Literature DB >> 28070730

CADD medicine: design is the potion that can cure my disease.

Eric S Manas1, Darren V S Green2.   

Abstract

The acronym "CADD" is often used interchangeably to refer to "Computer Aided Drug Discovery" and "Computer Aided Drug Design". While the former definition implies the use of a computer to impact one or more aspects of discovering a drug, in this paper we contend that computational chemists are most effective when they enable teams to apply true design principles as they strive to create medicines to treat human disease. We argue that teams must bring to bear multiple sub-disciplines of computational chemistry in an integrated manner in order to utilize these principles to address the multi-objective nature of the drug discovery problem. Impact, resourcing principles, and future directions for the field are also discussed, including areas of future opportunity as well as a cautionary note about hype and hubris.

Entities:  

Keywords:  CADD; Computational chemistry; Computer aided drug design; Group; Integration; Scientific strategy; Structure

Mesh:

Year:  2017        PMID: 28070730     DOI: 10.1007/s10822-016-0004-3

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  20 in total

1.  QSAR modeling: where have you been? Where are you going to?

Authors:  Artem Cherkasov; Eugene N Muratov; Denis Fourches; Alexandre Varnek; Igor I Baskin; Mark Cronin; John Dearden; Paola Gramatica; Yvonne C Martin; Roberto Todeschini; Viviana Consonni; Victor E Kuz'min; Richard Cramer; Romualdo Benigni; Chihae Yang; James Rathman; Lothar Terfloth; Johann Gasteiger; Ann Richard; Alexander Tropsha
Journal:  J Med Chem       Date:  2014-01-06       Impact factor: 7.446

2.  Project ranks billions of drug interactions.

Authors:  Sara Reardon
Journal:  Nature       Date:  2013-11-28       Impact factor: 49.962

3.  Fragment-Based Discovery of Low-Micromolar ATAD2 Bromodomain Inhibitors.

Authors:  Emmanuel H Demont; Chun-wa Chung; Rebecca C Furze; Paola Grandi; Anne-Marie Michon; Chris Wellaway; Nathalie Barrett; Angela M Bridges; Peter D Craggs; Hawa Diallo; David P Dixon; Clement Douault; Amanda J Emmons; Emma J Jones; Bhumika V Karamshi; Kelly Locke; Darren J Mitchell; Bernadette H Mouzon; Rab K Prinjha; Andy D Roberts; Robert J Sheppard; Robert J Watson; Paul Bamborough
Journal:  J Med Chem       Date:  2015-07-09       Impact factor: 7.446

4.  Exploitation of a Novel Binding Pocket in Human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Discovered through X-ray Fragment Screening.

Authors:  Alison J-A Woolford; Joseph E Pero; Sridhar Aravapalli; Valerio Berdini; Joseph E Coyle; Philip J Day; Andrew M Dodson; Pascal Grondin; Finn P Holding; Lydia Y W Lee; Peng Li; Eric S Manas; Joseph Marino; Agnes C L Martin; Brent W McCleland; Rachel L McMenamin; Christopher W Murray; Christopher E Neipp; Lee W Page; Vipulkumar K Patel; Florent Potvain; Sharna Rich; Ralph A Rivero; Kirsten Smith; Donald O Somers; Lionel Trottet; Ranganadh Velagaleti; Glyn Williams; Ren Xie
Journal:  J Med Chem       Date:  2016-05-20       Impact factor: 7.446

5.  Improving the passive permeability of macrocyclic peptides: Balancing permeability with other physicochemical properties.

Authors:  Praew Thansandote; Robert M Harris; Hannah L Dexter; Graham L Simpson; Sandeep Pal; Richard J Upton; Klara Valko
Journal:  Bioorg Med Chem       Date:  2014-11-28       Impact factor: 3.641

6.  GPU-accelerated molecular modeling coming of age.

Authors:  John E Stone; David J Hardy; Ivan S Ufimtsev; Klaus Schulten
Journal:  J Mol Graph Model       Date:  2010-07-08       Impact factor: 2.518

7.  D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.

Authors:  Symon Gathiaka; Shuai Liu; Michael Chiu; Huanwang Yang; Jeanne A Stuckey; You Na Kang; Jim Delproposto; Ginger Kubish; James B Dunbar; Heather A Carlson; Stephen K Burley; W Patrick Walters; Rommie E Amaro; Victoria A Feher; Michael K Gilson
Journal:  J Comput Aided Mol Des       Date:  2016-09-30       Impact factor: 3.686

8.  Computational fragment-based binding site identification by ligand competitive saturation.

Authors:  Olgun Guvench; Alexander D MacKerell
Journal:  PLoS Comput Biol       Date:  2009-07-10       Impact factor: 4.475

9.  Structure-Based Design of a Novel SMYD3 Inhibitor that Bridges the SAM-and MEKK2-Binding Pockets.

Authors:  Glenn S Van Aller; Alan P Graves; Patricia A Elkins; William G Bonnette; Patrick J McDevitt; Francesca Zappacosta; Roland S Annan; Tony W Dean; Dai-Shi Su; Christopher L Carpenter; Helai P Mohammad; Ryan G Kruger
Journal:  Structure       Date:  2016-04-07       Impact factor: 5.006

10.  Structure-Based Optimization of Naphthyridones into Potent ATAD2 Bromodomain Inhibitors.

Authors:  Paul Bamborough; Chun-wa Chung; Rebecca C Furze; Paola Grandi; Anne-Marie Michon; Robert J Sheppard; Heather Barnett; Hawa Diallo; David P Dixon; Clement Douault; Emma J Jones; Bhumika Karamshi; Darren J Mitchell; Rab K Prinjha; Christina Rau; Robert J Watson; Thilo Werner; Emmanuel H Demont
Journal:  J Med Chem       Date:  2015-07-31       Impact factor: 7.446

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  3 in total

1.  Contemporary Computational Applications and Tools in Drug Discovery.

Authors:  Philip B Cox; Rishi Gupta
Journal:  ACS Med Chem Lett       Date:  2022-06-01       Impact factor: 4.632

2.  BRADSHAW: a system for automated molecular design.

Authors:  Darren V S Green; Stephen Pickett; Chris Luscombe; Stefan Senger; David Marcus; Jamel Meslamani; David Brett; Adam Powell; Jonathan Masson
Journal:  J Comput Aided Mol Des       Date:  2019-10-21       Impact factor: 3.686

3.  COVID-19: CADD to the rescue.

Authors:  Abdulmujeeb T Onawole; Kazeem O Sulaiman; Temitope U Kolapo; Fatimo O Akinde; Rukayat O Adegoke
Journal:  Virus Res       Date:  2020-05-15       Impact factor: 3.303

  3 in total

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