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Journal articles on the topic 'Virtual compounds'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Karpov, P. A. "High-Throughput Screening of New Antimitotic Compounds Based on CSLabGrid Virtual Organization." Science and innovation 11, no. 1 (2015): 85–93. http://dx.doi.org/10.15407/scine11.01.085.

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Rahman, Md Mostafijur, Md Bayejid Hosen, M. Zakir Hossain Howlader, and Yearul Kabir. "Lead Molecule Prediction and Characterization for Designing MERS-CoV 3C-like Protease Inhibitors: An In silico Approach." Current Computer-Aided Drug Design 15, no. 1 (2018): 82–88. http://dx.doi.org/10.2174/1573409914666180629151906.

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Background: 3C-like protease also called the main protease is an essential enzyme for the completion of the life cycle of Middle East Respiratory Syndrome Coronavirus. In our study we predicted compounds which are capable of inhibiting 3C-like protease, and thus inhibit the lifecycle of Middle East Respiratory Syndrome Coronavirus using in silico methods. </P><P> Methods: Lead like compounds and drug molecules which are capable of inhibiting 3C-like protease was identified by structure-based virtual screening and ligand-based virtual screening method. Further, the compounds were va

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Saadat, Fatemeh, Soroush Sardari, and Bahram Maleki. "Virtual Screening of Anti-Mycobacterial Plant Compounds." Molecular Informatics 32, no. 9-10 (2013): 802–10. http://dx.doi.org/10.1002/minf.201300007.

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Li, Peng, Lili Yin, Bo Zhao, and Yuezhongyi Sun. "Virtual Screening of Drug Proteins Based on Imbalance Data Mining." Mathematical Problems in Engineering 2021 (May 22, 2021): 1–10. http://dx.doi.org/10.1155/2021/5585990.

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To address the imbalanced data problem in molecular docking-based virtual screening methods, this paper proposes a virtual screening method for drug proteins based on imbalanced data mining, which introduces machine learning technology into the virtual screening technology for drug proteins to deal with the imbalanced data problem in the virtual screening process and improve the accuracy of the virtual screening. First, to address the data imbalance problem caused by the large difference between the number of active compounds and the number of inactive compounds in the docking conformation gen

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Utsintong, Maleeruk, Piyanuch Rojsanga, Kwok-Yiu Ho, et al. "Virtual Screening against Acetylcholine Binding Protein." Journal of Biomolecular Screening 17, no. 2 (2011): 204–15. http://dx.doi.org/10.1177/1087057111421667.

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The nicotinic acetylcholine receptors (nAChRs) are a member of the ligand-gated ion channel family and play a key role in the transfer of information across neurological networks. The X-ray crystal structure of agonist-bound α7 acetylcholine binding protein (AChBP) has been recognized as the most appropriate template to model the ligand-binding domain of nAChR for studying the molecular mechanism of the receptor–ligand interactions. Virtual screening of the National Cancer Institute diversity set, a library of 1990 compounds with nonredundant pharmacophore profiles, using AutoDock against AChB

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Dagar, Komal, Shankar Gupta, Alamjot Singh та Vivek Asati. "In silico studies for the identification of potential thiazolidine-2,4-diones as α-amylase inhibitors". Pharmaspire 15, № 01 (2023): 48–53. http://dx.doi.org/10.56933/pharmaspire.2023.15109.

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Type 2 diabetes, which is characterized by hyperglycemia, is a chronic endocrine metabolic condition. α-amylase inhibitors may have a major therapeutic impact in type 2 diabetic mellitus. In the present study, virtual screening database preparation by R-group enumeration, virtual screening, docking study, and pharmacokinetics analysis was performed by taking α-amylase as a target. The results highlight the important binding features of novel thiazolidine-2,4-dione compounds as α-amylase inhibitors. An R-group enumeration study was performed for the generation of novel thiazolidine-2,4-dione de

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Ali, Omeed Akbar, Ayad Saadi Hameed, Firas Shawqi Algburi, Seyithan TAYSI, and Ilhami GULCIN. "Computational docking assisted designing of novel phosphate ester carrier for sulphamethoxazole drug as promising anti-bacterial compounds." Tikrit Journal of Pure Science 28, no. 5 (2023): 28–48. http://dx.doi.org/10.25130/tjps.v28i5.1477.

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Aiming to obtain new anti-bacterial agents, nine novel compounds(8-16) having the same essential moieties (phosphate ester, Schiff base and sulfonamide) were subjected to virtual molecular docking screening to investigate the interaction between these compounds and amino acids existing in the active site of dihydropteroate synthase. compounds (5-7) were synthesized, and on the basis of that, proposals for subsequent compounds were built. Virtual compounds were built based on previously prepared compounds (1-6). Docking score, root mean square deviation (RMSD), hydrogen bond type, Pi-Pi bond, s

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Qureshi, Shahrukh, Ravina Khandelwal, Maddala Madhavi, et al. "A Multi-target Drug Designing for BTK, MMP9, Proteasome and TAK1 for the Clinical Treatment of Mantle Cell Lymphoma." Current Topics in Medicinal Chemistry 21, no. 9 (2021): 790–818. http://dx.doi.org/10.2174/1568026621666210119112336.

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Background: Mantle cell lymphoma (MCL) is a type of non-Hodgkin lymphoma characterized by the mutation and overexpression of the cyclin D1 protein by the reciprocal chromosomal translocation t(11;14)(q13:q32). Aim: The present study aims to identify potential inhibition of MMP9, Proteasome, BTK, and TAK1 and determine the most suitable and effective protein target for the MCL. Methodology: Nine known inhibitors for MMP9, 24 for proteasome, 15 for BTK and 14 for TAK1 were screened. SB-3CT (PubChem ID: 9883002), oprozomib (PubChem ID: 25067547), zanubrutinib (PubChem ID: 135565884) and TAK1 inhi

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Rayevsky, O. V., O. M. Demchyk, P. A. Karpov та ін. "Structure-based virtual screening for new lead compounds targeted Plasmodium α-tubulin". Faktori eksperimental'noi evolucii organizmiv 28 (31 серпня 2021): 135–39. http://dx.doi.org/10.7124/feeo.v28.1389.

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Aim. Search for new dinitroaniline and phosphorothioamide compounds, capable of selective binding with Plasmodium α-tubulin, affecting its mitotic apparatus. Methods. Structural biology methods of computational prediction of protein-ligand interaction: molecular docking, molecular dynamics and pharmacophore analysis. Selection of compounds based on pharmacophore characteristics and virtual screening results. Results. The protocol and required structural conditions for target (α-tubulin of P. falciparum) preparation and correct modeling of the ligand-protein interaction (docking and virtual scr

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Scarpino, Bajusz, Proj, et al. "Discovery of Immunoproteasome Inhibitors Using Large-Scale Covalent Virtual Screening." Molecules 24, no. 14 (2019): 2590. http://dx.doi.org/10.3390/molecules24142590.

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Large-scale virtual screening of boronic acid derivatives was performed to identify nonpeptidic covalent inhibitors of the β5i subunit of the immunoproteasome. A hierarchical virtual screening cascade including noncovalent and covalent docking steps was applied to a virtual library of over 104,000 compounds. Then, 32 virtual hits were selected, out of which five were experimentally confirmed. Biophysical and biochemical tests showed micromolar binding affinity and time-dependent inhibitory potency for two compounds. These results validate the computational protocol that allows the screening of

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Wang, Zhe, Huiyong Sun, Chao Shen, et al. "Combined strategies in structure-based virtual screening." Physical Chemistry Chemical Physics 22, no. 6 (2020): 3149–59. http://dx.doi.org/10.1039/c9cp06303j.

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Ren, Ji-Xia, Rui-Tao Zhang, and Hui Zhang. "Identifying Novel ATX Inhibitors via Combinatory Virtual Screening Using Crystallography-Derived Pharmacophore Modelling, Docking Study, and QSAR Analysis." Molecules 25, no. 5 (2020): 1107. http://dx.doi.org/10.3390/molecules25051107.

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Autotaxin (ATX) is considered as an interesting drug target for the therapy of several diseases. The goal of the research was to detect new ATX inhibitors which have novel scaffolds by using virtual screening. First, based on two diverse receptor-ligand complexes, 14 pharmacophore models were developed, and the 14 models were verified through a big test database. Those pharmacophore models were utilized to accomplish virtual screening. Next, for the purpose of predicting the probable binding poses of compounds and then carrying out further virtual screening, docking-based virtual screening was

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Jamal, Azfar. "In-silico Identification of the Novel Anti EGFR Compounds from Ginger Through Virtual Screening and Molecular Docking Analysis." Journal of Pioneering Medical Sciences 14, Special Issue 1 (2025): 232–39. https://doi.org/10.47310/jpms202514s0130.

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Introduction: The EGFR receptor tyrosine kinase is revealed to be the critical biomarker involved in cancer metastasis and proliferation. The FDA approved drugs have shown an outstanding result in cancer treatment but these drugs suffer a lot of side effects, so there is a need to identify the novel phytochemicals that may have anti-EGFR activity. Methodology: The protein EGFR was retrieved from the PDB along with the hetero atoms attached with the crystal structure. The chosen 86 ginger compounds were downloaded from TIP database in 3D sdf format. Using the PyRx virtual screeing tool the targ

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SEIDAKHMETOVA, Roza B., Leila I. ARYSTAN, Gulmira M. MULDAEVA, Leila S. HAYDARGALIEVA, and Zhangeldy S. NURMAGANBETOV. "ASSESSMENT OF NEUROPROTECTIVE EFFECTS OF ALKALOID COMPOUNDS." Periódico Tchê Química 17, no. 35 (2020): 1–11. http://dx.doi.org/10.52571/ptq.v17.n35.2020.01_seidakhmetova_pgs_1_11.pdf.

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Beta-carboline alkaloids show a wide range of psychopharmacological effects (for example, some beta-carboline alkaloids facilitate dopaminergic transmission and interact with dopaminergic receptors D1 and D2 in the striatum). This article presents data on neuroprotective effects of alkaloid compounds using computer simulation methods, docking-based virtual screening, and experimental pharmacology. The purpose of the study was to investigate the neuroprotective/stress-protective action of new derivatives of alkaloid compounds using the methods of computer simulation, docking-based virtual scree

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Ohue, Masahito, Yuki Kojima, and Takatsugu Kosugi. "Generating Potential Protein-Protein Interaction Inhibitor Molecules Based on Physicochemical Properties." Molecules 28, no. 15 (2023): 5652. http://dx.doi.org/10.3390/molecules28155652.

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Protein-protein interactions (PPIs) are associated with various diseases; hence, they are important targets in drug discovery. However, the physicochemical empirical properties of PPI-targeted drugs are distinct from those of conventional small molecule oral pharmaceuticals, which adhere to the ”rule of five (RO5)”. Therefore, developing PPI-targeted drugs using conventional methods, such as molecular generation models, is challenging. In this study, we propose a molecular generation model based on deep reinforcement learning that is specialized for the production of PPI inhibitors. By introdu

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Hsieh, Chia-Ju, Sam Giannakoulias, E. James Petersson, and Robert H. Mach. "Computational Chemistry for the Identification of Lead Compounds for Radiotracer Development." Pharmaceuticals 16, no. 2 (2023): 317. http://dx.doi.org/10.3390/ph16020317.

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The use of computer-aided drug design (CADD) for the identification of lead compounds in radiotracer development is steadily increasing. Traditional CADD methods, such as structure-based and ligand-based virtual screening and optimization, have been successfully utilized in many drug discovery programs and are highlighted throughout this review. First, we discuss the use of virtual screening for hit identification at the beginning of drug discovery programs. This is followed by an analysis of how the hits derived from virtual screening can be filtered and culled to highly probable candidates t

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Brummond, Kay M., John R. Goodell, Matthew G. LaPorte, Lirong Wang та Xiang-Qun Xie. "Synthesis and in silico screening of a library of β-carboline-containing compounds". Beilstein Journal of Organic Chemistry 8 (10 липня 2012): 1048–58. http://dx.doi.org/10.3762/bjoc.8.117.

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The synthesis of a library of tetrahydro-β-carboline-containing compounds in milligram quantities is described. Among the unique heterocyclic frameworks are twelve tetrahydroindolizinoindoles, six tetrahydrocyclobutanindoloquinolizinones and three tetrahydrocyclopentenoneindolizinoindolones. These compounds were selected from a virtual combinatorial library of 11,478 compounds. Physical chemical properties were calculated and most of them are in accordance with Lipinski’s rules. Virtual docking and ligand-based target evaluations were performed for the β-carboline library compounds and selecte

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B Billones, Junie, Juriel Kristan F Ramirez, Yves Ira A ReyeS, and Abdul Rashid B Sampaco III. "Virtual Screening of Compounds Against Mycobacterium tuberculosis Maltosyltransferase GlgE." Acta Scientific Pharmaceutical Sciences 3, no. 6 (2019): 77–85. http://dx.doi.org/10.31080/asps.2019.03.0281.

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TilakVijay, Jakkanaboina, Kandimalla Vivek Babu та Addepally Uma. "Virtual screening of novel compounds as potential ERα inhibitors". Bioinformation 15, № 5 (2019): 321–32. http://dx.doi.org/10.6026/97320630015321.

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Alvia-Giler, Yomira Belén, Homero Antonio Zambrano-Ferrín, Carlos Andrés Mera-Santos, and Lenin Adrián Vera-Rosado. "Impact of virtual environments on learning binary inorganic compounds." International research journal of engineering, IT & scientific research 10, no. 4 (2024): 87–94. http://dx.doi.org/10.21744/irjeis.v10n4.2444.

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The purpose of the research was to determine the effectiveness of virtual environments in learning binary inorganic compounds at the BGU level of the “San Isidro” Educational Unit. For this purpose, the research had a quantitative approach. Data collection was carried out through knowledge tests on the students (control and experimental group). The results obtained showed that at the control group level a mean of 3.86 was calculated, showing a standard deviation of 1.509 and a mean standard error of 0.302. On the other hand, the calculation showed that, for the experimental group, a mean of 4.

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Gabrielsen, Mari, Rafał Kurczab, Agata Siwek, et al. "Identification of Novel Serotonin Transporter Compounds by Virtual Screening." Journal of Chemical Information and Modeling 54, no. 3 (2014): 933–43. http://dx.doi.org/10.1021/ci400742s.

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Zaslavskiy, Mikhail, Simon Jégou, Eric W. Tramel, and Gilles Wainrib. "ToxicBlend: Virtual screening of toxic compounds with ensemble predictors." Computational Toxicology 10 (May 2019): 81–88. http://dx.doi.org/10.1016/j.comtox.2019.01.001.

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Froes, Thamires Quadros, Miriam C. C. Melo, Gloria E. P. Souza, Marcelo Santos Castilho, and Denis M. Soares. "Virtual screening and biological evaluation of novel antipyretic compounds." Chemical Biology & Drug Design 90, no. 5 (2017): 739–52. http://dx.doi.org/10.1111/cbdd.12995.

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Chen, Kuan-Chung, Wen-Yuan Lee, Hsin-Yi Chen, and Calvin Yu-Chian Chen. "In SilicoInvestigation of Potential TRAF6 Inhibitor from Traditional Chinese Medicine against Cancers." BioMed Research International 2014 (2014): 1–14. http://dx.doi.org/10.1155/2014/429486.

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It has been indicated that tumor necrosis factor receptor-associated factor-6 (TRAF6) will upregulate the expression of hypoxia-inducible factor-1α(HIF-1α) and promote tumor angiogenesis. TRAF6 proteins can be treated as drug target proteins for a differentiation therapy against cancers. As structural disordered disposition in the protein may induce the side-effect and reduce the occupancy for ligand to bind with target protein, PONDR-Fit protocol was performed to predict the disordered disposition in TRAF6 protein before virtual screening. TCM compounds from the TCM Database@Taiwan were emplo

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Yuniarta, Tegar Achsendo, I. Gede Ari Sumartha, Taufik Muhammad Fakih, Rosita Handayani, and Dwi Syah Fitra Ramadhan. "Discovery of Potential Prolyl-tRNA Synthetase Allosteric Inhibitor Through Virtual Screening and In Vitro Assay against Plasmodium falciparum." Jordan Journal of Pharmaceutical Sciences 16, no. 4 (2023): 880–900. http://dx.doi.org/10.35516/jjps.v16i4.1027.

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Objectives: This study aimed to identify novel antimalarial compounds based on allosteric inhibitor of prolyl-tRNA synthetase using hierarchical virtual screening. Materials and Methods: Pharmacophore model was designed initially, based on the structure-activity relationships data between several pyrazole-urea analogues and their IC50 enzymatic value. The model obtained was applied to screen ZINC15 database, after which followed by drug-likeness, toxicophore, and PAINS filter. The hit compounds were docked against P. falciparum prolyl-tRNA synthetase enzyme, using validated docking method. The

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Tsai, Tsung-Lin, and Thy-Hou Lin. "Virtual Screening of Some Active Human Macrophage Migration Inhibitory Factor Antagonists." Journal of Biomolecular Screening 19, no. 7 (2014): 1116–23. http://dx.doi.org/10.1177/1087057114523317.

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Macrophage migration inhibitory factor (MIF) is an autocrine- and paracrine-acting cytokine that is involved in several inflammatory, autoimmune, infectious, and oncogenic diseases. Clinical data have shown that inhibition of MIF, especially its tautomerase activity, with small compounds has been beneficial in some disease models. A virtual screening (VS) experiment is conducted for searching some active compounds to inhibit the tautomerase activity of MIF from the ZINC database. By using an x-ray–determined structure OXIM-11 as the query and an in-house developed two-dimensional scaffold comp

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Setiawan, Muhammad Teguh, and Arry Yanuar. "VIRTUAL SCREENING AND MOLECULAR DYNAMICS SIMULATION OF COMPOUNDS FROM THE HERBAL DATABASE OF INDONESIA AGAINST HISTONE DEACETYLASE 2." International Journal of Applied Pharmaceutics 10, no. 1 (2018): 235. http://dx.doi.org/10.22159/ijap.2018.v10s1.52.

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Objective: This study aimed to find the herbal compounds from the database of Indonesian herbs with potential for use as histone deacetylase 2 (HDAC2)enzyme inhibitors through virtual screening using the LigandScout program.Methods: Virtual screening was conducted using LigandScout 4.09.3, AutodockZN, and AutoDockTools.Results: The virtual screening process resulted in 10 compounds with the highest pharmacophore fit score rating, from which five compounds withthe best criteria for molecular dynamics simulations were selected: Boesenbergin B, pongachalcone I, 6,8-diprenylgenistein, marmin, and

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Kollár, Levente, György Gábor Frenczy, Matic Proj, et al. "Virtual Screening and Biochemical Testing of Borocycles as Immunoproteasome Inhibitors." Periodica Polytechnica Chemical Engineering 65, no. 3 (2021): 292–98. http://dx.doi.org/10.3311/ppch.17202.

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Inhibition of the immunoproteasome (iCP) offers new opportunities in the treatment of cancer, autoimmune disorders and neurodegenerative diseases. Inspired by the success of boronic acids as proteasome inhibitors we have complied a virtual library of commercially available 5- and 6-membered borocycles and performed a structure based virtual screening against the chymotrypsin-like (β5i) subunit of the iCP. The top scored docking poses were visually inspected to select compounds for experimental testing. Six compounds with 5-membered ring and another six compounds with 6-membered ring were subje

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Ahmad Fuad, Fazia Adyani, and Nurhainis Ogu Salim. "Analogues of Oxamate, Pyruvate, and Lactate as Potential Inhibitors of Plasmodium knowlesi Lactate Dehydrogenase Identified Using Virtual Screening and Verified via Inhibition Assays." Processes 10, no. 11 (2022): 2443. http://dx.doi.org/10.3390/pr10112443.

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Malaria management remains a challenge, due to the resistance of malaria parasites to current antimalarial agents. This resistance consequently delays the global elimination of malaria throughout the world. Hence, the demand is increasing for new and effective antimalarial drugs. The identification of potential drugs that target Pk-LDH can be obtained through virtual screening analyses, as this has been previously applied to discover Pf-LDH inhibitors. In this study, the selected candidates from our virtual screening analyses were subsequently tested against purified Pk-LDH, and verified throu

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Seo, Hyowon, Difan Zhang, and T. Alan Hatton. "Experimental and Virtual Screening of Phenazine and Phenothiazine Derivatives in Aqueous Solution for Electrochemical Carbon Capture." ECS Meeting Abstracts MA2023-01, no. 27 (2023): 1772. http://dx.doi.org/10.1149/ma2023-01271772mtgabs.

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Molecular redox-active compounds, including quinone and aza-aromatics, have emerged as tools for capturing carbon dioxide using renewable electricity. Given the vast and highly diverse chemical space of the candidate compounds, accessing their electrochemical properties in a rapid way is attractive for both experimental and virtual screening approaches. Here we present a study on the experimental screening of a series of commercial redox-active compounds. Phenazine and phenothiazine dyes have been experimentally tested for applications in electrochemical carbon capture, for which they are find

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Krishnan, Preethi, Andrew K. Smith, Glen E. P. Ropella, Lopamudra Dutta, Ryan C. Kennedy, and C. Anthony Hunt. "Utilizing virtual experiments to increase understanding of discrepancies involving in vitro-to-in vivo predictions of hepatic clearance." PLOS ONE 17, no. 7 (2022): e0269775. http://dx.doi.org/10.1371/journal.pone.0269775.

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Predictions of xenobiotic hepatic clearance in humans using in vitro-to-in vivo extrapolation methods are frequently inaccurate and problematic. Multiple strategies are being pursued to disentangle responsible mechanisms. The objective of this work is to evaluate the feasibility of using insights gained from independent virtual experiments on two model systems to begin unraveling responsible mechanisms. The virtual culture is a software analog of hepatocytes in vitro, and the virtual human maps to hepatocytes within a liver within an idealized model human. Mobile objects (virtual compounds) ma

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Babkov, D. A., A. S. Taran, A. A. Shevchenko, et al. "Virtual and experimental screening of new melatonin bioisosteres for the treatment of glaucoma." Acta Biomedica Scientifica 9, no. 1 (2024): 116–28. http://dx.doi.org/10.29413/abs.2024-9.1.12.

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Background. Melatonin is an endogenous regulator of intraocular pressure (IOP), but its effectiveness as a drug for glaucoma treatment is limited.The aim of the study. To develop and to validate a virtual screening method to identify bioisosteric analogs of melatonin that are promising for study as agents that reduce intraocular pressure.Results. A database containing structural and experimental affinity information for 48 individual reference compounds was created. Risk assessments for mutagenic, carcinogenic, irritant and reproductive toxicity were performed in DataWarrior based on substruct

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Sasi Priya, S. V. S., Syed Hussain Basha, and D. R. Harish Kumar. "In-silico anticancer potential of active constituents from “Glycyrrhiza uralensis” targeting PPAR gamma protein." Research Journal of Chemistry and Environment 26, no. 5 (2022): 30–44. http://dx.doi.org/10.25303/2605rjce3044.

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The aim of the study is to anticipate the lead molecule from the phytochemical constituents of “Glycyrrhiza uralensis” which acts on PPAR γ receptor and causes cell proliferation and inhibits cell migration in cancer disease. PyRx virtual screening (Auto docking Vina) software and Schrodinger Maestro version 11.5 were used to screen the compounds anticancer activity. Python Molecular Viewer 1.5.6 (PMV 1.5.6) was used for semi flexible docking between the chemical compounds and PPAR γ protein receptor. Schrodinger Maestro version 11.5 was used to study the molecular dynamic simulation studies.

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Graham, Christian, and Nory B. Jones. "Intelligent Virtual Assistant's Impact on Technical Proficiency within Virtual Teams." International Journal of Virtual and Personal Learning Environments 6, no. 1 (2016): 41–61. http://dx.doi.org/10.4018/ijvple.2016010104.

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Information-systems development continues to be a difficult process, particularly for virtual teams that do not have the luxury of meeting face-to-face. The research literature on this topic reinforces this point: the greater part of database systems development projects ends in failure. The use of virtual teams to complete projects further compounds these failures. However, recent developments in intelligent virtual assistants (IVAs), such as Siri, Cortana, or Watson, have created opportunities to automate the systems-development process and improve success rates. Specifically, the use of a v

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Spiegel, Jacob, and Hanoch Senderowitz. "Evaluation of QSAR Equations for Virtual Screening." International Journal of Molecular Sciences 21, no. 21 (2020): 7828. http://dx.doi.org/10.3390/ijms21217828.

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Quantitative Structure Activity Relationship (QSAR) models can inform on the correlation between activities and structure-based molecular descriptors. This information is important for the understanding of the factors that govern molecular properties and for designing new compounds with favorable properties. Due to the large number of calculate-able descriptors and consequently, the much larger number of descriptors combinations, the derivation of QSAR models could be treated as an optimization problem. For continuous responses, metrics which are typically being optimized in this process are r

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Suay-García, Beatriz, Jose I. Bueso-Bordils, Antonio Falcó, Gerardo M. Antón-Fos, and Pedro A. Alemán-López. "Virtual Combinatorial Chemistry and Pharmacological Screening: A Short Guide to Drug Design." International Journal of Molecular Sciences 23, no. 3 (2022): 1620. http://dx.doi.org/10.3390/ijms23031620.

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Traditionally, drug development involved the individual synthesis and biological evaluation of hundreds to thousands of compounds with the intention of highlighting their biological activity, selectivity, and bioavailability, as well as their low toxicity. On average, this process of new drug development involved, in addition to high economic costs, a period of several years before hopefully finding a drug with suitable characteristics to drive its commercialization. Therefore, the chemical synthesis of new compounds became the limiting step in the process of searching for or optimizing leads

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Sanjeev Sharma, Anshul. "Comparative Study of Imaginary Compounds against Plasmodium Falciparum." INTERANTIONAL JOURNAL OF SCIENTIFIC RESEARCH IN ENGINEERING AND MANAGEMENT 07, no. 10 (2023): 1–11. http://dx.doi.org/10.55041/ijsrem25974.

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In the pursuit of developing innovative antimalarial medications, particularly targeting the pernicious Plasmodium falciparum, computational methods have assumed an increasingly crucial role. analysis of three primary computational techniques: Ligand-based Virtual Screening (LBVS), Molecular Docking, and Quantitative Structure-Activity Relationships (QSAR) in the realm of antimalarial drug discovery. The initial technique, LBVS, has swiftly become an invaluable asset for identifying novel drugs. Molecular docking proves invaluable in virtually screening extensive compound libraries, identifyin

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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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Kanakaveti, Vishnupriya, Sakthivel Rathinasamy, Suresh K. Rayala, and Michael Gromiha. "Forging New Scaffolds from Old: Combining Scaffold Hopping and Hierarchical Virtual Screening for Identifying Novel Bcl-2 Inhibitors." Current Topics in Medicinal Chemistry 19, no. 13 (2019): 1162–72. http://dx.doi.org/10.2174/1568026619666190618142432.

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Background: Though virtual screening methods have proven to be potent in various instances, the technique is practically incomplete to quench the need of drug discovery process. Thus, the quest for novel designing approaches and chemotypes for improved efficacy of lead compounds has been intensified and logistic approaches such as scaffold hopping and hierarchical virtual screening methods were evolved. Till now, in all the previous attempts these two approaches were applied separately. Objective: In the current work, we made a novel attempt in terms of blending scaffold hopping and hierarchic

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Kamakia, Faith, Stephen Ouma, and Richard Kagia. "Virtual screening of zinc compounds similar to NSAIDS with better pharmacodynamic and pharmacokinetic profiles." F1000Research 12 (April 26, 2023): 444. http://dx.doi.org/10.12688/f1000research.132017.1.

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BACKGROUND: Pain is a common symptom that is managed in both outpatients and inpatients. There are many side effects associated with opioids such as respiratory depression, constipation, hyperalgesia, and tolerance. Non- steroidal anti-inflammatory drugs cause gastrointestinal tract (GIT) irritation and may be a risk factor for developing peptic ulcer disease. This study aimed to generate active analgesic agents from known analgesics, determine the docking scores of these agents to their receptors, determine the pharmacokinetic properties of these agents, and evaluate their toxicity profiles.

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Salman, Saad, Fahad H. Shah, Jawaria Idrees, et al. "Virtual screening of immunomodulatory medicinal compounds as promising anti-SARS-CoV-2 inhibitors." Future Virology 15, no. 5 (2020): 267–75. http://dx.doi.org/10.2217/fvl-2020-0079.

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Aim: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a pernicious viral disease, causes acute respiratory distress responsible for mortality and morbidity worldwide. To screen different immunomodulatory medicinal compounds to unravel their interaction with SARS-CoV-2 viral proteins. Materials & methods: A library of immunomodulatory medicinal compounds with antiviral capability were analyzed against SARS proteases, spike protein and nonstructural proteins (NSP-9, 15) using Autodock vina. Results: Out of more than 300 medicinal compounds, only six compounds: arzanol, ferulic a

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Alqahtani, Leena S., Ahmad Salah Alkathiri, Abdulrahman Alzahrani, et al. "Structure-Based Virtual Screening of Antiviral Compounds Targeting the Norovirus RdRp Protein." Advancements in Life Sciences 11, no. 2 (2024): 488. http://dx.doi.org/10.62940/als.v11i2.2830.

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Background: Human noroviruses (NV) are the primary etiological organisms causing acute gastroenteritis around the world, causing severe morbidity and imposing a significant economic burden. The RNA-dependent RNA polymerase (RdRp) is essential for viral replication and could be a promising target for anti-NV therapeutics. Despite the discovery of a few NV RdRp inhibitors, the majority of these pharmaceuticals have demonstrated limited efficacy in inhibiting viral replication in cellular models.Methods: In this study, computational screening of antiviral compounds was conducted targeting the NV

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Tajane, Pravin, Swapnil Deshmukh, Amit Lunkad, and Manoj Tare. "Discovery of mTOR Receptor Modulators Targeting Breast Cancer by Hybrid of Virtual Screening and Molecular Docking Approach." INTERNATIONAL JOURNAL OF PHARMACEUTICAL QUALITY ASSURANCE 15, no. 02 (2024): 743–48. http://dx.doi.org/10.25258/ijpqa.15.2.30.

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This research paper presents a comprehensive approach integrating virtual screening and molecular docking to identify potential therapeutic candidates. Pharmacophore-based virtual screening was employed to assess the structural similarities of compounds to a reference molecule, revealing promising candidates with high similarity scores. Subsequently, molecular docking studies were conducted to predict the binding affinities of these compounds to the target receptor, 4DRH. CHEMBL3775006 emerged as a lead candidate, demonstrating both structural resemblance and strong binding affinity to the tar

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Li, Kaiwen, Zean Li, Yiran Tao та ін. "Discovering novel P38α inhibitors for the treatment of prostate cancer through virtual screening methods". Future Medicinal Chemistry 11, № 24 (2019): 3125–37. http://dx.doi.org/10.4155/fmc-2019-0223.

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Aim: P38α plays a crucial role in the development of castration-resistant prostate cancer. Discovering novel inhibitors of P38α offers potential for the development of new anticancer drugs. Methods & results: Compounds from the Chemdiv and Enamine virtual libraries were filtered to construct the P38α inhibitor-like library. A total of 58 new P38α inhibitors were discovered via virtual screening; these included three compounds (compound 1, 5, 9) with kinase IC50 of below 10 μM. In vitro, these three compounds have the potential to suppress the viabilities of prostate cancer cell lines, howe

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da Silva, Luciane S., Uessiley R. Barbosa, Lívia do C. Silva, Célia MA Soares, Maristela Pereira, and Roosevelt A. da Silva. "Identification of a new antifungal compound against isocitrate lyase of Paracoccidioides brasiliensis." Future Microbiology 14, no. 18 (2019): 1589–606. http://dx.doi.org/10.2217/fmb-2019-0166.

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Aim: To perform virtual screening of compounds based on natural products targeting isocitrate lyase of Paracoccidioides brasiliensis. Materials & methods: Homology modeling and molecular dynamics simulations were applied in order to obtain conformational models for virtual screening. The selected hits were tested in vitro against enzymatic activity of ICL of the dimorphic fungus P. brasiliensis and growth of the Paracoccidioides spp. The cytotoxicity and selectivity index of the compounds were defined. Results & conclusion: Carboxamide, lactone and β-carboline moieties were identified

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Lin, Shao-Long, Yan-Song Chen, Ruo-Yu Liu, et al. "Synergistic acceleration of machine learning and molecular docking for prostate-specific antigen ligand design." RSC Advances 14, no. 12 (2024): 8240–50. http://dx.doi.org/10.1039/d3ra08550c.

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By employing a million-level virtual screening to obtain potential PSA compounds and effectively guiding the synthesis using machine learning methods, we obtained lead compounds that exhibited significantly improved binding affinity for PSA.

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Aloqbi, Akram Ahmed. "Identification of Novel STAT3 Dimerization Inhibitor Through Structure-Based Virtual Screening for Cancer Management." Advancements in Life Sciences 11, no. 2 (2024): 508. http://dx.doi.org/10.62940/als.v11i2.2975.

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Background: Signal transducer and activator of transcription 3 (STAT3) is a transcription factor that controls cell proliferation, differentiation, angiogenesis, and immunological responses. In many human malignancies, abnormal STAT3 activation promotes tumor growth via oncogenic gene expression, resulting in tumor malignancy. Many drugs with clinically authorized analogues that are used as STAT3 inhibitors for cancer therapy have several drawbacks in terms of stability and toxicity.Methods: This study used PyRx 0.8 tool to screen the Traditional Chinese Medicine (TCM) database of about 32,364

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Ouyang, Ruizhuo, Jinyao Liu, Shen Wang, et al. "Virtual Screening-Based Study of Novel Anti-Cancer Drugs Targeting G-Quadruplex." Pharmaceutics 15, no. 5 (2023): 1414. http://dx.doi.org/10.3390/pharmaceutics15051414.

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In order to develop new anti-cancer drugs more efficiently and reduce side effects based on active drug targets, the virtual drug screening was carried out through the target of G-quadruplexes and 23 hit compounds were, thus, screened out as potential anticancer drugs. Six classical G-quadruplex complexes were introduced as query molecules, and the three-dimensional similarity of molecules was calculated by shape feature similarity (SHAFTS) method so as to reduce the range of potential compounds. Afterwards, the molecular docking technology was utilized to perform the final screening followed

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Ani, R., Roshini Manohar, Gayathri Anil, and O. S. Deepa. "Virtual Screening of Drug Likeness using Tree Based Ensemble Classifier." Biomedical and Pharmacology Journal 11, no. 3 (2018): 1513–19. http://dx.doi.org/10.13005/bpj/1518.

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In earlier years, the Drug discovery process took years to identify and process a Drug. It takes a normal of 12 years for a Drug to travel from the research lab to the patient. With the introduction of Machine Learning in Drug discovery, the whole process turned out to be simple. The utilization of computational tools in the early stages of Drug development has expanded in recent decades. A computational procedure carried out in Drug discovery process is Virtual Screening (VS). VS are used to identify the compounds which can bind to a Drug target. The preliminary process before analyzing the b

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PHAM, Quan Minh, and Long Quoc PHAM. "VIRTUAL SCREENING STATEGIES IN DRUG DISCOVERY – A BRIEF OVERVIEW." Vietnam Journal of Science and Technology 59, no. 4 (2021): 415. http://dx.doi.org/10.15625/2525-2518/59/4/16003.

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Computer-aided drug design has now become a compulsory tool in the drug discovery and development process which uses computational approaches to discover potential compounds with expected biological activities. Firstly, this review provides a comprehensive introduction of the virtual screening technique, knowledge and advances in both SBVS and LBVS strategies also presented. Secondly, recent database of compounds provided worldwide and drug-like parameters which are helpful in supporting the VS process will be discussed. These information will provides a good platform to estimate the advance o

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