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Application of computational methods for anticancer drug discovery, design, and optimization

Diego Prada-Gracia, Sara Huerta-Yépez, Liliana M. Moreno-Vargas
2016 Boletín Médico del Hospital Infantil de México  
From hit identification to lead optimization, techniques such as ligand- or structure-based virtual screening are widely used in many discovery efforts.  ...  In this paper, we review the concept of rational design presenting some of the most representative examples of molecules identified by means of it.  ...  The identification of small molecules and the process of transforming these into high-content lead series are key activities in modern drug discovery.  ... 
doi:10.1016/j.bmhimx.2016.10.006 pmid:29421286 pmcid:PMC7110968 fatcat:3dom2uh5jjg5jarfxcc74d7oxi

Hierarchical virtual screening approaches in small molecule drug discovery

Ashutosh Kumar, Kam Y.J. Zhang
2015 Methods  
Several virtual screening studies are discussed to demonstrate the successful application of hierarchical virtual screening in small molecule drug discovery.  ...  In this review, we focus on different hierarchical virtual screening strategies and their application in the discovery of small molecule modulators of important drug targets.  ...  Among many ways of identifying initial hits in drug discovery, highthroughput screening (HTS) and virtual screening (VS) are most common.  ... 
doi:10.1016/j.ymeth.2014.07.007 pmid:25072167 pmcid:PMC7129923 fatcat:t5mu2qmh5ncz3gwu3k2wnfr3t4

Application of computational methods for anticancer drug discovery, design, and optimization

Diego Prada-Gracia, Sara Huerta-Yépez, Liliana M. Moreno-Vargas
2016 Boletín Médico Del Hospital Infantil de México (English Edition)  
From hit identification to lead optimization, techniques such as ligand-or structurebased virtual screening are widely used in many discovery efforts.  ...  In this paper, we review the concept of rational design presenting some of the most representative examples of molecules identified by means of it.  ...  The identification of small molecules and the process of transforming these into high-content lead series are key activities in modern drug discovery.  ... 
doi:10.1016/j.bmhime.2017.11.040 fatcat:qna2hfewqzbrxbwi4fn4muop4m

Neccessasity of Bio-imaging Hybrid Approaches Accelerating Drug Discovery Process (Mini-Review)

Iliyana Samardzhieva, Aamir Khan
2018 International Journal of Computer Applications  
In particular, High Content Screening (HCS) and Virtual Screening (VS) are reviewed, and their respective examples are discussed to gain insight into state-of-the-art bio-imaging methodologies used for  ...  This paper summarizes current trends in bio-imaging technologies and their application on the process of drug discovery.  ...  The compound screening phase aims to find the 'hit' molecule.  ... 
doi:10.5120/ijca2018917564 fatcat:uou6hcalprcihfwdl5hyl4jr5q

MEMES: Machine learning framework for Enhanced MolEcular Screening

Sarvesh Mehta, Siddhartha Laghuvarapu, Yashaswi Pathak, Aaftaab Sethi, Mallika Alvala, U. Deva Deva Priyakumar
2021 Chemical Science  
In drug discovery applications, high throughput virtual screening exercises are routinely performed to determine an initial set of candidate molecules referred to as "hits".  ...  In such an experiment, each molecule...  ...  The first step in the process after target identification and validation is to identify hit molecules, where potential strong binding drug-like molecules against a drug target are identified using computational  ... 
doi:10.1039/d1sc02783b pmid:34659706 pmcid:PMC8442698 fatcat:aqxn7wxzujd5fdzuqn5rkphfpa

DeepMalaria: Artificial Intelligence Driven Discovery of Potent Antiplasmodials

Arash Keshavarzi Arshadi, Milad Salem, Jennifer Collins, Jiann Shiun Yuan, Debopam Chakrabarti
2020 Frontiers in Pharmacology  
The traditional drug discovery approach of high throughput screening (HTS) of large compound libraries for identification of new drug leads is time-consuming and resource intensive.  ...  While virtual in silico screening is a solution to this problem, however, the generalization of the models is not ideal.  ...  ACKNOWLEDGMENTS We would like to thank Farnam Kavehei for providing graphical figures in Figure 1 . Also, we appreciate Dr. Taj Azarian for his critical comments on the manuscript.  ... 
doi:10.3389/fphar.2019.01526 pmid:32009951 pmcid:PMC6974622 fatcat:grxbzsgdz5et3cnso5enpgvmbe

How can natural products serve as a viable source of lead compounds for the development of new/novel anti-malarials?

Eric Guantai, Kelly Chibale
2011 Malaria Journal  
This has spurred intensive drug discovery endeavours geared towards identifying novel, highly active anti-malarial drugs, and the identification of quality leads from natural sources would greatly augment  ...  The current reality is that other than compounds that have their foundation in historic natural products, there are no other compounds in drug discovery as part of lead optimization projects and preclinical  ...  Promising analogs designed or identified in this way may be expanded and developed further by introduction of (bio)isosteric substitutions suggested by scaffold hopping techniques, or by the application  ... 
doi:10.1186/1475-2875-10-s1-s2 pmid:21411013 pmcid:PMC3059460 fatcat:uwiasrdyhfckfhadaaoevk3wue

Idea2Data: Towards a New Paradigm for Drug Discovery

Christos A Nicolaou, Christine Humblet, Hong Hu, Eva-Marie Martín de la Nava, Frank C. Dorsey, Thomas M. Castle, Keith Ian Burton, Haitao Hu, Jorg Hendle, Michael J. Hickey, Joel Duerksen, Jibo Wang (+1 others)
2019 ACS Medicinal Chemistry Letters  
Available physical collections, typically used during hit identification, are of the order of 106 compounds but represent only a small fraction of the small molecule drug-like chemical space.  ...  and experimental components of the drug discovery process.  ...  A key step in the small molecule drug discovery process involves the identification of so-called hit compounds, chemical structures with measurable although typically weak activity that can serve as tools  ... 
doi:10.1021/acsmedchemlett.8b00488 pmid:30891127 pmcid:PMC6421544 fatcat:k5tax75o5jds5ifymiblgf3u3m

Computer-aided drug discovery

Jürgen Bajorath
2015 F1000Research  
Approaches are highlighted that aid in the identification and optimization of new drug candidates.  ...  If applied in a scientifically meaningful way, computational methods improve the ability to identify and evaluate potential drug molecules, but there remain weaknesses in the methods that preclude naïve  ...  small molecules.  ... 
doi:10.12688/f1000research.6653.1 pmid:26949519 pmcid:PMC4756805 fatcat:phphuefryzdjdkhxn2cx57mrb4

Inhibitors of DNA Methyltransferases From Natural Sources: A Computational Perspective

Fernanda I. Saldívar-González, Alejandro Gómez-García, David E. Chávez-Ponce de León, Norberto Sánchez-Cruz, Javier Ruiz-Rios, B. Angélica Pilón-Jiménez, José L. Medina-Franco
2018 Frontiers in Pharmacology  
Examples of computational approaches surveyed in this work are docking, similarity-based virtual screening, and pharmacophore modeling.  ...  It is also discussed the chemoinformatic-guided exploration of the chemical space of naturally occurring compounds as epigenetic modulators which may have significant implications in epigenetic drug discovery  ...  We foresee an augmented hit and led identification efforts based on natural products combining approaches such as high-throughput screening, structure-, ligand-based in silico screening, structure-based  ... 
doi:10.3389/fphar.2018.01144 pmid:30364171 pmcid:PMC6191485 fatcat:oiog4cmcena7zpzyoulka5uoqa

Virtual screening and fast automated docking methods

Gisbert Schneider, Hans-Joachim Böhm
2002 Drug Discovery Today  
Recent advances in high-throughput protein structure determination and in computational chemistry have refocussed attention on virtual screening and fast automated docking methods.  ...  We also provide several examples of where virtual screening has proved successful, highlighting the usefulness of the approach.  ...  w Virtual screening (VS) methods contribute to the drug discovery process in various ways [1, 2] .  ... 
doi:10.1016/s1359-6446(01)02091-8 pmid:11790605 fatcat:uvtu2kyj3bhypa3h6o4lyewunu

Virtual screening and fast automated docking methods

Gisbert Schneider, Hans-Joachim Böhm
2002 Drug Discovery Today  
Recent advances in high-throughput protein structure determination and in computational chemistry have refocussed attention on virtual screening and fast automated docking methods.  ...  We also provide several examples of where virtual screening has proved successful, highlighting the usefulness of the approach.  ...  w Virtual screening (VS) methods contribute to the drug discovery process in various ways [1, 2] .  ... 
doi:10.1016/s1359-6446(02)00004-1 fatcat:hyzelgvstzfcnn4bok5jf4qrtu

Computer-Aided Drug Design: An Innovative Tool for Modeling

Pranita P. Kore, Madhavi M. Mutha, Rishikesh V. Antre, Rajesh J. Oswal, Sandip S. Kshirsagar
2012 Open Journal of Medicinal Chemistry  
In present review we reported a brief history of CADD, DNA as target, receptor theory, structure optimization, structure-based drug design, virtual high-throughput screening (vHTS), graph machines.  ...  In the early stage of a drug discovery process, researchers may be faced with little or no structure activity relationship (SAR) information.  ...  This is followed by the development of a virtual screening protocol initialized by either docking of small molecules from the library or building these structures in the active site by employing De novo  ... 
doi:10.4236/ojmc.2012.24017 fatcat:5iax3xh7xjhejefmxg5to4ox6u

Shifting from the single to the multitarget paradigm in drug discovery

José L. Medina-Franco, Marc A. Giulianotti, Gregory S. Welmaker, Richard A. Houghten
2013 Drug Discovery Today  
Thus, there has been augmented interest in identifying drugs that interact with specific targets.  ...  Drug discovery has undergone transformations over the years, moving from in vivo models to a single target-selective drug for a single mechanism.  ...  This work was supported by NIDA grant R01 DA031370-02 (to R.A.H.).  ... 
doi:10.1016/j.drudis.2013.01.008 pmid:23340113 pmcid:PMC3642214 fatcat:nhvzmjmbsvf2vddogi6faaqa2y

Application of NMR and Molecular Docking in Structure-Based Drug Discovery [chapter]

Jaime L. Stark, Robert Powers
2011 Topics in current chemistry  
This review will highlight the use of NMR ligand affinity screens and molecular docking in drug discovery and describe recent examples where the two techniques were combined to identify new and effective  ...  High-throughput screening (HTS) is the primary method used by the pharmaceutical industry to identify initial lead compounds.  ...  Thus, combining NMR with virtual screens may provide a more efficient approach to lead identification and drug discovery.  ... 
doi:10.1007/128_2011_213 pmid:21915777 pmcid:PMC6628936 fatcat:5eomzv4nzbehzf7wje5yfbp6qe
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