1
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Sternicki LM, Poulsen SA. Fragment-based drug discovery campaigns guided by native mass spectrometry. RSC Med Chem 2024; 15:2270-2285. [PMID: 39026646 PMCID: PMC11253872 DOI: 10.1039/d4md00273c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/19/2024] [Indexed: 07/20/2024] Open
Abstract
Native mass spectrometry (nMS) is well established as a biophysical technique for characterising biomolecules and their interactions with endogenous or investigational small molecule ligands. The high sensitivity mass measurements make nMS particularly well suited for applications in fragment-based drug discovery (FBDD) screening campaigns where the detection of weakly binding ligands to a target biomolecule is crucial. We first reviewed the contributions of nMS to guiding FBDD hit identification in 2013, providing a comprehensive perspective on the early adoption of nMS for fragment screening. Here we update this initial progress with a focus on contributions of nMS that have guided FBDD for the period 2014 until end of 2023. We highlight the development of nMS adoption in FBDD in the context of other biophysical fragment screening techniques. We also discuss the roadmap for increased adoption of nMS for fragment screening beyond soluble proteins, including for guiding the discovery of fragments supporting advances in PROTAC discovery, RNA-binding small molecules and covalent therapeutic drug discovery.
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Affiliation(s)
- Louise M Sternicki
- Griffith Institute for Drug Discovery, Griffith University Nathan Brisbane Queensland 4111 Australia
- ARC Centre for Fragment-Based Design Australia
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery, Griffith University Nathan Brisbane Queensland 4111 Australia
- ARC Centre for Fragment-Based Design Australia
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2
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Andrés Libreros-Zúñiga G, Pavão E Pavão D, de Morais Barroso V, Cristina de Moraes Roso Mesquita N, Fehelberg Pinto Braga S, Oliva G, Salgado Ferreira R, Ishida K, Vinicius Bertacine Dias M. Integration of biophysical and biological approaches to validate fragment-like compounds targeting l,d-transpeptidases from Mycobacterium tuberculosis. Bioorg Chem 2024; 142:106960. [PMID: 37944368 DOI: 10.1016/j.bioorg.2023.106960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/12/2023]
Abstract
Tuberculosis is one of the major causes of death worldwide; more than a million people die every year because of this infection. The constant emergency of Mycobacterium tuberculosis resistant strains against the most used treatments also contributes to the burden caused by this disease. Consequently, the development of new alternative therapies against this disease is constantly required. In recent years, only a few molecules have reached the market as new antituberculosis agents. The mycobacterial cell wall biosynthesis is for a longstanding considered an important target for drug development. Particularly, in M. tuberculosis, the peptidoglycan cross-links are predominantly formed by nonclassical bridges between the third residues of adjacent tetrapeptides. The responsible enzymes for these reactions are ld-transpeptidases (Ldts), for which M. tuberculosis has five paralogues. Although these enzymes are distinct from the penicillin-binding proteins (PBPs), they can also be inactivated by β-lactam antibiotics, but since M. tuberculosis has a chromosomal β-lactamase, most of the antibiotics of these classes can be degraded. Thus, to identify alternative scaffolds for the development of new antimicrobials against tuberculosis, we have integrated several fragment-based drug discovery techniques. Based on that, we identified and validated a number of small molecules that could be the starting point in the synthesis of more potent inhibitors against at least two Ldts from M. tuberculosis, LdtMt2 and LdtMt3. Eight identified molecules inhibited the Ldts activity in at least 20%, and three of them have antimycobacterial activity. The cell ultrastructural analysis suggested that one of the best compounds induced severe effects on the septum and cell wall morphologies, which corroborates our target-based approach to identifying new Ldts hits.
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Affiliation(s)
- Gerardo Andrés Libreros-Zúñiga
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil; IBILCE, São Paulo State University, Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo 15054-000, Brazil; Department of Microbiology, Faculty of Health, University of Valle, Calle 4B # 36-00, 760043, Cali, Valle del Cauca, Colombia.
| | - Danilo Pavão E Pavão
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil
| | - Vinicius de Morais Barroso
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil
| | | | - Saulo Fehelberg Pinto Braga
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais. Av. Antônio Carlos, 6627 - Belo Horizonte, 31270-901 Minas Gerais, Brazil
| | - Glaucius Oliva
- Institute of Physics of São Carlos, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, Brazil
| | - Rafaela Salgado Ferreira
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais. Av. Antônio Carlos, 6627 - Belo Horizonte, 31270-901 Minas Gerais, Brazil
| | - Kelly Ishida
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil
| | - Marcio Vinicius Bertacine Dias
- Department of Microbiology, Institute of Biomedical Science, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, São Paulo 05508-900, Brazil; IBILCE, São Paulo State University, Rua Cristóvão Colombo, 2265, São José do Rio Preto, São Paulo 15054-000, Brazil; Department of Chemistry, University of Warwick, Coventry CV4 7AL, England.
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3
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Roughley SD. Five Years of the KNIME Vernalis Cheminformatics Community Contribution. Curr Med Chem 2020; 27:6495-6522. [PMID: 30182834 PMCID: PMC8206202 DOI: 10.2174/0929867325666180904113616] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 07/19/2018] [Accepted: 07/19/2018] [Indexed: 11/22/2022]
Abstract
Since the official release as a KNIME Community Contribution in June 2013, the Vernalis KNIME nodes have increased from a single node (the 'PDB Connector' node) to around 126 nodes (November 2017; Version 1.12.0); furthermore, a number of nodes have been adopted into the core KNIME product. In this review, we provide a brief timeline of the development of the current public release and an overview of the current nodes. We will focus in more detail on three particular areas: nodes accessing publicly available information via web services, nodes providing cheminformatics functionality without recourse to a cheminformatics toolkit, and nodes using one of the cheminformatics toolkits present in KNIME. We will conclude with a number of case studies demonstrating the use of KNIME at Vernalis.
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Affiliation(s)
- Stephen D. Roughley
- Department of Chemistry & Cheminformatics, Vernalis Research Ltd, Granta Park, Great Abington, CambridgeCB21 6GB, UK
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4
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Tsopelas F, Tsantili-Kakoulidou A. Advances with weak affinity chromatography for fragment screening. Expert Opin Drug Discov 2019; 14:1125-1135. [DOI: 10.1080/17460441.2019.1648425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Fotios Tsopelas
- Laboratory of Inorganic and Analytical Chemistry, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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5
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Affiliation(s)
- Brian Raymer
- Medicine Design, Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Samit K. Bhattacharya
- Medicine Design, Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States
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6
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Abstract
Click chemistry has emerged as a powerful tool in our arsenal for unlocking new biology. This includes its utility in both chemical biology and drug discovery. An emerging application of click chemistry is in the development of biochemical assays for high-throughput screening to identify new chemical probes and drug leads. This Feature Article will discuss the advancements in click chemistry that were necessary for the development of a new class of biochemical assay, catalytic enzyme-linked click chemistry assay or cat-ELCCA. Inspired by enzyme immunoassays, cat-ELCCA was designed as a click chemistry-based amplification assay where bioorthogonally-tagged analytes and enzymes are used in place of the enzyme-linked secondary antibodies used in immunoassays. The result is a robust assay format with demonstrated applicability in several important areas of biology and drug discovery, including post-translational modifications, pre-microRNA maturation, and protein-protein and RNA-protein interactions. Through the use of cat-ELCCA and other related click chemistry-based assays, new chemical probes for interrogating promising drug targets have been discovered. These examples will be discussed, in addition to a future outlook on the impact of this approach in probe and drug discovery.
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Affiliation(s)
- Amanda L Garner
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 1600 Huron Parkway, NCRC B520, Ann Arbor, Michigan 48109, USA.
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7
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Song JM, Menon A, Mitchell DC, Johnson OT, Garner AL. High-Throughput Chemical Probing of Full-Length Protein-Protein Interactions. ACS COMBINATORIAL SCIENCE 2017; 19:763-769. [PMID: 29112379 PMCID: PMC5939945 DOI: 10.1021/acscombsci.7b00128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human biology is regulated by a complex network of protein-protein interactions (PPIs), and disruption of this network has been implicated in many diseases. However, the targeting of PPIs remains a challenging area for chemical probe and drug discovery. Although many methodologies have been put forth to facilitate these efforts, new technologies are still needed. Current biochemical assays for PPIs are typically limited to motif-domain and domain-domain interactions, and assays that will enable the screening of full-length protein systems, which are more biologically relevant, are sparse. To overcome this barrier, we have developed a new assay technology, "PPI catalytic enzyme-linked click chemistry assay" or PPI cat-ELCCA, which utilizes click chemistry to afford catalytic signal amplification. To validate this approach, we have applied PPI cat-ELCCA to the eIF4E-4E-BP1 and eIF4E-eIF4G PPIs, key regulators of cap-dependent mRNA translation. Using these examples, we have demonstrated that PPI cat-ELCCA is amenable to full-length proteins, large (>200 kDa) and small (∼12 kDa), and is readily adaptable to automated high-throughput screening. Thus, PPI cat-ELCCA represents a powerful new tool in the toolbox of assays available to scientists interested in the targeting of disease-relevant PPIs.
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Affiliation(s)
- James M. Song
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Arya Menon
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dylan C. Mitchell
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Oleta T. Johnson
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Amanda L. Garner
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
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8
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9
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Shipe WD, Sharik SS, Barrow JC, McGaughey GB, Theberge CR, Uslaner JM, Yan Y, Renger JJ, Smith SM, Coleman PJ, Cox CD. Discovery and Optimization of a Series of Pyrimidine-Based Phosphodiesterase 10A (PDE10A) Inhibitors through Fragment Screening, Structure-Based Design, and Parallel Synthesis. J Med Chem 2015; 58:7888-94. [PMID: 26378882 DOI: 10.1021/acs.jmedchem.5b00983] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- William D. Shipe
- Departments
of †Discovery Chemistry, ‡Chemistry Modeling
and Informatics, §Neuroscience, and ∥Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Steven S. Sharik
- Departments
of †Discovery Chemistry, ‡Chemistry Modeling
and Informatics, §Neuroscience, and ∥Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - James C. Barrow
- Departments
of †Discovery Chemistry, ‡Chemistry Modeling
and Informatics, §Neuroscience, and ∥Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Georgia B. McGaughey
- Departments
of †Discovery Chemistry, ‡Chemistry Modeling
and Informatics, §Neuroscience, and ∥Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Cory R. Theberge
- Departments
of †Discovery Chemistry, ‡Chemistry Modeling
and Informatics, §Neuroscience, and ∥Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Jason M. Uslaner
- Departments
of †Discovery Chemistry, ‡Chemistry Modeling
and Informatics, §Neuroscience, and ∥Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Youwei Yan
- Departments
of †Discovery Chemistry, ‡Chemistry Modeling
and Informatics, §Neuroscience, and ∥Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - John J. Renger
- Departments
of †Discovery Chemistry, ‡Chemistry Modeling
and Informatics, §Neuroscience, and ∥Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Sean M. Smith
- Departments
of †Discovery Chemistry, ‡Chemistry Modeling
and Informatics, §Neuroscience, and ∥Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Paul J. Coleman
- Departments
of †Discovery Chemistry, ‡Chemistry Modeling
and Informatics, §Neuroscience, and ∥Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, United States
| | - Christopher D. Cox
- Departments
of †Discovery Chemistry, ‡Chemistry Modeling
and Informatics, §Neuroscience, and ∥Structural Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, United States
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10
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Kopra K, Härmä H. Quenching resonance energy transfer (QRET): a single-label technique for inhibitor screening and interaction studies. N Biotechnol 2015; 32:575-80. [PMID: 25721971 DOI: 10.1016/j.nbt.2015.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 02/10/2015] [Accepted: 02/13/2015] [Indexed: 12/01/2022]
Abstract
The increased number of therapeutic targets has led to a growing need for screening methods enabling possible inhibitor compound selection. Information for new therapeutic targets has been found mostly from sequencing of the human genome but this knowledge cannot be directly converted into clinically relevant drug molecules. After target identification, the multistep drug development process takes many years and hundreds of millions of dollars are spent without certainty of the outcome. The first and the most critical step in the drug development process is hit selection. The optimal high throughput screening method should provide the highest possible number of true positive hits for further studies and lead discovery. The result should be achieved with low material consumption in a rapid and automated process. Radioactive label based methods are sensitive, but due to the problems arising from the radioactivity, luminescence-based methods have become increasingly popular in screening. In this review, the time-resolved luminescence based quenching resonance energy transfer (QRET) technique is discussed for primary screening.
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Affiliation(s)
- Kari Kopra
- Institute of Biomedicine, Department of Cell Biology and Anatomy, University of Turku, Kiinamyllynkatu 10, 3rd Floor, FI-20520 Turku, Finland.
| | - Harri Härmä
- Institute of Biomedicine, Department of Cell Biology and Anatomy, University of Turku, Kiinamyllynkatu 10, 3rd Floor, FI-20520 Turku, Finland
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11
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Chen H, Zhou X, Wang A, Zheng Y, Gao Y, Zhou J. Evolutions in fragment-based drug design: the deconstruction-reconstruction approach. Drug Discov Today 2015; 20:105-13. [PMID: 25263697 PMCID: PMC4305461 DOI: 10.1016/j.drudis.2014.09.015] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/18/2014] [Accepted: 09/17/2014] [Indexed: 12/21/2022]
Abstract
Recent advances in the understanding of molecular recognition and protein-ligand interactions have facilitated rapid development of potent and selective ligands for therapeutically relevant targets. Over the past two decades, a variety of useful approaches and emerging techniques have been developed to promote the identification and optimization of leads that have high potential for generating new therapeutic agents. Intriguingly, the innovation of a fragment-based drug design (FBDD) approach has enabled rapid and efficient progress in drug discovery. In this critical review, we focus on the construction of fragment libraries and the advantages and disadvantages of various fragment-based screening (FBS) for constructing such libraries. We also highlight the deconstruction-reconstruction strategy by utilizing privileged fragments of reported ligands.
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Affiliation(s)
- Haijun Chen
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, PR China; Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Xiaobin Zhou
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, PR China
| | - Ailan Wang
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, PR China
| | - Yunquan Zheng
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, PR China
| | - Yu Gao
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, PR China
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA.
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12
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Kutchukian PS, Wassermann AM, Lindvall MK, Wright SK, Ottl J, Jacob J, Scheufler C, Marzinzik A, Brooijmans N, Glick M. Large scale meta-analysis of fragment-based screening campaigns: privileged fragments and complementary technologies. ACTA ACUST UNITED AC 2014; 20:588-96. [PMID: 25550355 DOI: 10.1177/1087057114565080] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/02/2014] [Indexed: 11/15/2022]
Abstract
A first step in fragment-based drug discovery (FBDD) often entails a fragment-based screen (FBS) to identify fragment "hits." However, the integration of conflicting results from orthogonal screens remains a challenge. Here we present a meta-analysis of 35 fragment-based campaigns at Novartis, which employed a generic 1400-fragment library against diverse target families using various biophysical and biochemical techniques. By statistically interrogating the multidimensional FBS data, we sought to investigate three questions: (1) What makes a fragment amenable for FBS? (2) How do hits from different fragment screening technologies and target classes compare with each other? (3) What is the best way to pair FBS assay technologies? In doing so, we identified substructures that were privileged for specific target classes, as well as fragments that were privileged for authentic activity against many targets. We also revealed some of the discrepancies between technologies. Finally, we uncovered a simple rule of thumb in screening strategy: when choosing two technologies for a campaign, pairing a biochemical and biophysical screen tends to yield the greatest coverage of authentic hits.
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Affiliation(s)
- Peter S Kutchukian
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA Current address: Merck, Boston, MA, USA
| | | | - Mika K Lindvall
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - S Kirk Wright
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Johannes Ottl
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Jaison Jacob
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | - Natasja Brooijmans
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA Current address: Blueprint Medicines, Cambridge, MA, USA
| | - Meir Glick
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
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13
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Walker S, Meisenberg C, Bibby RA, Askwith T, Williams G, Rininsland FH, Pearl LH, Oliver AW, El-Khamisy S, Ward S, Atack JR. Development of an oligonucleotide-based fluorescence assay for the identification of tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors. Anal Biochem 2014; 454:17-22. [PMID: 24637157 PMCID: PMC4007590 DOI: 10.1016/j.ab.2014.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 02/03/2014] [Accepted: 03/06/2014] [Indexed: 01/17/2023]
Abstract
Topoisomerase 1 (TOP1) generates transient nicks in the DNA to relieve torsional stress encountered during the cellular processes of transcription, replication, and recombination. At the site of the nick there is a covalent linkage of TOP1 with DNA via a tyrosine residue. This reversible TOP1-cleavage complex intermediate can become trapped on DNA by TOP1 poisons such as camptothecin, or by collision with replication or transcription machinery, thereby causing protein-linked DNA single- or double-strand breaks and resulting in cell death. Tyrosyl-DNA phosphodiesterase 1 (TDP1) is a key enzyme involved in the repair of TOP1-associated DNA breaks via hydrolysis of 3'-phosphotyrosine bonds. Inhibition of TDP1 is therefore an attractive strategy for targeting cancer cells in conjunction with TOP1 poisons. Existing methods for monitoring the phosphodiesterase activity of TDP1 are generally gel based or of high cost. Here we report a novel, oligonucleotide-based fluorescence assay that is robust, sensitive, and suitable for high-throughput screening of both fragment and small compound libraries for the detection of TDP1 inhibitors. We further validated the assay using whole cell extracts, extending its potential application to determine of TDP1 activity in clinical samples from patients undergoing chemotherapy.
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Affiliation(s)
- Sarah Walker
- Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| | - Cornelia Meisenberg
- Wellcome Trust DNA Repair Group, Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Rachel A Bibby
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, University of Sussex, Science Park Road, Brighton BN1 9RQ, UK
| | - Trevor Askwith
- Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| | - Gareth Williams
- Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK
| | | | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, University of Sussex, Science Park Road, Brighton BN1 9RQ, UK
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, University of Sussex, Science Park Road, Brighton BN1 9RQ, UK
| | - Sherif El-Khamisy
- Wellcome Trust DNA Repair Group, Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK; Mammalian Genome Stability Group, Kreb's Institute, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK.
| | - Simon Ward
- Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK.
| | - John R Atack
- Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, UK.
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14
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Shang E, Yuan Y, Chen X, Liu Y, Pei J, Lai L. De Novo Design of Multitarget Ligands with an Iterative Fragment-Growing Strategy. J Chem Inf Model 2014; 54:1235-41. [DOI: 10.1021/ci500021v] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Erchang Shang
- BNLMS, State Key
Laboratory for Structural Chemistry of Unstable
and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yaxia Yuan
- Center
for Quantitative Biology, AAIS, Peking University, Beijing 100871, China
| | - Xinyi Chen
- BNLMS, State Key
Laboratory for Structural Chemistry of Unstable
and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ying Liu
- BNLMS, State Key
Laboratory for Structural Chemistry of Unstable
and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, AAIS, Peking University, Beijing 100871, China
| | - Jianfeng Pei
- Center
for Quantitative Biology, AAIS, Peking University, Beijing 100871, China
| | - Luhua Lai
- BNLMS, State Key
Laboratory for Structural Chemistry of Unstable
and Stable Species, College of Chemistry
and Molecular Engineering, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, AAIS, Peking University, Beijing 100871, China
- Peking-Tsinghua
Center for Life Sciences, Peking University, Beijing 100871, China
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15
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Beresini MH, Liu Y, Dawes TD, Clark KR, Orren L, Schmidt S, Turincio R, Jones SW, Rodriguez RA, Thana P, Hascall D, Gross DP, Skelton NJ. Small-Molecule Library Subset Screening as an Aid for Accelerating Lead Identification. ACTA ACUST UNITED AC 2014; 19:758-70. [DOI: 10.1177/1087057114522515] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 12/26/2013] [Indexed: 12/25/2022]
Abstract
Several small-compound library subsets (14,000 to 56,000) have been established to complement screening of a larger Genentech corporate library (~1,300,000). Two validation sets (~1% of the total library) containing compounds representative of the main library were chosen by selection of plates or individual compounds. Use of these subsets guided selection of assay configuration, validated assay reproducibility, and provided estimates of hit rates expected from our full library. A larger diversity subset representing the scaffold diversity of the full library (3.4% of the total) was designed for screening more challenging targets with limited reagent availability or low-throughput assays. Retrospective analysis of this subset showed hit rates similar to those of the main library while recovering a higher proportion of hit scaffolds. Finally, a property-restricted diversity set called the “in-between library” was established to identify ligand-efficient compounds of molecular size between those typically found in fragment and high-throughput screening libraries. It was screened at fivefold higher concentrations than the main library to facilitate identification of less potent yet ligand-efficient compounds. Taken together, this work underscores the value of generating multiple purpose-focused, diversity-based library subsets that are designed using computational approaches coupled with internal screening data analyses to accelerate the lead discovery process.
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Affiliation(s)
- Maureen H. Beresini
- Department of Biochemical & Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Yichin Liu
- Department of Biochemical & Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Timothy D. Dawes
- Department of Biochemical & Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Kevin R. Clark
- Department of Biochemical & Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Linda Orren
- Department of Biochemical & Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Stephen Schmidt
- Department of Biochemical & Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Rebecca Turincio
- Department of Biochemical & Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Steven W. Jones
- Department of Biochemical & Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Richard A. Rodriguez
- Department of Biochemical & Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Peter Thana
- Department of Biochemical & Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Daniel Hascall
- Department of Biochemical & Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Daniel P. Gross
- Department of Biochemical & Cellular Pharmacology, Genentech Inc, South San Francisco, CA, USA
| | - Nicholas J. Skelton
- Department of Discovery Chemistry, Genentech Inc, South San Francisco, CA, USA
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16
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Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery. Proc Natl Acad Sci U S A 2013; 110:12984-9. [PMID: 23872845 DOI: 10.1073/pnas.1304045110] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In fragment-based drug discovery, the weak affinities exhibited by fragments pose significant challenges for screening. Biophysical techniques are used to address this challenge, but there is no clear consensus on which cascade of methods is best suited to identify fragment hits that ultimately translate into bound X-ray structures and provide bona fide starting points for synthesis. We have benchmarked an integrated biophysical approach for fragment screening and validation against Mycobacterium tuberculosis pantothenate synthetase. A primary screen of 1,250 fragments library was performed by thermal shift, followed by secondary screen using one-dimensional NMR spectroscopy (water ligand observed gradient spectroscopy and saturation transfer difference binding experiments) and ultimate hit validation by isothermal titration calorimetry and X-ray crystallography. Our multibiophysical approach identified three distinct binding sites for fragments and laid a solid foundation for successful structure-based elaboration into potent inhibitors.
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17
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Holler TP, Evdokimov AG, Narasimhan L. Structural biology approaches to antibacterial drug discovery. Expert Opin Drug Discov 2013; 2:1085-101. [PMID: 23484874 DOI: 10.1517/17460441.2.8.1085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Antibacterial drug discovery has undertaken a major experiment in the 12 years since the first bacterial genomes were sequenced. Genome mining has identified hundreds of potential targets that have been distilled to a relatively small number of broad-spectrum targets ('low-hanging fruit') using the genetics tools of modern microbiology. Prosecuting these targets with high-throughput screens has led to a disappointingly small number of lead series that have mostly evaporated under closer scrutiny. In the meantime, multi-drug resistant pathogens are becoming a serious challenge in the clinic and the community and the number of pharmaceutical firms pursuing antibacterial discovery has declined. Filling the antibacterial development pipeline with novel chemical series is a significant challenge that will require the collaboration of scientists from many disciplines. Fortunately, advancements in the tools of structural biology and of in silico modeling are opening up new avenues of research that may help deal with the problems associated with discovering novel antibiotics.
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Affiliation(s)
- Tod P Holler
- Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor, MI 48105, USA +1 734 622 5954 ; +1 734 622 2963 ; Tod.Holler@pfizer. com
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18
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Fernández-Bachiller MI, Horatscheck A, Lisurek M, Rademann J. Alzheimer's disease: identification and development of β-secretase (BACE-1) binding fragments and inhibitors by dynamic ligation screening (DLS). ChemMedChem 2013; 8:1041-56. [PMID: 23757181 DOI: 10.1002/cmdc.201300078] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 04/25/2013] [Indexed: 11/12/2022]
Abstract
The application of dynamic ligation screening (DLS), a methodology for fragment-based drug discovery (FBDD), to the aspartic protease β-secretase (BACE-1) is reported. For this purpose, three new fluorescence resonance energy transfer (FRET) substrates were designed and synthesized. Their kinetic parameters (Vmax , KM , and kcat ) were determined and compared with a commercial substrate. Secondly, a peptide aldehyde was designed as a chemically reactive inhibitor (CRI) based on the Swedish mutation substrate sequence. Incubation of this CRI with the protease, a FRET substrate, and one amine per well taken from an amine library, which was assembled by a maximum common substructure (MCS) approach, revealed the fragment 3-(3-aminophenyl)-2H-chromen-2-one (1) to be a competitive BACE-1 inhibitor that enhanced the activity of the CRI. Irreversibly formed fragment combination products of 1 with the initial peptide sequence were active and confirmed the targeting of the active site through the ethane-1,2-diamine isostere. Finally, structure-assisted combination of fragment 1 with secondary fragments that target the S1 site in hit optimization yielded novel, entirely fragment-based BACE-1 inhibitors with up to 30-fold improved binding affinity. Interactions with the protein were explained by molecular modeling studies, which indicate that the new fragment combinations interact with the catalytic aspartic acid dyad, as well as with the adjacent binding sites required for potency.
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Affiliation(s)
- María Isabel Fernández-Bachiller
- Medicinal Chemistry Department, Leibniz Institut für Molekulare Pharmakologie (FMP) Campus Berlin-Buch, Robert-Rössle Str. 10, 13125 Berlin, Germany
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19
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Abstract
The SHAPES method is one of several fragment-based drug discovery methods developed in the last decade. Molecules containing drug-like fragments are screened using NMR methods to find weakly binding (0.1 μM to multi-mM) hits that are then transformed into potent, viable leads. This review analyzes ten years of SHAPES screens, in which potent leads were found for 70 - 80% of the targets screened, and discusses lessons learned about how best to apply fragment-based lead discovery in the pharmaceutical environment. Detailed examples of lead discovery and optimization for the kinases REDK and MK2 are given. Finally, future directions are considered and a strategy is proposed for increasing efficiency by coupling fragment-based screening with receptor-assisted inhibitor design (NMR-RAID).
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Affiliation(s)
- Christopher Lepre
- Vertex Pharmaceuticals, Inc., 130 Waverly Street, Cambridge, MA 02139, USA +1 617 444 6627 ;
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20
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Dolezal O, Doughty L, Hattarki MK, Fazio VJ, Caradoc-Davies TT, Newman J, Peat TS. Fragment Screening for the Modelling Community: SPR, ITC, and Crystallography. Aust J Chem 2013. [DOI: 10.1071/ch13302] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The SAMPL (Statistical Assessment of the Modelling of Proteins and Ligands) challenge brought together experimentalists and modellers in an effort to improve our understanding of chemical and biochemical systems so better modelling tools can be developed. The most recent challenge, SAMPL3, held at Stanford University in August 2011, was an attempt to improve the methods used to predict how small fragment compounds bind to proteins, and the protein chosen for this test was bovine trypsin. Surface plasmon resonance was used to screen 500 compounds from a Maybridge fragment library and these compounds were subsequently used to soak crystals of trypsin and the best hits were also characterised by isothermal titration calorimetry. We present methods used for the surface plasmon resonance and the isothermal titration calorimetry experiments, as well as the results for these methods and those compounds that were found in the crystal structures.
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21
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Francis CL, Kenny PW, Dolezal O, Saubern S, Kruger M, Savage GP, Peat TS, Ryan JH. Construction of the CSIRO Fragment Library. Aust J Chem 2013. [DOI: 10.1071/ch13325] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A fundamental component of a successful fragment screening program is a productive fragment library, one that delivers hit fragments with potential for pharmaceutical development. A proprietary fragment library was developed by identifying and extracting subsets of CSIRO’s Compound Collection using two complimentary approaches. Over time, the use of surface plasmon resonance as a front-line screening tool has enabled identification and exclusion of problematic compounds and led to a more reliable fragment screening library.
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22
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Lau WF, Withka JM, Hepworth D, Magee TV, Du YJ, Bakken GA, Miller MD, Hendsch ZS, Thanabal V, Kolodziej SA, Xing L, Hu Q, Narasimhan LS, Love R, Charlton ME, Hughes S, van Hoorn WP, Mills JE. Design of a multi-purpose fragment screening library using molecular complexity and orthogonal diversity metrics. J Comput Aided Mol Des 2011; 25:621-36. [PMID: 21604056 DOI: 10.1007/s10822-011-9434-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 05/06/2011] [Indexed: 11/26/2022]
Abstract
Fragment Based Drug Discovery (FBDD) continues to advance as an efficient and alternative screening paradigm for the identification and optimization of novel chemical matter. To enable FBDD across a wide range of pharmaceutical targets, a fragment screening library is required to be chemically diverse and synthetically expandable to enable critical decision making for chemical follow-up and assessing new target druggability. In this manuscript, the Pfizer fragment library design strategy which utilized multiple and orthogonal metrics to incorporate structure, pharmacophore and pharmacological space diversity is described. Appropriate measures of molecular complexity were also employed to maximize the probability of detection of fragment hits using a variety of biophysical and biochemical screening methods. In addition, structural integrity, purity, solubility, fragment and analog availability as well as cost were important considerations in the selection process. Preliminary analysis of primary screening results for 13 targets using NMR Saturation Transfer Difference (STD) indicates the identification of uM-mM hits and the uniqueness of hits at weak binding affinities for these targets.
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Affiliation(s)
- Wan F Lau
- Pfizer Global Research and Development (PGRD), Groton, CT 06340, USA.
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23
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Abstract
A successful fragment-based lead discovery (FBLD) campaign largely depends on the content of the fragment collection being screened. To design a successful fragment collection, several factors must be considered, including collection size, property filters, hit follow-up considerations, and screening methods. In this chapter, we will discuss each factor and how it was applied to the design and assembly of one or more fragment collections in a major pharmaceutical company setting. We will also present examples and statistics of screening results from such collections and how subsequent collections can be improved. Lastly, we will provide a summary comparison of selected fragment collections from literature.
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24
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Combining biophysical screening and X-ray crystallography for fragment-based drug discovery. Top Curr Chem (Cham) 2011; 317:115-43. [PMID: 21837555 DOI: 10.1007/128_2011_225] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Over the past decade, fragment-based drug discovery (FBDD) has gained importance for the generation of novel ideas to inspire synthetic chemistry. In order to identify small molecules that bind to a target protein, multiple approaches have been utilized by various groups in the pharmaceutical industry and by academic groups. The combination of fragment screening by biophysical methods and in particular with surface plasmon resonance technologies (SPR) together with the visualization of the binding properties by X-ray crystallography offers a number of benefits. Screening by SPR identifies ligands for a target protein as well as provides an assessment of the binding properties with respect to affinity, stoichiometry, and specificity of the interaction. Despite the huge technology advances of the past years, X-ray crystallography is still a resource-intensive technology, and SPR binding data provides excellent measures to prioritize X-ray experiments and consequently enable a better success rate in obtaining structural information. Information on the chemical structures of fragments binding to a protein can be used to perform similarity searches in compound libraries in order to establish structure-activity relationships as well as to explore particular scaffolds. At Roche we have applied this workflow for a number of targets and the experiences will be outlined in this review.
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25
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How to Avoid Rediscovering the Known. Methods Enzymol 2011. [DOI: 10.1016/b978-0-12-381274-2.00007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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26
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Computational medicinal chemistry in fragment-based drug discovery: what, how and when. Future Med Chem 2011; 3:95-134. [DOI: 10.4155/fmc.10.277] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The use of fragment-based drug discovery (FBDD) has increased in the last decade due to the encouraging results obtained to date. In this scenario, computational approaches, together with experimental information, play an important role to guide and speed up the process. By default, FBDD is generally considered as a constructive approach. However, such additive behavior is not always present, therefore, simple fragment maturation will not always deliver the expected results. In this review, computational approaches utilized in FBDD are reported together with real case studies, where applicability domains are exemplified, in order to analyze them, and then, maximize their performance and reliability. Thus, a proper use of these computational tools can minimize misleading conclusions, keeping the credit on FBDD strategy, as well as achieve higher impact in the drug-discovery process. FBDD goes one step beyond a simple constructive approach. A broad set of computational tools: docking, R group quantitative structure–activity relationship, fragmentation tools, fragments management tools, patents analysis and fragment-hopping, for example, can be utilized in FBDD, providing a clear positive impact if they are utilized in the proper scenario – what, how and when. An initial assessment of additive/non-additive behavior is a critical point to define the most convenient approach for fragments elaboration.
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27
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Abstract
Fragment-based drug discovery (FBDD) has emerged in the past decade as a powerful tool for discovering drug leads. The approach first identifies starting points: very small molecules (fragments) that are about half the size of typical drugs. These fragments are then expanded or linked together to generate drug leads. Although the origins of the technique date back some 30 years, it was only in the mid-1990s that experimental techniques became sufficiently sensitive and rapid for the concept to be become practical. Since that time, the field has exploded: FBDD has played a role in discovery of at least 18 drugs that have entered the clinic, and practitioners of FBDD can be found throughout the world in both academia and industry. Literally dozens of reviews have been published on various aspects of FBDD or on the field as a whole, as have three books (Jahnke and Erlanson, Fragment-based approaches in drug discovery, 2006; Zartler and Shapiro, Fragment-based drug discovery: a practical approach, 2008; Kuo, Fragment based drug design: tools, practical approaches, and examples, 2011). However, this chapter will assume that the reader is approaching the field with little prior knowledge. It will introduce some of the key concepts, set the stage for the chapters to follow, and demonstrate how X-ray crystallography plays a central role in fragment identification and advancement.
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28
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Boettcher A, Ruedisser S, Erbel P, Vinzenz D, Schiering N, Hassiepen U, Rigollier P, Mayr LM, Woelcke J. Fragment-Based Screening by Biochemical Assays. ACTA ACUST UNITED AC 2010; 15:1029-41. [DOI: 10.1177/1087057110380455] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fragment-based screening (FBS) has gained acceptance in the pharmaceutical industry as an attractive approach for the identification of new chemical starting points for drug discovery programs in addition to classical strategies such as high-throughput screening. There is the concern that screening of fragments at high µM concentrations in biochemical assays results in increased false-positive and false-negative rates. Here the authors systematically compare the data quality of FBS obtained by enzyme activity-based fluorescence intensity, fluorescence lifetime, and mobility shift assays with the data quality from surface plasmon resonance (SPR) and nuclear magnetic resonance (NMR) methods. The serine protease trypsin and the matrix metalloprotease MMP12 were selected as model systems. For both studies, 352 fragments were selected each. From the data generated, all 3 biochemical protease assay methods can be used for screening of fragments with low false-negative and low false-positive rates, comparable to those achieved with the SPR-based assays. It can also be concluded that only fragments with a solubility higher than the screening concentration determined by means of NMR should be used for FBS purposes. Extrapolated to 10,000 fragments, the biochemical assays speed up the primary FBS process by approximately a factor of 10 and reduce the protease consumption by approximately 10,000-fold compared to NMR protein observation experiments.
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Affiliation(s)
- Andreas Boettcher
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Simon Ruedisser
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Paulus Erbel
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Daniela Vinzenz
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Nikolaus Schiering
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Ulrich Hassiepen
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Pascal Rigollier
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Lorenz M. Mayr
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
| | - Julian Woelcke
- Novartis Institutes for BioMedical Research (NIBR), Expertise Platform Proteases (EPP), Novartis Pharma AG, Basel, Switzerland
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29
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Kobayashi M, Retra K, Figaroa F, Hollander JG, Ab E, Heetebrij RJ, Irth H, Siegal G. Target Immobilization as a Strategy for NMR-Based Fragment Screening. ACTA ACUST UNITED AC 2010; 15:978-89. [DOI: 10.1177/1087057110375614] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fragment-based drug discovery (FBDD) has become a widely accepted tool that is complementary to high-throughput screening (HTS) in developing small-molecule inhibitors of pharmaceutical targets. Because a fragment campaign can only be as successful as the hit matter found, it is critical that the first stage of the process be optimized. Here the authors compare the 3 most commonly used methods for hit discovery in FBDD: high concentration screening (HCS), solution ligand-observed nuclear magnetic resonance (NMR), and surface plasmon resonance (SPR). They selected the commonly used saturation transfer difference (STD) NMR spectroscopy and the proprietary target immobilized NMR screening (TINS) as representative of the array of possible NMR methods. Using a target typical of FBDD campaigns, the authors find that HCS and TINS are the most sensitive to weak interactions. They also find a good correlation between TINS and STD for tighter binding ligands, but the ability of STD to detect ligands with affinity weaker than 1 mM KD is limited. Similarly, they find that SPR detection is most suited to ligands that bind with KD better than 1 mM. However, the good correlation between SPR and potency in a bioassay makes this a good method for hit validation and characterization studies.
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Affiliation(s)
| | - Kim Retra
- Biomolecular Analysis and Spectroscopy, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije University Amsterdam, Amsterdam, The Netherlands
| | | | | | - Eiso Ab
- ZoBio B.V, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | | | - Hubertus Irth
- Biomolecular Analysis and Spectroscopy, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije University Amsterdam, Amsterdam, The Netherlands
| | - Gregg Siegal
- ZoBio B.V, Einsteinweg 55, 2333CC, Leiden, The Netherlands
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
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30
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Murray CW, Blundell TL. Structural biology in fragment-based drug design. Curr Opin Struct Biol 2010; 20:497-507. [DOI: 10.1016/j.sbi.2010.04.003] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 03/26/2010] [Accepted: 04/14/2010] [Indexed: 10/19/2022]
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31
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Godemann R, Madden J, Krämer J, Smith M, Fritz U, Hesterkamp T, Barker J, Höppner S, Hallett D, Cesura A, Ebneth A, Kemp J. Fragment-based discovery of BACE1 inhibitors using functional assays. Biochemistry 2009; 48:10743-51. [PMID: 19799414 DOI: 10.1021/bi901061a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Novel nonpeptidic inhibitors of beta-secretase (BACE1) have been discovered by employing a fragment-based biochemical screening approach. A diverse library of 20000 low-molecular weight compounds were screened and yielded 26 novel hits that were confirmed by biochemical and surface plasmon resonance secondary assays. We describe here fragment inhibitors cocrystallized with BACE1 in a flap open and flap closed conformation as determined by X-ray crystallography.
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32
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The multiple roles of computational chemistry in fragment-based drug design. J Comput Aided Mol Des 2009; 23:459-73. [PMID: 19533374 DOI: 10.1007/s10822-009-9284-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 05/18/2009] [Indexed: 10/20/2022]
Abstract
Fragment-based drug discovery (FBDD) represents a change in strategy from the screening of molecules with higher molecular weights and physical properties more akin to fully drug-like compounds, to the screening of smaller, less complex molecules. This is because it has been recognised that fragment hit molecules can be efficiently grown and optimised into leads, particularly after the binding mode to the target protein has been first determined by 3D structural elucidation, e.g. by NMR or X-ray crystallography. Several studies have shown that medicinal chemistry optimisation of an already drug-like hit or lead compound can result in a final compound with too high molecular weight and lipophilicity. The evolution of a lower molecular weight fragment hit therefore represents an attractive alternative approach to optimisation as it allows better control of compound properties. Computational chemistry can play an important role both prior to a fragment screen, in producing a target focussed fragment library, and post-screening in the evolution of a drug-like molecule from a fragment hit, both with and without the available fragment-target co-complex structure. We will review many of the current developments in the area and illustrate with some recent examples from successful FBDD discovery projects that we have conducted.
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33
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Blomberg N, Cosgrove DA, Kenny PW, Kolmodin K. Design of compound libraries for fragment screening. J Comput Aided Mol Des 2009; 23:513-25. [DOI: 10.1007/s10822-009-9264-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2008] [Accepted: 02/16/2009] [Indexed: 01/15/2023]
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34
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Hesterkamp T, Whittaker M. Fragment-based activity space: smaller is better. Curr Opin Chem Biol 2008; 12:260-8. [PMID: 18316043 DOI: 10.1016/j.cbpa.2008.02.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 01/29/2008] [Accepted: 02/02/2008] [Indexed: 12/18/2022]
Abstract
Fragment-based drug discovery has the potential to supersede traditional high throughput screening based drug discovery for molecular targets amenable to structure determination. This is because the chemical diversity coverage is better accomplished by a fragment collection of reasonable size than by larger HTS collections. Furthermore, fragments have the potential to be efficient target binders with higher probability than more elaborated drug-like compounds. The selection of the fragment screening technique is driven by sensitivity and throughput considerations, and we advocate in the present article the use of high concentration bioassays in conjunction with NMR-based hit confirmation. Subsequent ligand X-ray structure determination of the fragment ligand in complex with the target protein by co-crystallisation or crystal soaking can focus on confirmed binders.
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35
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Ciulli A, Abell C. Fragment-based approaches to enzyme inhibition. Curr Opin Biotechnol 2007; 18:489-96. [PMID: 17959370 DOI: 10.1016/j.copbio.2007.09.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 09/07/2007] [Accepted: 09/12/2007] [Indexed: 01/28/2023]
Abstract
Fragment-based approaches have provided a new paradigm for small-molecule drug discovery. The methodology is complementary to high-throughput screening approaches, starting from fragments of low molecular complexity and high ligand efficiency, and building up to more potent inhibitors. The approach, which depends heavily on a number of biophysical techniques, is now being taken up by more groups in both industry and academia. This article describes key aspects of the process and highlights recent developments and applications.
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Affiliation(s)
- Alessio Ciulli
- University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
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36
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Hajduk PJ, Greer J. A decade of fragment-based drug design: strategic advances and lessons learned. Nat Rev Drug Discov 2007; 6:211-9. [PMID: 17290284 DOI: 10.1038/nrd2220] [Citation(s) in RCA: 753] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Since the early 1990s, several technological and scientific advances - such as combinatorial chemistry, high-throughput screening and the sequencing of the human genome - have been heralded as remedies to the problems facing the pharmaceutical industry. The use of these technologies in some form is now well established at most pharmaceutical companies; however, the return on investment in terms of marketed products has not met expectations. Fragment-based drug design is another tool for drug discovery that has emerged in the past decade. Here, we describe the development and evolution of fragment-based drug design, analyse the role that this approach can have in combination with other discovery technologies and highlight the impact that fragment-based methods have made in progressing new medicines into the clinic.
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Affiliation(s)
- Philip J Hajduk
- Pharmaceutical Discovery Division, Abbott Laboratories, Abbott Park, Illinois 60064, USA.
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37
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Congreve M, Murray CW, Carr R, Rees DC. Chapter 28 Fragment-Based Lead Discovery. ANNUAL REPORTS IN MEDICINAL CHEMISTRY VOLUME 42 2007. [DOI: 10.1016/s0065-7743(07)42028-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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38
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Erlanson DA. Fragment-based lead discovery: a chemical update. Curr Opin Biotechnol 2006; 17:643-52. [PMID: 17084612 DOI: 10.1016/j.copbio.2006.10.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Revised: 09/10/2006] [Accepted: 10/20/2006] [Indexed: 11/24/2022]
Abstract
Fragment-based lead discovery constructs drug leads from small molecular fragments. In theory, this is a highly efficient method for drug discovery, and the technique has become enormously popular in the past few years. In this review, I describe how a variety of approaches in fragment-based lead discovery--including NMR, X-ray crystallography, mass spectrometry, functional screening, and in silico screening--have produced drug leads. Although the examples show that the technique can reliably generate potent molecules, there is still much work to be done to maintain the efficiency of molecules' binding affinities as fragments are linked, expanded, and otherwise improved.
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Affiliation(s)
- Daniel A Erlanson
- Sunesis Pharmaceuticals, Inc., 341 Oyster Point Boulevard, South San Francisco, CA 94080, USA.
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