Access the full text.
Sign up today, get DeepDyve free for 14 days.
A. Gaulton, L. Bellis, A. Bento, Jon Chambers, M. Davies, A. Hersey, Yvonne Light, S. McGlinchey, D. Michalovich, B. Al-Lazikani, John Overington (2011)
ChEMBL: a large-scale bioactivity database for drug discoveryNucleic Acids Research, 40
A. Schreyer, T. Blundell (2012)
USRCAT: real-time ultrafast shape recognition with pharmacophoric constraintsJournal of Cheminformatics, 4
Y. Martin, J. Kofron, L. Traphagen (2002)
Do structurally similar molecules have similar biological activity?Journal of medicinal chemistry, 45 19
L. Xue, Jürgen Bajorath (2000)
Molecular descriptors in chemoinformatics, computational combinatorial chemistry, and virtual screening.Combinatorial chemistry & high throughput screening, 3 5
A. Kooistra, Stefan Mordalski, Gáspár Pándy-Szekeres, M. Esguerra, Alibek Mamyrbekov, Christian Munk, G. Keserü, D. Gloriam (2020)
GPCRdb in 2021: integrating GPCR sequence, structure and functionNucleic Acids Research, 49
G. Morris, R. Huey, William Lindstrom, M. Sanner, R. Belew, D. Goodsell, A. Olson (2009)
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibilityJournal of Computational Chemistry, 30
RS Bohacek (1996)
3Med Res Rev, 16
R. Bohacek, C. McMartin, W. Guida (1996)
The art and practice of structure‐based drug design: A molecular modeling perspectiveMedicinal Research Reviews, 16
W. Walters (2018)
Virtual Chemical Libraries.Journal of medicinal chemistry, 62 3
Niu Huang, B. Shoichet, J. Irwin (2006)
Benchmarking sets for molecular docking.Journal of medicinal chemistry, 49 23
J. Baell, Georgina Holloway (2010)
New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays.Journal of medicinal chemistry, 53 7
O. Grygorenko, D. Volochnyuk, S. Ryabukhin, D. Judd (2020)
The symbiotic relationship between drug discovery and organic chemistry.Chemistry
P. Finn, G. Morris (2013)
Shape‐based similarity searching in chemical databasesWiley Interdisciplinary Reviews: Computational Molecular Science, 3
Compounds catalog and screening sets
Michael Mysinger, Michael Carchia, J. Irwin, B. Shoichet (2012)
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better BenchmarkingJournal of Medicinal Chemistry, 55
O. Grygorenko, D. Radchenko, Igor Dziuba, A. Chuprina, Kateryna Gubina, Yurii Moroz (2020)
Generating Multibillion Chemical Space of Readily Accessible Screening CompoundsiScience, 23
Christopher, A. Lipinski, Beryl, W. Dominy, Paul, J. Feeney (2001)
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings.Advanced drug delivery reviews, 46 1-3
A. Nicholls, G. McGaughey, R. Sheridan, A. Good, G. Warren, M. Mathieu, S. Muchmore, Scott Brown, J. Grant, James Haigh, Neysa Nevins, Ajay Jain, B. Kelley (2010)
Molecular Shape and Medicinal Chemistry: A PerspectiveJournal of Medicinal Chemistry, 53
Fernanda Saldívar-González, C. Huerta-García, J. Medina‐Franco (2020)
Chemoinformatics-based enumeration of chemical libraries: a tutorialJournal of Cheminformatics, 12
D. Radchenko, V. Naumchyk, Igor Dziuba, A. Kyrylchuk, Kateryna Gubina, Yurii Moroz, O. Grygorenko (2021)
One-pot parallel synthesis of 1,3,5-trisubstituted 1,2,4-triazolesMolecular Diversity, 26
D. Huggins, A. Venkitaraman, D. Spring (2011)
Rational methods for the selection of diverse screening compounds.ACS chemical biology, 6 3
C. Stoddart (2016)
Is there a reproducibility crisis in scienceNature
Hans Matter (1997)
Selecting optimally diverse compounds from structure databases: a validation study of two-dimensional and three-dimensional molecular descriptors.Journal of medicinal chemistry, 40 8
E. Schonbrunn, S. Betzi, Riazul Alam, Mathew Martin, A. Becker, Huijong Han, Rawle Francis, R. Chakrasali, Sudhakar Jakkaraj, Aslamuzzaman Kazi, S. Sebti, C. Cubitt, A. Gebhard, L. Hazlehurst, J. Tash, Gunda Georg (2013)
Development of highly potent and selective diaminothiazole inhibitors of cyclin-dependent kinases.Journal of medicinal chemistry, 56 10
(2007)
Enamine real database : making chemical diversity real
Georgi Kanev, C. Graaf, B. Westerman, I. Esch, A. Kooistra (2020)
KLIFS: an overhaul after the first 5 years of supporting kinase researchNucleic Acids Research, 49
R. Bruns, Ian Watson (2012)
Rules for identifying potentially reactive or promiscuous compounds.Journal of medicinal chemistry, 55 22
Andrey Bogolubsky, Yurii Moroz, Olena Savych, S. Pipko, Angelika Konovets, M. Platonov, O. Vasylchenko, V. Hurmach, O. Grygorenko (2018)
An Old Story in the Parallel Synthesis World: An Approach to Hydantoin Libraries.ACS combinatorial science, 20 1
Jiankun Lyu, Sheng Wang, T. Balius, I. Singh, A. Levit, Yurii Moroz, Matthew O’Meara, T. Che, Enkhjargal Algaa, Kateryna Tolmachova, A. Tolmachev, B. Shoichet, B. Roth, J. Irwin (2019)
Ultra-large library docking for discovering new chemotypesNature, 566
M. Seddon, D. Cosgrove, M. Packer, V. Gillet (2018)
Alignment-Free Molecular Shape Comparison Using Spectral Geometry: The FrameworkJournal of chemical information and modeling, 59 1
A. Nadin, Channa Hattotuwagama, I. Churcher (2012)
Lead-oriented synthesis: a new opportunity for synthetic chemistry.Angewandte Chemie, 51 5
Sereina Riniker, G. Landrum (2013)
Open-source platform to benchmark fingerprints for ligand-based virtual screeningJournal of Cheminformatics, 5
L. Fan, L. Tan, Zhangcheng Chen, Jianzhong Qi, Fen Nie, Zhipu Luo, Jianjun Cheng, Sheng Wang (2020)
Haloperidol bound D2 dopamine receptor structure inspired the discovery of subtype selective ligandsNature Communications, 11
Olena Savych, Yuliya Kuchkovska, Andrey Bogolyubsky, A. Konovets, Kateryna Gubina, S. Pipko, Anton Zhemera, A. Grishchenko, Dmytro Khomenko, V. Brovarets, Roman Doroschuk, Yurii Moroz, O. Grygorenko (2019)
One-pot Parallel Synthesis of 5-(Dialkylamino)tetrazoles.ACS combinatorial science
White Rose, Research Online, R. Ashton, P. Willett, Mark Ashton, J. Barnard, F. Casset, M. Charlton, G. Downs, D. Gorse, J. Holliday, R. Lahana, P. Willett
Promoting Access to White Rose Research Papers Identification of Diverse Database Subsets Using Property-based and Fragment-based Molecular Descriptions
E. Pettersen, Thomas Goddard, Conrad Huang, Gregory Couch, Daniel Greenblatt, E. Meng, T. Ferrin (2004)
UCSF Chimera—A visualization system for exploratory research and analysisJournal of Computational Chemistry, 25
M. Sanner (1999)
Python: a programming language for software integration and development.Journal of molecular graphics & modelling, 17 1
CA Lipinski, F Lombardo, BW Dominy, PJ Feeney (2001)
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settingsAdv Drug Deliv Rev, 46
Jayme Dahlin, M. Walters (2016)
How to Triage PAINS-Full Research.Assay and drug development technologies, 14 3
Woong-Hee Shin, Xiaolei Zhu, M. Bures, D. Kihara (2015)
Three-Dimensional Compound Comparison Methods and Their Application in Drug DiscoveryMolecules, 20
Swarit Jasial, Ye Hu, Martin Vogt, J. Bajorath (2016)
Activity-relevant similarity values for fingerprints and implications for similarity searchingF1000Research, 5
Adrià Cereto-Massagué, María Ojeda, Cristina Valls, M. Mulero, S. García-Vallvé, G. Pujadas (2015)
Molecular fingerprint similarity search in virtual screening.Methods, 71
D. Veber, Stephen Johnson, Hung‐Yuan Cheng, B. Smith, K. Ward, K. Kopple (2002)
Molecular properties that influence the oral bioavailability of drug candidates.Journal of medicinal chemistry, 45 12
J. Irwin, Khanh Tang, Jennifer Young, Chinzorig Dandarchuluun, Benjamin Wong, Munkhzul Khurelbaatar, Yurii Moroz, J. Mayfield, R. Sayle (2020)
ZINC20 - A Free Ultralarge-Scale Chemical Database for Ligand DiscoveryJournal of chemical information and modeling
M Ashton, J Barnard, F Casset (2002)
Identification of diverse database subsets using property-based and fragment-based molecular descriptionsQuant Struct-ActRelat, 21
(2016)
2016) RDKit: Open-Source Cheminformatics Software
In the emerging field of drug discovery, rapid virtual screening methods become extremely valuable, especially when dealing with ultra-large databases of organic small bioactive molecules. In this work, we present a fast, computationally resource-efficient, and simple workflow for screening targeted compound libraries generated from ultra-large virtual chemical space. This workflow aims to find compounds with similar molecular 3D shapes with reference ones, and at the same time to expand chemical diversity and to identify new and potentially active scaffolds. This pipeline ensures the enrichment of the generated libraries with novel chemotypes. Also, it was shown that delicate tailoring of the physicochemical parameters of the search set ensures that all library compounds will possess desired property distributions. A visual inspection has shown that found structures bind to the receptor in the same way as the reference ones. Using our screening workflow, we have created a number of conventional protein-targeted libraries: the GPCRs Targeted Library (531 K compounds) and the Protein Kinases Targeted Library (113 K compounds). The described pipeline and scripts are freely accessible at: https://github.com/ChemSpace-LLC/usrcat_sim.Graphical abstract[graphic not available: see fulltext]
Molecular Diversity – Springer Journals
Published: Apr 1, 2023
Keywords: Computer-aided drug discovery; 3D Shape recognition; USRCAT; Ligand-based drug discovery; Novel chemotypes
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.