Literature DB >> 30595456

How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals.

John D Westbrook1, Stephen K Burley2.   

Abstract

Discovery and development of 210 new molecular entities (NMEs; new drugs) approved by the US Food and Drug Administration 2010-2016 was facilitated by 3D structural information generated by structural biologists worldwide and distributed on an open-access basis by the PDB. The molecular targets for 94% of these NMEs are known. The PDB archive contains 5,914 structures containing one of the known targets and/or a new drug, providing structural coverage for 88% of the recently approved NMEs across all therapeutic areas. More than half of the 5,914 structures were published and made available by the PDB at no charge, with no restrictions on usage >10 years before drug approval. Citation analyses revealed that these 5,914 PDB structures significantly affected the very large body of publicly funded research reported in publications on the NME targets that motivated biopharmaceutical company investment in discovery and development programs that produced the NMEs.
Copyright © 2018 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  FAIR principles; PDB; RCSB PDB; Research Collaboratory for Structural Bioinformatics Protein Databank; Worldwide PDB; biopharmaceutical industry; data deposition; drugs; macromolecular crystallography; new molecular entities; open access; wwPDB

Mesh:

Substances:

Year:  2018        PMID: 30595456      PMCID: PMC7325526          DOI: 10.1016/j.str.2018.11.007

Source DB:  PubMed          Journal:  Structure        ISSN: 0969-2126            Impact factor:   5.006


  49 in total

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Review 2.  Leveraging SBDD in protein therapeutic development: antibody engineering.

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6.  Landscape of Innovation for Cardiovascular Pharmaceuticals: From Basic Science to New Molecular Entities.

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Journal:  Clin Ther       Date:  2017-06-23       Impact factor: 3.393

7.  Atomic positions in rhombohedral 2-zinc insulin crystals.

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8.  Crystal structure of the complex between programmed death-1 (PD-1) and its ligand PD-L2.

Authors:  Eszter Lázár-Molnár; Qingrong Yan; Erhu Cao; Udupi Ramagopal; Stanley G Nathenson; Steven C Almo
Journal:  Proc Natl Acad Sci U S A       Date:  2008-07-18       Impact factor: 11.205

9.  Structural basis for blocking PD-1-mediated immune suppression by therapeutic antibody pembrolizumab.

Authors:  Zhenkun Na; Siok Ping Yeo; Sakshibeedu R Bharath; Matthew W Bowler; Esra Balıkçı; Cheng-I Wang; Haiwei Song
Journal:  Cell Res       Date:  2016-06-21       Impact factor: 25.617

10.  BioMagResBank.

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Journal:  Nucleic Acids Res       Date:  2007-11-04       Impact factor: 16.971

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  27 in total

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Authors:  Simon H Connell; Sekazi K Mtingwa; Tabbetha Dobbins; Nkem Khumbah; Brian Masara; Edward P Mitchell; Lawrence Norris; Prosper Ngabonziza; Tshepo Ntsoane; Herman Winick
Journal:  Biophys Rev       Date:  2019-07-12

2.  The Protein Data Bank Archive.

Authors:  Sameer Velankar; Stephen K Burley; Genji Kurisu; Jeffrey C Hoch; John L Markley
Journal:  Methods Mol Biol       Date:  2021

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Authors:  Przemyslaw J Porebski; Grzegorz Bokota; Barat S Venkataramany; Wladek Minor
Journal:  Protein Sci       Date:  2019-10-25       Impact factor: 6.725

4.  RCSB Protein Data Bank: Enabling biomedical research and drug discovery.

Authors:  David S Goodsell; Christine Zardecki; Luigi Di Costanzo; Jose M Duarte; Brian P Hudson; Irina Persikova; Joan Segura; Chenghua Shao; Maria Voigt; John D Westbrook; Jasmine Y Young; Stephen K Burley
Journal:  Protein Sci       Date:  2019-11-29       Impact factor: 6.725

5.  Pre- and Post-publication Verification for Reproducible Data Mining in Macromolecular Crystallography.

Authors:  John R Helliwell
Journal:  Methods Mol Biol       Date:  2022

6.  Simplified quality assessment for small-molecule ligands in the Protein Data Bank.

Authors:  Chenghua Shao; John D Westbrook; Changpeng Lu; Charmi Bhikadiya; Ezra Peisach; Jasmine Y Young; Jose M Duarte; Robert Lowe; Sijian Wang; Yana Rose; Zukang Feng; Stephen K Burley
Journal:  Structure       Date:  2022-01-12       Impact factor: 5.006

Review 7.  Impact of the Protein Data Bank on antineoplastic approvals.

Authors:  John D Westbrook; Rose Soskind; Brian P Hudson; Stephen K Burley
Journal:  Drug Discov Today       Date:  2020-02-14       Impact factor: 7.851

8.  Deciphering collaborative sidechain motions in proteins during molecular dynamics simulations.

Authors:  Bruck Taddese; Antoine Garnier; Hervé Abdi; Daniel Henrion; Marie Chabbert
Journal:  Sci Rep       Date:  2020-09-28       Impact factor: 4.379

9.  Modernized uniform representation of carbohydrate molecules in the Protein Data Bank.

Authors:  Chenghua Shao; Zukang Feng; John D Westbrook; Ezra Peisach; John Berrisford; Yasuyo Ikegawa; Genji Kurisu; Sameer Velankar; Stephen K Burley; Jasmine Y Young
Journal:  Glycobiology       Date:  2021-09-20       Impact factor: 4.313

10.  PDB-101: Educational resources supporting molecular explorations through biology and medicine.

Authors:  Christine Zardecki; Shuchismita Dutta; David S Goodsell; Robert Lowe; Maria Voigt; Stephen K Burley
Journal:  Protein Sci       Date:  2021-10-18       Impact factor: 6.725

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