docking simulation of pyrazoline analogues. One of diketopiperazine derivates that have similar structure to pyrazoline has antibacterial activity against Staphylococcus aureus (S. aureus). Vina is AutoDock- improved program that capable for molecular screening based on free-energy and binding conformation prediction between ligand and protein target. The aim of these studies is to screen diketopiperazine derivates on dehydrosqualene synthase of S. aureus using Vina. Diketopiperazine derivates, curcumin analogu

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Abdulaali Sahib, Mohammed, and Monther Faisal Mahdi. "Identification of Indole Derivatives as Selective Cyclooxygenase-2 Inhibitors by Virtual Screening and Molecular Dynamic Simulation." Turkish Computational and Theoretical Chemistry 9, no. 2 (2024): 19–32. https://doi.org/10.33435/tcandtc.1442939.

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Selective COX-2 inhibitors present a promising strategy in pain management due to their reduced adverse effects compared to non-selective COX inhibitors targeting COX-1. This study focuses on the design and virtual exploration of 8 indole derivatives using molecular docking, ADMET, and molecular dynamics (MD) simulations. Molecular docking highlighted the significance of hydrophobic and hydrophilic amino acid residues for ligand stability, with compounds 4 and 5 exhibiting notably strong in silico affinities to COX-2 (docking scores of -11.349 kcal/mol and -10.872 kcal/mol, respectively). Mole

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Brescia, Valerio. "Computational Analysis and Phytochemical Screening Targeting Dihydrolipoamide Dehydrogenase (DLD) for Alzheimer's Disease: A Molecular Dynamics Simulation Study." European journal of volunteering and community-based projects 1, no. 2 (2024): 70–94. https://doi.org/10.5281/zenodo.12683808.

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<strong>Abstract: </strong>The decreasing rate of metabolisms within the mitochondrial is connected to the progressive characterization of Alzheimer's Disease (AD). Dihydrolipoamide dehydrogenase (dld), and DLD1 are specific chemicals comprised of two enzymes/complexes of protein; pyruvate dehydrogenase and α-ketoglutarate dehydrogenase physiologically related to AD and have a noteworthy function in energy metabolism. The present computational study was designed to envisage a rational screening of natural phytochemical compounds against DLD1 in AD. The molecular docking and virtual scree

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Zong, Keli, Lei Xu, Yuxin Hou, et al. "Virtual Screening and Molecular Dynamics Simulation Study of Influenza Polymerase PB2 Inhibitors." Molecules 26, no. 22 (2021): 6944. http://dx.doi.org/10.3390/molecules26226944.

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Influenza A virus is the main cause of worldwide epidemics and annual influenza outbreaks in humans. In this study, a virtual screen was performed to identify compounds that interact with the PB2 cap-binding domain (CBD) of influenza A polymerase. A virtual screening workflow based on Glide docking was used to screen an internal database containing 8417 molecules, and then the output compounds were selected based on solubility, absorbance, and structural fingerprints. Of the 16 compounds selected for biological evaluation, six compounds were identified that rescued cells from H1N1 virus-mediat

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De Paris, Renata, Fábio A. Frantz, Osmar Norberto de Souza, and Duncan D. A. Ruiz. "wFReDoW: A Cloud-Based Web Environment to Handle Molecular Docking Simulations of a Fully Flexible Receptor Model." BioMed Research International 2013 (2013): 1–12. http://dx.doi.org/10.1155/2013/469363.

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Molecular docking simulations of fully flexible protein receptor (FFR) models are coming of age. In our studies, an FFR model is represented by a series of different conformations derived from a molecular dynamic simulation trajectory of the receptor. For each conformation in the FFR model, a docking simulation is executed and analyzed. An important challenge is to perform virtual screening of millions of ligands using an FFR model in a sequential mode since it can become computationally very demanding. In this paper, we propose a cloud-based web environment, called web Flexible Receptor Docki

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Khan, Azhar, Sunil Sharma, Abhishek Gehlot, Mona Gupta, and Mahboob Alam. "Antifungal screening and molecular docking simulation of silica supported synthesized sitosteryl hydrogen phthalate using microwave irradiation." Chemical Industry 74, no. 6 (2020): 377–88. http://dx.doi.org/10.2298/hemind200709028k.

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In this study, steroidal sitosteryl hydrogen phthalate (stigmast-5-en-3b-yl hydrogen phthalate) was synthesized by the reaction of 3b-sitosterol and phthalic anhydride using silica gel as a solid support under microwave irradiation (MWI). The comparative study of microwave assisted synthesis and conventional synthesis of the steroidal compound in a hazardous solvent revealed that the former method provided shortened reaction times at increased yields. The compounds obtained by the two procedures were characterized by infrared spectroscopy, proton, carbon-13 nuclear magnetic resonance (1H and 1

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Singh, Swati, Tamal Das, Manika Awasthi, Veda P. Pandey, Brijesh Pandey, and Upendra N. Dwivedi. "DNA topoisomerase-directed anticancerous alkaloids: ADMET-based screening, molecular docking, and dynamics simulation." Biotechnology and Applied Biochemistry 63, no. 1 (2015): 125–37. http://dx.doi.org/10.1002/bab.1346.

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Tang, Haiyan, Kai Ren, Guanjie Wang, Rong Zhang, and Long Zhang. "Computational design of phosphoinositide 3-kinase gamma (PI3Kg) inhibitors as a newer therapy for rheumatoid arthritis." Tropical Journal of Pharmaceutical Research 20, no. 4 (2022): 775–81. http://dx.doi.org/10.4314/tjpr.v20i4.17.

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    Purpose: To develop a potential therapy for rheumatoid arthritis (RA) by altering factors involved in the pathogenesis of the disease. Methods: Molecular docking simulation-based virtual screening was performed against phosphoinositide-3-kinase gamma (PI3Kg) to identify potential leads that may serve as anti-rheumatoid arthritic agents through their interactions and binding energies with the target receptor, followed by their optimization for improvement of their pharmacokinetics and toxicity profiles. Results: Molecular docking simulation-based virtual

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Cao, Xiaoci, Guohong Xin, and Baoshuan Fang. "Molecular docking and molecular dynamics simulation studies on the effect of baicalein on breast and ovarian cancers." Tropical Journal of Pharmaceutical Research 22, no. 7 (2023): 1395–402. http://dx.doi.org/10.4314/tjpr.v22i7.6.

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Purpose: To carry out molecular docking and molecular dynamics simulation analysis on the effect of baicalein and its derivatives on breast cancer and ovarian cancer.Methods: The potential ligand binding site of cyclooxygenase-2 (COX-2) was predicted, and virtual screening was carried out on baicalein, a plant-based herbal compound, and its natural derivatives. Furthermore, molecular dynamics (MD) simulation was used to confirm the validity and stability of the docking protocol.Results: Molecular docking showed strong molecular interaction of baicalein and its derivatives with COX-2. The resul

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Zhou, Wei, Shiliang Li, Weiqiang Lu, et al. "Isoindole-1,3-dione derivatives as RSK2 inhibitors: synthesis, molecular docking simulation and SAR analysis." MedChemComm 7, no. 2 (2016): 292–96. http://dx.doi.org/10.1039/c5md00469a.

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Alzain, Abdulrahim A., Mohammed A. Almogaddam, Rayan Yousif, et al. "Molecular Docking, Molecular Dynamics Simulation, and Pharmacophore-Based Virtual Screening Unveil Natural Compounds with TIM-3 Inhibitory Activity." Journal of Pharmacy and Bioallied Sciences 17, Suppl 2 (2025): S1882—S1887. https://doi.org/10.4103/jpbs.jpbs_402_25.

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ABSTRACT Introduction: The aberrant expression of T cell immunoglobulin mucin-3 (TIM-3) has been linked to adaptive immunotherapy resistance and poor prognosis. Targeting TIM-3 has gained popularity due to positive outcomes in preclinical settings. Materials and method: This research explored the Supernatural 3.0 database for potential TIM-3 inhibitors. A pharmacophore-based virtual screening, molecular docking, and molecular dynamics simulations were conducted for 449,008 compounds. Compounds SN0085417 (-7.542 kcal/mol), SN0261906 (-7.036 kcal/mol), and SN0276180 (-6.871 kcal/mol) showed bett

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