Literature DB >> 23548177

Stochastic voyages into uncharted chemical space produce a representative library of all possible drug-like compounds.

Aaron M Virshup1, Julia Contreras-García, Peter Wipf, Weitao Yang, David N Beratan.   

Abstract

The "small molecule universe" (SMU), the set of all synthetically feasible organic molecules of 500 Da molecular weight or less, is estimated to contain over 10(60) structures, making exhaustive searches for structures of interest impractical. Here, we describe the construction of a "representative universal library" spanning the SMU that samples the full extent of feasible small molecule chemistries. This library was generated using the newly developed Algorithm for Chemical Space Exploration with Stochastic Search (ACSESS). ACSESS makes two important contributions to chemical space exploration: it allows the systematic search of the unexplored regions of the small molecule universe, and it facilitates the mining of chemical libraries that do not yet exist, providing a near-infinite source of diverse novel compounds.

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Year:  2013        PMID: 23548177      PMCID: PMC3670418          DOI: 10.1021/ja401184g

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  36 in total

1.  Designing focused libraries using MoSELECT.

Authors:  Valerie J Gillet; Peter Willett; Peter J Fleming; Darren V S Green
Journal:  J Mol Graph Model       Date:  2002-06       Impact factor: 2.518

2.  Towards the systematic exploration of chemical space.

Authors:  Mark Dow; Martin Fisher; Thomas James; Francesco Marchetti; Adam Nelson
Journal:  Org Biomol Chem       Date:  2011-10-04       Impact factor: 3.876

3.  Virtual exploration of the small-molecule chemical universe below 160 Daltons.

Authors:  Tobias Fink; Heinz Bruggesser; Jean-Louis Reymond
Journal:  Angew Chem Int Ed Engl       Date:  2005-02-25       Impact factor: 15.336

4.  Designing molecules by optimizing potentials.

Authors:  Mingliang Wang; Xiangqian Hu; David N Beratan; Weitao Yang
Journal:  J Am Chem Soc       Date:  2006-03-15       Impact factor: 15.419

5.  970 million druglike small molecules for virtual screening in the chemical universe database GDB-13.

Authors:  Lorenz C Blum; Jean-Louis Reymond
Journal:  J Am Chem Soc       Date:  2009-07-01       Impact factor: 15.419

6.  Predicting molecules--more realism, please!

Authors:  Roald Hoffmann; Paul von Ragué Schleyer; Henry F Schaefer
Journal:  Angew Chem Int Ed Engl       Date:  2008       Impact factor: 15.336

7.  Drug discovery: A question of library design.

Authors:  Philip J Hajduk; Warren R J D Galloway; David R Spring
Journal:  Nature       Date:  2011-02-03       Impact factor: 49.962

8.  Scaffold topologies. 2. Analysis of chemical databases.

Authors:  Michael J Wester; Sara N Pollock; Evangelos A Coutsias; Tharun Kumar Allu; Sorel Muresan; Tudor I Oprea
Journal:  J Chem Inf Model       Date:  2008-07-08       Impact factor: 4.956

9.  A gradient-directed Monte Carlo approach to molecular design.

Authors:  Xiangqian Hu; David N Beratan; Weitao Yang
Journal:  J Chem Phys       Date:  2008-08-14       Impact factor: 3.488

10.  Automated design of ligands to polypharmacological profiles.

Authors:  Jérémy Besnard; Gian Filippo Ruda; Vincent Setola; Keren Abecassis; Ramona M Rodriguiz; Xi-Ping Huang; Suzanne Norval; Maria F Sassano; Antony I Shin; Lauren A Webster; Frederick R C Simeons; Laste Stojanovski; Annik Prat; Nabil G Seidah; Daniel B Constam; G Richard Bickerton; Kevin D Read; William C Wetsel; Ian H Gilbert; Bryan L Roth; Andrew L Hopkins
Journal:  Nature       Date:  2012-12-13       Impact factor: 49.962

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  42 in total

1.  Mappability of drug-like space: towards a polypharmacologically competent map of drug-relevant compounds.

Authors:  Pavel Sidorov; Helena Gaspar; Gilles Marcou; Alexandre Varnek; Dragos Horvath
Journal:  J Comput Aided Mol Des       Date:  2015-11-12       Impact factor: 3.686

2.  Idea2Data: Toward a New Paradigm for Drug Discovery.

Authors:  Christos A Nicolaou; Christine Humblet; Hong Hu; Eva M Martin; Frank C Dorsey; Thomas M Castle; Keith Ian Burton; Haitao Hu; Jorg Hendle; Michael J Hickey; Joel Duerksen; Jibo Wang; Jon A Erickson
Journal:  ACS Med Chem Lett       Date:  2019-02-04       Impact factor: 4.345

3.  The octet rule in chemical space: generating virtual molecules.

Authors:  Rafel Israels; Astrid Maaß; Jan Hamaekers
Journal:  Mol Divers       Date:  2017-08-03       Impact factor: 2.943

Review 4.  Expanding the medicinal chemistry synthetic toolbox.

Authors:  Jonas Boström; Dean G Brown; Robert J Young; György M Keserü
Journal:  Nat Rev Drug Discov       Date:  2018-08-24       Impact factor: 84.694

5.  Ring system-based chemical graph generation for de novo molecular design.

Authors:  Tomoyuki Miyao; Hiromasa Kaneko; Kimito Funatsu
Journal:  J Comput Aided Mol Des       Date:  2016-06-14       Impact factor: 3.686

6.  Molecular docking screening using agonist-bound GPCR structures: probing the A2A adenosine receptor.

Authors:  David Rodríguez; Zhang-Guo Gao; Steven M Moss; Kenneth A Jacobson; Jens Carlsson
Journal:  J Chem Inf Model       Date:  2015-02-13       Impact factor: 4.956

7.  Advanced Multidimensional Separations in Mass Spectrometry: Navigating the Big Data Deluge.

Authors:  Jody C May; John A McLean
Journal:  Annu Rev Anal Chem (Palo Alto Calif)       Date:  2016-03-30       Impact factor: 10.745

8.  Chemical Space Mimicry for Drug Discovery.

Authors:  William Yuan; Dadi Jiang; Dhanya K Nambiar; Lydia P Liew; Michael P Hay; Joshua Bloomstein; Peter Lu; Brandon Turner; Quynh-Thu Le; Robert Tibshirani; Purvesh Khatri; Mark G Moloney; Albert C Koong
Journal:  J Chem Inf Model       Date:  2017-04-03       Impact factor: 4.956

9.  Molpher: a software framework for systematic chemical space exploration.

Authors:  David Hoksza; Petr Skoda; Milan Voršilák; Daniel Svozil
Journal:  J Cheminform       Date:  2014-03-21       Impact factor: 5.514

Review 10.  Ab Initio Machine Learning in Chemical Compound Space.

Authors:  Bing Huang; O Anatole von Lilienfeld
Journal:  Chem Rev       Date:  2021-08-13       Impact factor: 60.622

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