Structure-based virtual screening of chemical libraries for drug discovery

Ghosh, Sutapa; Nie, Anmin; An, Jing; Huang, Ziwei

doi:10.1016/j.cbpa.2006.04.002

Cited by 218 publications

(177 citation statements)

References 48 publications

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“…Virtual screening techniques have recently emerged as a complementary technique to traditional high-throughput screening technologies employed in the pharmaceutical industry (Shoichet 2004;Ghosh et al 2006;Cavasotto et al 2007). Using computer-aided methodologies, large numbers of compounds can be rapidly screened in order to efficiently eliminate non-binding compounds in silico, thus dramatically reducing the costs associated with preliminary testing in a drug discovery project.…”

Section: In Silico Methods In Drug Discoverymentioning

confidence: 99%

Structure-Based Approaches Targeting Oncogene Promoter G-Quadruplexes

Ma¹,

Yan²,

Leung³

et al. 2013

Oncogene and Cancer - From Bench to Clinic

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Section: In Silico Methods In Drug Discoverymentioning

confidence: 99%

Structure-Based Approaches Targeting Oncogene Promoter G-Quadruplexes

Ma¹,

Yan²,

Leung³

et al. 2013

Oncogene and Cancer - From Bench to Clinic

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“…It has been successfully applied in a number of programs, in particular, at the lead discovery stage, where high-throughput molecular docking can play an important role [17]. Now, the virtual screening is carried out by creating a folder directory called "virtual screening" containing sub folders called "ligands," etc., in the "ligand" folder ligand files are set up.…”

Section: Virtual Screening Using Autodockmentioning

confidence: 99%

Virtual Screening of potential inhibitors from Herbs for the treatment of Breast Cancer

Emerson

Khan²,

Bafna³

et al. 2017

Asian J Pharm Clin Res

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Objectives: Cancer is a disease which results in uncontrollable abnormal cells division and destruction of body tissues. Breast cancer occurs when malignant tumors develop in the breast. Breast cancer is the second leading cause of death among women. To study the role of herbs used in the treatment for breast cancer. To investigate the anti-breast cancer activity of compounds present on most common herbs and to analyse their interaction with amino acids in the active sites. Methods:Complementary and alternative medicine is often used for curing cancer mainly the breast cancer. Also certain studies support the benefits of herbal medicines over others among Complementary and alternative medicine. Herbal treatments are more popular due to less complications and more safety. We selected a dataset of 38 compounds and performed virtual screening to identify the potential inhibitor against the known protein target BRCA1 involved in breast cancer using AutoDock4 as docking software. The binding site analyses were carried out using Discovery studio.Results: From our study, we deduced that cimigenol (black cohosh) and glycyrrhetinic acid (licorice) were found to have the highest affinity with the target protein. The amino acid interactions with the top five compounds were also analysed. Conclusion:During the course of our research we explored over common herbs used globally in treatment for breast cancer. Virtual screening was performed using AutoDock to search ligands to identify those structures which are most likely to bind to the protein. The high affinity compounds can bind more efficiently to the BRCA1 receptor and, hence, has potential to emerge as lead compound in the treatment of breast cancer.

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“…Protein structures (apo, ligand-free; or holo, ligand-bound) are experimentally determined by X-ray crystallography and nuclear magnetic resonance (NMR). Alternatively, protein structure homology models can be a valuable alternative [3,[5][6][7][8][9][10][19][20][21][22][23]. Several in silico methods can be used in combination with experimental evidences to extract and organize the molecular information in order to assist the understanding of the structural and chemical basis involved in receptor-ligand binding affinity and biological activity.…”

Section: Structure-based Drug Designmentioning

confidence: 99%

Structure-Based Drug Design Strategies in Medicinal Chemistry

Andricopulo¹,

Salum²,

Abraham

2009

CTMC

133

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A broad variety of medicinal chemistry approaches can be used for the identification of hits, generation of leads, as well as to accelerate the development of high quality drug candidates. Structure-based drug design (SBDD) methods are becoming increasingly powerful, versatile and more widely used. This review summarizes current developments in structure-based virtual screening and receptor-based pharmacophores, highlighting achievements as well as challenges, along with the value of structure-based lead optimization, with emphasis on recent examples of successful applications for the identification of novel active compounds.Keywords: Structure-based drug design, medicinal chemistry, virtual screening, QSAR, pharmacophores. STRUCTURE-BASED DRUG DESIGNThe performance of biochemical processes and cell mechanisms are dependent upon complex and multiple noncovalent intermolecular interactions between proteins and small-molecule modulators. The understanding of the structural and chemical binding properties of important drug targets in biologically relevant pathways allows the design of small molecules capable of regulating or modulating specific target functions in the body that are closely linked to human diseases and disorders, through multiple intermolecular interactions within a well-defined binding pocket [1][2][3][4]. In general, the identification of promising hits for further optimization is a major challenge faced by the both pharmaceutical and academic laboratories. Although the trial-anderror nature is inherent in drug research, rational concepts and modern computational methods have become widely employed for lead selection and optimization.The use of three-dimensional (3D) protein structure information in the development of new biologically active molecules, which is termed Structure-Based Drug Design (SBDD), is a well-established, successful and highly attarctive strategy used by academic and pharmaceutical research laboratories worldwide [3][4][5][6][7][8]. As a creative and knowledgedriven approach, an essential requirement for structure-based studies is a substantial understanding of the spatial and energetic aspects that affect the binding affinities of proteinligand complexes. Considering that the shape and chemical nature of the binding site of a specific target protein are known, and the possible intermolecular interactions between ligands and the protein within its active site have been identified, this qualified information can be directly employed for the identification of new ligands and the optimization of lead compounds. This opens new possibilities to boost the search for lead molecules and to limit the number of compounds that need to be evaluated experimentally.Hits can be identified through the docking of smallmolecule ligands (selected from databases of chemical structures) into protein active sites or by using receptorbased pharmacophore models. Furthermore, drug candidates can be designed de novo by improving the complementary binding properties of lead compounds and the r...

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Structure-based virtual screening of chemical libraries for drug discovery

Cited by 218 publications

References 48 publications

Structure-Based Approaches Targeting Oncogene Promoter G-Quadruplexes

Structure-Based Approaches Targeting Oncogene Promoter G-Quadruplexes

Virtual Screening of potential inhibitors from Herbs for the treatment of Breast Cancer

Structure-Based Drug Design Strategies in Medicinal Chemistry

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