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Kirsch P, Hartman AM, Hirsch AKH, Empting M. Concepts and Core Principles of Fragment-Based Drug Design. Molecules 2019; 24:molecules24234309. [PMID: 31779114 PMCID: PMC6930586 DOI: 10.3390/molecules24234309] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/11/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
In this review, a general introduction to fragment-based drug design and the underlying concepts is given. General considerations and methodologies ranging from library selection/construction over biophysical screening and evaluation methods to in-depth hit qualification and subsequent optimization strategies are discussed. These principles can be generally applied to most classes of drug targets. The examples given for fragment growing, merging, and linking strategies at the end of the review are set in the fields of enzyme-inhibitor design and macromolecule–macromolecule interaction inhibition. Building upon the foundation of fragment-based drug discovery (FBDD) and its methodologies, we also highlight a few new trends in FBDD.
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Affiliation(s)
- Philine Kirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123 Saarbrücken, Germany
| | - Alwin M. Hartman
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Anna K. H. Hirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Martin Empting
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization (DDOP), Campus E8.1, 66123 Saarbrücken, Germany; (P.K.); (A.M.H.); (A.K.H.H.)
- Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 66123 Saarbrücken, Germany
- Correspondence: ; Tel.: +49-681-988-062-031
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Ashenden SK. Screening Library Design. Methods Enzymol 2018; 610:73-96. [PMID: 30390806 DOI: 10.1016/bs.mie.2018.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Thanks to technological advances and a greater understanding of the biological and chemical natures of targets and related diseases, high-throughput screening (HTS) has been allowed to be faster, cheaper, and more accessible. Yet, despite these increased technologies and understandings, the frequency of novel and drugs are being approved each year has not being increasing over the years. 2017 was considered a "bumper" year with a total of 46 approved drugs, over double that of the previous year. However, it is thought that part of the problem that HTS has not lived up to expectations is because of the contents of current chemical libraries. Therefore, new methods to design screening libraries are of great interest.
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Affiliation(s)
- Stephanie Kay Ashenden
- Department of Chemistry, Cambridge University, Cambridge, United Kingdom; Discovery Sciences, IMed Biotech Unit, AstraZeneca R&D, Cambridge, United Kingdom.
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Santa Maria JP, Park Y, Yang L, Murgolo N, Altman MD, Zuck P, Adam G, Chamberlin C, Saradjian P, Dandliker P, Boshoff HIM, Barry CE, Garlisi C, Olsen DB, Young K, Glick M, Nickbarg E, Kutchukian PS. Linking High-Throughput Screens to Identify MoAs and Novel Inhibitors of Mycobacterium tuberculosis Dihydrofolate Reductase. ACS Chem Biol 2017; 12:2448-2456. [PMID: 28806050 DOI: 10.1021/acschembio.7b00468] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Though phenotypic and target-based high-throughput screening approaches have been employed to discover new antibiotics, the identification of promising therapeutic candidates remains challenging. Each approach provides different information, and understanding their results can provide hypotheses for a mechanism of action (MoA) and reveal actionable chemical matter. Here, we describe a framework for identifying efficacy targets of bioactive compounds. High throughput biophysical profiling against a broad range of targets coupled with machine learning was employed to identify chemical features with predicted efficacy targets for a given phenotypic screen. We validate the approach on data from a set of 55 000 compounds in 24 historical internal antibacterial phenotypic screens and 636 bacterial targets screened in high-throughput biophysical binding assays. Models were built to reveal the relationships between phenotype, target, and chemotype, which recapitulated mechanisms for known antibacterials. We also prospectively identified novel inhibitors of dihydrofolate reductase with nanomolar antibacterial efficacy against Mycobacterium tuberculosis. Molecular modeling provided structural insight into target-ligand interactions underlying selective killing activity toward mycobacteria over human cells.
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Affiliation(s)
- John P. Santa Maria
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Yumi Park
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Lihu Yang
- Department of Chemistry, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - Nicholas Murgolo
- Department of Information & Analytics, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - Michael D. Altman
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Paul Zuck
- Research Science, Merck Sharp & Dohme Corp., North Wales, Pennsylvania, United States
| | - Greg Adam
- Department of Pharmacology, Merck Sharp & Dohme Corp., North Wales, Pennsylvania, United States
| | - Chad Chamberlin
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter Saradjian
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter Dandliker
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Helena I. M. Boshoff
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Clifton E. Barry
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Charles Garlisi
- Department of Pharmacology, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - David B. Olsen
- Neglected Tropical Disease Discovery, Merck Sharp & Dohme Corp., West Point, Pennsylvania, United States
| | - Katherine Young
- Neglected Tropical Disease Discovery, Merck Sharp & Dohme Corp., West Point, Pennsylvania, United States
| | - Meir Glick
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Elliott Nickbarg
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter S. Kutchukian
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
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