Literature DB >> 28257191

Chemical Space Mimicry for Drug Discovery.

William Yuan1,2, Dadi Jiang2, Dhanya K Nambiar2, Lydia P Liew3, Michael P Hay3, Joshua Bloomstein2, Peter Lu2, Brandon Turner2, Quynh-Thu Le2, Robert Tibshirani4, Purvesh Khatri2,5, Mark G Moloney6, Albert C Koong2.   

Abstract

We describe a new library generation method, Machine-based Identification of Molecules Inside Characterized Space (MIMICS), that generates sets of molecules inspired by a text-based input. MIMICS-generated libraries were found to preserve distributions of properties while simultaneously increasing structural diversity. Newly identified MIMICS-generated compounds were found to be bioactive as inhibitors of specific components of the unfolded protein response (UPR) and the VEGFR2 pathway in cell-based assays, thus confirming the applicability of this methodology toward drug design applications. Wider application of MIMICS could facilitate the efficient utilization of chemical space.

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Year:  2017        PMID: 28257191      PMCID: PMC5802964          DOI: 10.1021/acs.jcim.6b00754

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   4.956


  11 in total

1.  Molecular shape diversity of combinatorial libraries: a prerequisite for broad bioactivity.

Authors:  Wolfgang H B Sauer; Matthias K Schwarz
Journal:  J Chem Inf Comput Sci       Date:  2003 May-Jun

2.  Inhibition of angiogenesis and invasion by 3,3'-diindolylmethane is mediated by the nuclear factor-kappaB downstream target genes MMP-9 and uPA that regulated bioavailability of vascular endothelial growth factor in prostate cancer.

Authors:  Dejuan Kong; Yiwei Li; Zhiwei Wang; Sanjeev Banerjee; Fazlul H Sarkar
Journal:  Cancer Res       Date:  2007-04-01       Impact factor: 12.701

3.  PaDEL-descriptor: an open source software to calculate molecular descriptors and fingerprints.

Authors:  Chun Wei Yap
Journal:  J Comput Chem       Date:  2010-12-17       Impact factor: 3.376

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

Authors:  Aaron M Virshup; Julia Contreras-García; Peter Wipf; Weitao Yang; David N Beratan
Journal:  J Am Chem Soc       Date:  2013-05-02       Impact factor: 15.419

5.  Catalytic activity of Matrix metalloproteinase-19 is essential for tumor suppressor and anti-angiogenic activities in nasopharyngeal carcinoma.

Authors:  King Chi Chan; Josephine Mun Yee Ko; Hong Lok Lung; Radislav Sedlacek; Zeng-Feng Zhang; Dian-Zhong Luo; Zhen-Bo Feng; Shuang Chen; Honglin Chen; Kwok Wah Chan; Sai Wah Tsao; Daniel Tsin-Tien Chua; Eugene R Zabarovsky; Eric J Stanbridge; Maria Li Lung
Journal:  Int J Cancer       Date:  2011-04-01       Impact factor: 7.396

6.  Identification of an Ire1alpha endonuclease specific inhibitor with cytotoxic activity against human multiple myeloma.

Authors:  Ioanna Papandreou; Nicholas C Denko; Michael Olson; Heleen Van Melckebeke; Sofie Lust; Arvin Tam; David E Solow-Cordero; Donna M Bouley; Fritz Offner; Maho Niwa; Albert C Koong
Journal:  Blood       Date:  2010-11-16       Impact factor: 22.113

Review 7.  Targeting the IRE1α-XBP1 branch of the unfolded protein response in human diseases.

Authors:  Dadi Jiang; Maho Niwa; Albert C Koong
Journal:  Semin Cancer Biol       Date:  2015-05-16       Impact factor: 15.707

8.  BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities.

Authors:  Tiqing Liu; Yuhmei Lin; Xin Wen; Robert N Jorissen; Michael K Gilson
Journal:  Nucleic Acids Res       Date:  2006-12-01       Impact factor: 16.971

9.  Strategy to discover diverse optimal molecules in the small molecule universe.

Authors:  Chetan Rupakheti; Aaron Virshup; Weitao Yang; David N Beratan
Journal:  J Chem Inf Model       Date:  2015-02-19       Impact factor: 4.956

10.  ChemBank: a small-molecule screening and cheminformatics resource database.

Authors:  Kathleen Petri Seiler; Gregory A George; Mary Pat Happ; Nicole E Bodycombe; Hyman A Carrinski; Stephanie Norton; Steve Brudz; John P Sullivan; Jeremy Muhlich; Martin Serrano; Paul Ferraiolo; Nicola J Tolliday; Stuart L Schreiber; Paul A Clemons
Journal:  Nucleic Acids Res       Date:  2007-10-18       Impact factor: 16.971

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  12 in total

Review 1.  Rethinking drug design in the artificial intelligence era.

Authors:  Petra Schneider; W Patrick Walters; Alleyn T Plowright; Norman Sieroka; Jennifer Listgarten; Robert A Goodnow; Jasmin Fisher; Johanna M Jansen; José S Duca; Thomas S Rush; Matthias Zentgraf; John Edward Hill; Elizabeth Krutoholow; Matthias Kohler; Jeff Blaney; Kimito Funatsu; Chris Luebkemann; Gisbert Schneider
Journal:  Nat Rev Drug Discov       Date:  2019-12-04       Impact factor: 84.694

2.  Application of Generative Autoencoder in De Novo Molecular Design.

Authors:  Thomas Blaschke; Marcus Olivecrona; Ola Engkvist; Jürgen Bajorath; Hongming Chen
Journal:  Mol Inform       Date:  2017-12-13       Impact factor: 3.353

Review 3.  A Structure-Based Drug Discovery Paradigm.

Authors:  Maria Batool; Bilal Ahmad; Sangdun Choi
Journal:  Int J Mol Sci       Date:  2019-06-06       Impact factor: 5.923

4.  CReM: chemically reasonable mutations framework for structure generation.

Authors:  Pavel Polishchuk
Journal:  J Cheminform       Date:  2020-04-22       Impact factor: 5.514

5.  MolFinder: an evolutionary algorithm for the global optimization of molecular properties and the extensive exploration of chemical space using SMILES.

Authors:  Yongbeom Kwon; Juyong Lee
Journal:  J Cheminform       Date:  2021-03-18       Impact factor: 5.514

6.  Combining generative artificial intelligence and on-chip synthesis for de novo drug design.

Authors:  Francesca Grisoni; Berend J H Huisman; Alexander L Button; Michael Moret; Kenneth Atz; Daniel Merk; Gisbert Schneider
Journal:  Sci Adv       Date:  2021-06-11       Impact factor: 14.136

7.  Molecular generative model based on conditional variational autoencoder for de novo molecular design.

Authors:  Jaechang Lim; Seongok Ryu; Jin Woo Kim; Woo Youn Kim
Journal:  J Cheminform       Date:  2018-07-11       Impact factor: 5.514

8.  Enhancing reaction-based de novo design using a multi-label reaction class recommender.

Authors:  Gian Marco Ghiandoni; Michael J Bodkin; Beining Chen; Dimitar Hristozov; James E A Wallace; James Webster; Valerie J Gillet
Journal:  J Comput Aided Mol Des       Date:  2020-02-28       Impact factor: 3.686

Review 9.  Machine Learning Methods in Drug Discovery.

Authors:  Lauv Patel; Tripti Shukla; Xiuzhen Huang; David W Ussery; Shanzhi Wang
Journal:  Molecules       Date:  2020-11-12       Impact factor: 4.411

10.  AI in drug development: a multidisciplinary perspective.

Authors:  Víctor Gallego; Roi Naveiro; Carlos Roca; David Ríos Insua; Nuria E Campillo
Journal:  Mol Divers       Date:  2021-07-12       Impact factor: 3.364

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