1
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Wu PP, Cao BR, Tian FY, Gao ZB. Development of SV2A Ligands for Epilepsy Treatment: A Review of Levetiracetam, Brivaracetam, and Padsevonil. Neurosci Bull 2024; 40:594-608. [PMID: 37897555 PMCID: PMC11127901 DOI: 10.1007/s12264-023-01138-2] [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: 03/27/2023] [Accepted: 08/16/2023] [Indexed: 10/30/2023] Open
Abstract
Epilepsy is a common neurological disorder that is primarily treated with antiseizure medications (ASMs). Although dozens of ASMs are available in the clinic, approximately 30% of epileptic patients have medically refractory seizures; other limitations in most traditional ASMs include poor tolerability and drug-drug interactions. Therefore, there is an urgent need to develop alternative ASMs. Levetiracetam (LEV) is a first-line ASM that is well tolerated, has promising efficacy, and has little drug-drug interaction. Although it is widely accepted that LEV acts through a unique therapeutic target synaptic vesicle protein (SV) 2A, the molecular basis of its action remains unknown. Even so, the next-generation SV2A ligands against epilepsy based on the structure of LEV have achieved clinical success. This review highlights the research and development (R&D) process of LEV and its analogs, brivaracetam and padsevonil, to provide ideas and experience for the R&D of novel ASMs.
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Affiliation(s)
- Peng-Peng Wu
- Center for Neurological and Psychiatric Research and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bi-Rong Cao
- Center for Neurological and Psychiatric Research and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fu-Yun Tian
- Center for Neurological and Psychiatric Research and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China.
| | - Zhao-Bing Gao
- Center for Neurological and Psychiatric Research and Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China.
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2
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León R, Soto-Delgado J, Montero E, Vargas M. Development of Computational Approaches with a Fragment-Based Drug Design Strategy: In Silico Hsp90 Inhibitors Discovery. Int J Mol Sci 2021; 22:ijms222413226. [PMID: 34948022 PMCID: PMC8706391 DOI: 10.3390/ijms222413226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 01/21/2023] Open
Abstract
A semi-exhaustive approach and a heuristic search algorithm use a fragment-based drug design (FBDD) strategy for designing new inhibitors in an in silico process. A deconstruction reconstruction process uses a set of known Hsp90 ligands for generating new ones. The deconstruction process consists of cutting off a known ligand in fragments. The reconstruction process consists of coupling fragments to develop a new set of ligands. For evaluating the approaches, we compare the binding energy of the new ligands with the known ligands.
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Affiliation(s)
- Roberto León
- Facultad de Ingeniería, Universidad Andres Bello, Viña del Mar 2531015, Chile; (E.M.); (M.V.)
- Correspondence: (R.L.); (J.S.-D.)
| | - Jorge Soto-Delgado
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Viña del Mar 2531015, Chile
- Correspondence: (R.L.); (J.S.-D.)
| | - Elizabeth Montero
- Facultad de Ingeniería, Universidad Andres Bello, Viña del Mar 2531015, Chile; (E.M.); (M.V.)
| | - Matías Vargas
- Facultad de Ingeniería, Universidad Andres Bello, Viña del Mar 2531015, Chile; (E.M.); (M.V.)
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3
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Zheng S, Lei Z, Ai H, Chen H, Deng D, Yang Y. Deep scaffold hopping with multimodal transformer neural networks. J Cheminform 2021; 13:87. [PMID: 34774103 PMCID: PMC8590293 DOI: 10.1186/s13321-021-00565-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/31/2021] [Indexed: 11/10/2022] Open
Abstract
Scaffold hopping is a central task of modern medicinal chemistry for rational drug design, which aims to design molecules of novel scaffolds sharing similar target biological activities toward known hit molecules. Traditionally, scaffolding hopping depends on searching databases of available compounds that can't exploit vast chemical space. In this study, we have re-formulated this task as a supervised molecule-to-molecule translation to generate hopped molecules novel in 2D structure but similar in 3D structure, as inspired by the fact that candidate compounds bind with their targets through 3D conformations. To efficiently train the model, we curated over 50 thousand pairs of molecules with increased bioactivity, similar 3D structure, but different 2D structure from public bioactivity database, which spanned 40 kinases commonly investigated by medicinal chemists. Moreover, we have designed a multimodal molecular transformer architecture by integrating molecular 3D conformer through a spatial graph neural network and protein sequence information through Transformer. The trained DeepHop model was shown able to generate around 70% molecules having improved bioactivity together with high 3D similarity but low 2D scaffold similarity to the template molecules. This ratio was 1.9 times higher than other state-of-the-art deep learning methods and rule- and virtual screening-based methods. Furthermore, we demonstrated that the model could generalize to new target proteins through fine-tuning with a small set of active compounds. Case studies have also shown the advantages and usefulness of DeepHop in practical scaffold hopping scenarios.
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Affiliation(s)
- Shuangjia Zheng
- School of Data and Computer Science, Sun Yat-Sen University, China, 132 East Circle at University City, Guangzhou, 510006, China
| | - Zengrong Lei
- Fermion Technology Co., Ltd, 1088 Newport East Road, Guangzhou, 510335, China
| | - Haitao Ai
- Fermion Technology Co., Ltd, 1088 Newport East Road, Guangzhou, 510335, China
| | - Hongming Chen
- Centre of Chemistry and Chemical Biology, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510530, China
| | - Daiguo Deng
- Fermion Technology Co., Ltd, 1088 Newport East Road, Guangzhou, 510335, China.
| | - Yuedong Yang
- School of Data and Computer Science, Sun Yat-Sen University, China, 132 East Circle at University City, Guangzhou, 510006, China.
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4
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Feder D, Mohd-Pahmi SH, Hussein WM, Guddat LW, McGeary RP, Schenk G. Rational Design of Potent Inhibitors of a Metallohydrolase Using a Fragment-Based Approach. ChemMedChem 2021; 16:3342-3359. [PMID: 34331400 DOI: 10.1002/cmdc.202100486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Indexed: 11/08/2022]
Abstract
Metallohydrolases form a large group of enzymes that have fundamental importance in a broad range of biological functions. Among them, the purple acid phosphatases (PAPs) have gained attention due to their crucial role in the acquisition and use of phosphate by plants and also as a promising target for novel treatments of bone-related disorders and cancer. To date, no crystal structure of a mammalian PAP with drug-like molecules bound near the active site is available. Herein, we used a fragment-based design approach using structures of a mammalian PAP in complex with the MaybridgeTM fragment CC063346, the amino acid L-glutamine and the buffer molecule HEPES, as well as various solvent molecules to guide the design of highly potent and efficient mammalian PAP inhibitors. These inhibitors have improved aqueous solubility when compared to the clinically most promising PAP inhibitors available to date. Furthermore, drug-like fragments bound in newly discovered binding sites mapped out additional scaffolds for further inhibitor discovery, as well as scaffolds for the design of inhibitors with novel modes of action.
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Affiliation(s)
- Daniel Feder
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Siti H Mohd-Pahmi
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Waleed M Hussein
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Luke W Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ross P McGeary
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.,Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
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5
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Wang J, Zheng S, Chen J, Yang Y. Meta Learning for Low-Resource Molecular Optimization. J Chem Inf Model 2021; 61:1627-1636. [PMID: 33729779 DOI: 10.1021/acs.jcim.0c01416] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The goal of molecular optimization (MO) is to discover molecules that acquire improved pharmaceutical properties over a known starting molecule. Despite many recent successes of new approaches for MO, these methods were typically developed for particular properties with rich annotated training examples. Thus, these approaches are difficult to implement in real scenes where only a small amount of pharmaceutical data is usually available due to the expense and significant effort required for the data collection. Here, we propose a new approach, Meta-MO, for molecular optimization with a handful of training samples based on the well-recognized first-order meta-learning algorithms. By using a set of meta tasks with rich training samples, Meta-MO trains a meta model through the meta-learning optimization and adapts the learned model to new low-resource MO tasks. Meta-MO was shown to consistently outperform several pretraining and multitask training procedures, providing an average improvement in the success rate of 4.3% on a large-scale bioactivity data set with diverse target variations. We also observed that Meta-MO resulted in the best performing models across fine-tuning sets with only dozens of samples. To the best of our knowledge, this is the first study to apply meta learning to MO tasks. More importantly, such a strategy could be further extended to many low-resource scenarios in real-world drug design.
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Affiliation(s)
- Jiahao Wang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Shuangjia Zheng
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China.,Galixir Technologies (Beijing) Limited, Beijing 100083, China
| | - Jianwen Chen
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuedong Yang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou 510006, China.,Key Laboratory of Machine Intelligence and Advanced Computing (MOE), Sun Yat-sen University, Guangzhou 510000, China
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6
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Yang Y, Zheng S, Su S, Zhao C, Xu J, Chen H. SyntaLinker: automatic fragment linking with deep conditional transformer neural networks. Chem Sci 2020; 11:8312-8322. [PMID: 34123096 PMCID: PMC8163338 DOI: 10.1039/d0sc03126g] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/21/2020] [Indexed: 12/18/2022] Open
Abstract
Linking fragments to generate a focused compound library for a specific drug target is one of the challenges in fragment-based drug design (FBDD). Hereby, we propose a new program named SyntaLinker, which is based on a syntactic pattern recognition approach using deep conditional transformer neural networks. This state-of-the-art transformer can link molecular fragments automatically by learning from the knowledge of structures in medicinal chemistry databases (e.g. ChEMBL database). Conventionally, linking molecular fragments was viewed as connecting substructures that were predefined by empirical rules. In SyntaLinker, however, the rules of linking fragments can be learned implicitly from known chemical structures by recognizing syntactic patterns embedded in SMILES notations. With deep conditional transformer neural networks, SyntaLinker can generate molecular structures based on a given pair of fragments and additional restrictions. Case studies have demonstrated the advantages and usefulness of SyntaLinker in FBDD.
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Affiliation(s)
- Yuyao Yang
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City Guangzhou 510006 China
- Center of Chemistry and Chemical Biology, Guangzhou Regenerative Medicine and Health Guangdong Laboratory Guangzhou 510530 China
| | - Shuangjia Zheng
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City Guangzhou 510006 China
| | - Shimin Su
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City Guangzhou 510006 China
- Center of Chemistry and Chemical Biology, Guangzhou Regenerative Medicine and Health Guangdong Laboratory Guangzhou 510530 China
| | - Chao Zhao
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City Guangzhou 510006 China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, 132 East Circle at University City Guangzhou 510006 China
| | - Hongming Chen
- Center of Chemistry and Chemical Biology, Guangzhou Regenerative Medicine and Health Guangdong Laboratory Guangzhou 510530 China
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7
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Hopkins BT, Bame E, Bell N, Bohnert T, Bowden-Verhoek JK, Bui M, Cancilla MT, Conlon P, Cullen P, Erlanson DA, Fan J, Fuchs-Knotts T, Hansen S, Heumann S, Jenkins TJ, Marcotte D, McDowell B, Mertsching E, Negrou E, Otipoby KL, Poreci U, Romanowski MJ, Scott D, Silvian L, Yang W, Zhong M. Optimization of novel reversible Bruton's tyrosine kinase inhibitors identified using Tethering-fragment-based screens. Bioorg Med Chem 2019; 27:2905-2913. [PMID: 31138459 DOI: 10.1016/j.bmc.2019.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 01/06/2023]
Abstract
Since the approval of ibrutinib for the treatment of B-cell malignancies in 2012, numerous clinical trials have been reported using covalent inhibitors to target Bruton's tyrosine kinase (BTK) for oncology indications. However, a formidable challenge for the pharmaceutical industry has been the identification of reversible, selective, potent molecules for inhibition of BTK. Herein, we report application of Tethering-fragment-based screens to identify low molecular weight fragments which were further optimized to improve on-target potency and ADME properties leading to the discovery of reversible, selective, potent BTK inhibitors suitable for pre-clinical proof-of-concept studies.
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Affiliation(s)
- Brian T Hopkins
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States.
| | - Eris Bame
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Noah Bell
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Tonika Bohnert
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | | | - Minna Bui
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Mark T Cancilla
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Patrick Conlon
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Patrick Cullen
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Daniel A Erlanson
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Junfa Fan
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Tarra Fuchs-Knotts
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Stig Hansen
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Stacey Heumann
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Tracy J Jenkins
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Douglas Marcotte
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Bob McDowell
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | | | - Ella Negrou
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Kevin L Otipoby
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Urjana Poreci
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Michael J Romanowski
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Daniel Scott
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Laura Silvian
- Biogen Inc., 225 Binney Street, Cambridge, MA 02142, United States
| | - Wenjin Yang
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
| | - Min Zhong
- Sunesis Pharmaceuticals, Inc., 395 Oyster Point Boulevard, South San Francisco, CA 94080, United States
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8
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Molecular Insights into the Fungus-Specific Serine/Threonine Protein Phosphatase Z1 in Candida albicans. mBio 2016; 7:mBio.00872-16. [PMID: 27578752 PMCID: PMC4999541 DOI: 10.1128/mbio.00872-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The opportunistic pathogen Candida is one of the most common causes of nosocomial bloodstream infections. Because candidemia is associated with high mortality rates and because the incidences of multidrug-resistant Candida are increasing, efforts to identify novel targets for the development of potent antifungals are warranted. Here, we describe the structure and function of the first member of a family of protein phosphatases that is specific to fungi, protein phosphatase Z1 (PPZ1) from Candida albicans We show that PPZ1 not only is active but also is as susceptible to inhibition by the cyclic peptide inhibitor microcystin-LR as its most similar human homolog, protein phosphatase 1α (PP1α [GLC7 in the yeast Saccharomyces cerevisiae]). Unexpectedly, we also discovered that, despite its 66% sequence identity to PP1α, the catalytic domain of PPZ1 contains novel structural elements that are not present in PP1α. We then used activity and pulldown assays to show that these structural differences block a large subset of PP1/GLC7 regulatory proteins from effectively binding PPZ1, demonstrating that PPZ1 does not compete with GLC7 for its regulatory proteins. Equally important, these unique structural elements provide new pockets suitable for the development of PPZ1-specific inhibitors. Together, these studies not only reveal why PPZ1 does not negatively impact GLC7 activity in vivo but also demonstrate that the family of fungus-specific phosphatases-especially PPZ1 from C. albicans-are highly suitable targets for the development of novel drugs that specifically target C. albicans without cross-reacting with human phosphatases. IMPORTANCE Candida albicans is a medically important human pathogen that is the most common cause of fungal infections in humans. In particular, approximately 46,000 cases of health care-associated candidiasis occur each year in the United States. Because these infections are associated with high mortality rates and because multiple species of Candida are becoming increasingly resistant to antifungals, there are increasing efforts to identify novel targets that are essential for C. albicans virulence. Here we use structural and biochemical approaches to elucidate how a member of a fungus-specific family of enzymes, serine/threonine phosphatase PPZ1, functions in C. albicans We discovered multiple unique features of PPZ1 that explain why it does not cross-react with, and in turn compete for, PP1-specific regulators, a long-standing question in the field. Most importantly, however, these unique features identified PPZ1 as a potential target for the development of novel antifungal therapeutics that will provide new, safe, and potent treatments for candidiasis in humans.
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9
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Mignani S, Huber S, Tomás H, Rodrigues J, Majoral JP. Compound high-quality criteria: a new vision to guide the development of drugs, current situation. Drug Discov Today 2016; 21:573-84. [PMID: 26802700 DOI: 10.1016/j.drudis.2016.01.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 02/08/2023]
Abstract
For several decades, the pharmaceutical industry has suffered due to major issues such as reductions of the number of FDA approved drugs and biologics. Several analyses have been highlighted that the 'druglikeness' is one of the strategies to improve succeed rates of screening such as, for instance, high-throughput screening (HTS), and then hits (as starting point), leads and clinical candidates. It is clear that the improvement of compound quality accelerates the drug discovery projects. The monitoring of several indices to avoid 'molecular obesity' (ADMET problems) of final drugs from good-quality 'low-fat' starting points represents today a powerful strategy of optimization process. The development of the new guides to find drugs highlighting attempts at improving the attrition rate from hits to final medicines by focusing on how to improve the druggability of hits, leads and drugs during the drug discovery process represents a key approach to design next better generation of medicines.
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Affiliation(s)
- Serge Mignani
- Université Paris Descartes, PRES Sorbonne Paris Cité, CNRS UMR 860, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologique, 45, rue des Saints Pères, 75006 Paris, France.
| | - Scot Huber
- SCYNEXIS, Inc., P.O. Box 12878, Research Triangle Park, NC 27709, USA
| | - Helena Tomás
- CQM - Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus Universitário da Penteada, 9000-390 Funchal, Portugal
| | - João Rodrigues
- CQM - Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus Universitário da Penteada, 9000-390 Funchal, Portugal.
| | - Jean-Pierre Majoral
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France; Université de Toulouse, UPS, INPT, 31077 Toulouse Cedex 4, France.
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10
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The Role of Biotin in Bacterial Physiology and Virulence: a Novel Antibiotic Target for
Mycobacterium tuberculosis. Microbiol Spectr 2016; 4. [DOI: 10.1128/microbiolspec.vmbf-0008-2015] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
Biotin is an essential cofactor for enzymes present in key metabolic pathways such as fatty acid biosynthesis, replenishment of the tricarboxylic acid cycle, and amino acid metabolism. Biotin is synthesized
de novo
in microorganisms, plants, and fungi, but this metabolic activity is absent in mammals, making biotin biosynthesis an attractive target for antibiotic discovery. In particular, biotin biosynthesis plays important metabolic roles as the sole source of biotin in all stages of the
Mycobacterium tuberculosis
life cycle due to the lack of a transporter for scavenging exogenous biotin. Biotin is intimately associated with lipid synthesis where the products form key components of the mycobacterial cell membrane that are critical for bacterial survival and pathogenesis. In this review we discuss the central role of biotin in bacterial physiology and highlight studies that demonstrate the importance of its biosynthesis for virulence. The structural biology of the known biotin synthetic enzymes is described alongside studies using structure-guided design, phenotypic screening, and fragment-based approaches to drug discovery as routes to new antituberculosis agents.
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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: 80] [Impact Index Per Article: 8.9] [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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Catalytic activation of pre-substrates via dynamic fragment assembly on protein templates. Nat Commun 2014; 5:5170. [PMID: 25403979 DOI: 10.1038/ncomms6170] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 09/08/2014] [Indexed: 11/09/2022] Open
Abstract
Sensitive detection of small molecule fragments binding to defined sites of biomacromolecules is still a considerable challenge. Here we demonstrate that protein-binding fragments are able to induce enzymatic reactions on the protein surface via dynamic fragment ligation. Fragments binding to the S1 pocket of serine proteases containing a nitrogen, oxygen or sulphur nucleophile are found to activate electrophilic pre-substrates through a reversible, covalent ligation reaction. The dynamic ligation reaction positions the pre-substrate molecule at the active site of the protein thereby inducing its enzymatic cleavage. Catalytic activation of pre-substrates is confirmed by fluorescence spectroscopy and by high-performance liquid chromatography. The approach is investigated with 3 pre-substrates and 14 protein-binding fragments and the specific activation and the templating effect exerted by the enzyme is quantified for each protease-fragment-pre-substrate combination. The described approach enables the site-specific identification of protein-binding fragments, the functional characterization of enzymatic sites and the quantitative analysis of protein template-assisted ligation reactions.
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Abstract
More research effort needs to be invested in antimicrobial drug development to address the increasing threat of multidrug-resistant organisms. The enzyme DHPS has been a validated drug target for over 70 years as the target for the highly successful sulfa drugs. The use of sulfa drugs has been compromised by the widespread presence of resistant organisms and the adverse side effects associated with their use. Despite the large amount of structural information available for DHPS, few recent publications address the possibility of using this knowledge for novel drug design. This article reviews the relevant papers and patents that report promising new small-molecule inhibitors of DHPS, and discuss these data in light of new insights into the DHPS catalytic mechanism and recently determined crystal structures of DHPS bound to potent small-molecule inhibitors. This new functional understanding confirms that DHPS deserves further consideration as an antimicrobial drug target.
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14
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Hanessian S, Babonneau V, Boyer N, Mannoury la Cour C, Millan MJ, De Nanteuil G. Design and synthesis of potential dual NK(1)/NK(3) receptor antagonists. Bioorg Med Chem Lett 2013; 24:510-4. [PMID: 24374277 DOI: 10.1016/j.bmcl.2013.12.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 12/04/2013] [Accepted: 12/09/2013] [Indexed: 11/17/2022]
Abstract
The tachykinin NK1 and NK3 receptors are a novel drug target for schizophrenia in order to treat not only the positive and cognitive symptoms, but also the associated co-morbid depression and sleep disturbances associated with the disease. A novel class of peptidomimetic derivatives based on a versatile phenylglycine central core was synthesized and tested in vitro as dual NK1/NK3 receptor antagonists. From this series emerged compounds with good NK1 receptor affinity, although only modest dual NK1/NK3 receptor affinity was observed with one of these analogs.
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Affiliation(s)
- Stephen Hanessian
- Department of Chemistry, Université de Montréal, PO Box 6128, Station Centre-Ville, Montréal, Que. H3C 3J7, Canada.
| | - Vincent Babonneau
- Department of Chemistry, Université de Montréal, PO Box 6128, Station Centre-Ville, Montréal, Que. H3C 3J7, Canada
| | - Nicolas Boyer
- Department of Chemistry, Université de Montréal, PO Box 6128, Station Centre-Ville, Montréal, Que. H3C 3J7, Canada
| | - Clotilde Mannoury la Cour
- Department of Psychopharmacology, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy/Seine, France
| | - Mark J Millan
- Department of Psychopharmacology, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy/Seine, France
| | - Guillaume De Nanteuil
- Neuroscience Chemistry Research Unit, Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
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15
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Yuan H, Tai W, Hu S, Liu H, Zhang Y, Yao S, Ran T, Lu S, Ke Z, Xiong X, Xu J, Chen Y, Lu T. Fragment-based strategy for structural optimization in combination with 3D-QSAR. J Comput Aided Mol Des 2013; 27:897-915. [DOI: 10.1007/s10822-013-9687-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 10/24/2013] [Indexed: 12/14/2022]
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Kell DB. Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it. FEBS J 2013; 280:5957-80. [PMID: 23552054 DOI: 10.1111/febs.12268] [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] [Received: 02/03/2013] [Revised: 03/20/2013] [Accepted: 03/26/2013] [Indexed: 12/16/2022]
Abstract
Despite the sequencing of the human genome, the rate of innovative and successful drug discovery in the pharmaceutical industry has continued to decrease. Leaving aside regulatory matters, the fundamental and interlinked intellectual issues proposed to be largely responsible for this are: (a) the move from 'function-first' to 'target-first' methods of screening and drug discovery; (b) the belief that successful drugs should and do interact solely with single, individual targets, despite natural evolution's selection for biochemical networks that are robust to individual parameter changes; (c) an over-reliance on the rule-of-5 to constrain biophysical and chemical properties of drug libraries; (d) the general abandoning of natural products that do not obey the rule-of-5; (e) an incorrect belief that drugs diffuse passively into (and presumably out of) cells across the bilayers portions of membranes, according to their lipophilicity; (f) a widespread failure to recognize the overwhelmingly important role of proteinaceous transporters, as well as their expression profiles, in determining drug distribution in and between different tissues and individual patients; and (g) the general failure to use engineering principles to model biology in parallel with performing 'wet' experiments, such that 'what if?' experiments can be performed in silico to assess the likely success of any strategy. These facts/ideas are illustrated with a reasonably extensive literature review. Success in turning round drug discovery consequently requires: (a) decent systems biology models of human biochemical networks; (b) the use of these (iteratively with experiments) to model how drugs need to interact with multiple targets to have substantive effects on the phenotype; (c) the adoption of polypharmacology and/or cocktails of drugs as a desirable goal in itself; (d) the incorporation of drug transporters into systems biology models, en route to full and multiscale systems biology models that incorporate drug absorption, distribution, metabolism and excretion; (e) a return to 'function-first' or phenotypic screening; and (f) novel methods for inferring modes of action by measuring the properties on system variables at all levels of the 'omes. Such a strategy offers the opportunity of achieving a state where we can hope to predict biological processes and the effect of pharmaceutical agents upon them. Consequently, this should both lower attrition rates and raise the rates of discovery of effective drugs substantially.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry, The University of Manchester, UK; Manchester Institute of Biotechnology, The University of Manchester, UK
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Deng X, Kong LM, Zhao Y, He J, Peng LY, Li Y, Zhao QS. Exploring of drug leads from diversity-oriented Michael-acceptor library derived from natural products. NATURAL PRODUCTS AND BIOPROSPECTING 2012. [PMCID: PMC4131632 DOI: 10.1007/s13659-012-0071-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Xu Deng
- />State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
- />Graduate University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Ling-Mei Kong
- />State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
- />Graduate University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yu Zhao
- />State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Juan He
- />State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Li-Yan Peng
- />State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Yan Li
- />State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Qin-Shi Zhao
- />State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
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Cardoso R, Love R, Nilsson CL, Bergqvist S, Nowlin D, Yan J, Liu KKC, Zhu J, Chen P, Deng YL, Dyson HJ, Greig MJ, Brooun A. Identification of Cys255 in HIF-1α as a novel site for development of covalent inhibitors of HIF-1α/ARNT PasB domain protein-protein interaction. Protein Sci 2012; 21:1885-96. [PMID: 23033253 DOI: 10.1002/pro.2172] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 09/26/2012] [Accepted: 09/27/2012] [Indexed: 12/11/2022]
Abstract
The heterodimer HIF-1α (hypoxia inducible factor)/HIF-β (also known as ARNT-aryl hydrocarbon nuclear translocator) is a key mediator of cellular response to hypoxia. The interaction between these monomer units can be modified by the action of small molecules in the binding interface between their C-terminal heterodimerization (PasB) domains. Taking advantage of the presence of several cysteine residues located in the allosteric cavity of HIF-1α PasB domain, we applied a cysteine-based reactomics "hotspot identification" strategy to locate regions of HIF-1α PasB domain critical for its interaction with ARNT. COMPOUND 5 was identified using a mass spectrometry-based primary screening strategy and was shown to react specifically with Cys255 of the HIF-1α PasB domain. Biophysical characterization of the interaction between PasB domains of HIF-1α and ARNT revealed that covalent binding of COMPOUND 5 to Cys255 reduced binding affinity between HIF-1α and ARNT PasB domains approximately 10-fold. Detailed NMR structural analysis of HIF-1α-PasB-COMPOUND 5 conjugate showed significant local conformation changes in the HIF-1α associated with key residues involved in the HIF-1α/ARNT PasB domain interaction as revealed by the crystal structure of the HIF-1α/ARNT PasB heterodimer. Our screening strategy could be applied to other targets to identify pockets surrounding reactive cysteines suitable for development of small molecule modulators of protein function.
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Affiliation(s)
- Rosa Cardoso
- Oncology Chemistry, Worldwide Research and Development, Pfizer Inc., San Diego, California 92121, USA
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Feder D, Hussein WM, Clayton DJ, Kan MW, Schenk G, McGeary RP, Guddat LW. Identification of Purple Acid Phosphatase Inhibitors by Fragment-Based Screening: Promising New Leads for Osteoporosis Therapeutics. Chem Biol Drug Des 2012; 80:665-74. [DOI: 10.1111/cbdd.12001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Salon JA, Lodowski DT, Palczewski K. The significance of G protein-coupled receptor crystallography for drug discovery. Pharmacol Rev 2012; 63:901-37. [PMID: 21969326 DOI: 10.1124/pr.110.003350] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Crucial as molecular sensors for many vital physiological processes, seven-transmembrane domain G protein-coupled receptors (GPCRs) comprise the largest family of proteins targeted by drug discovery. Together with structures of the prototypical GPCR rhodopsin, solved structures of other liganded GPCRs promise to provide insights into the structural basis of the superfamily's biochemical functions and assist in the development of new therapeutic modalities and drugs. One of the greatest technical and theoretical challenges to elucidating and exploiting structure-function relationships in these systems is the emerging concept of GPCR conformational flexibility and its cause-effect relationship for receptor-receptor and receptor-effector interactions. Such conformational changes can be subtle and triggered by relatively small binding energy effects, leading to full or partial efficacy in the activation or inactivation of the receptor system at large. Pharmacological dogma generally dictates that these changes manifest themselves through kinetic modulation of the receptor's G protein partners. Atomic resolution information derived from increasingly available receptor structures provides an entrée to the understanding of these events and practically applying it to drug design. Supported by structure-activity relationship information arising from empirical screening, a unified structural model of GPCR activation/inactivation promises to both accelerate drug discovery in this field and improve our fundamental understanding of structure-based drug design in general. This review discusses fundamental problems that persist in drug design and GPCR structural determination.
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Affiliation(s)
- John A Salon
- Department of Molecular Structure, Amgen Incorporated, Thousand Oaks, California, USA
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21
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Ward RA, Brassington C, Breeze AL, Caputo A, Critchlow S, Davies G, Goodwin L, Hassall G, Greenwood R, Holdgate GA, Mrosek M, Norman RA, Pearson S, Tart J, Tucker JA, Vogtherr M, Whittaker D, Wingfield J, Winter J, Hudson K. Design and synthesis of novel lactate dehydrogenase A inhibitors by fragment-based lead generation. J Med Chem 2012; 55:3285-306. [PMID: 22417091 DOI: 10.1021/jm201734r] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Lactate dehydrogenase A (LDHA) catalyzes the conversion of pyruvate to lactate, utilizing NADH as a cofactor. It has been identified as a potential therapeutic target in the area of cancer metabolism. In this manuscript we report our progress using fragment-based lead generation (FBLG), assisted by X-ray crystallography to develop small molecule LDHA inhibitors. Fragment hits were identified through NMR and SPR screening and optimized into lead compounds with nanomolar binding affinities via fragment linking. Also reported is their modification into cellular active compounds suitable for target validation work.
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Affiliation(s)
- Richard A Ward
- Oncology and Discovery Sciences iMEDs, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK.
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22
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Cheng Y, Judd TC, Bartberger MD, Brown J, Chen K, Fremeau RT, Hickman D, Hitchcock SA, Jordan B, Li V, Lopez P, Louie SW, Luo Y, Michelsen K, Nixey T, Powers TS, Rattan C, Sickmier EA, St Jean DJ, Wahl RC, Wen PH, Wood S. From fragment screening to in vivo efficacy: optimization of a series of 2-aminoquinolines as potent inhibitors of beta-site amyloid precursor protein cleaving enzyme 1 (BACE1). J Med Chem 2011; 54:5836-57. [PMID: 21707077 DOI: 10.1021/jm200544q] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using fragment-based screening of a focused fragment library, 2-aminoquinoline 1 was identified as an initial hit for BACE1. Further SAR development was supported by X-ray structures of BACE1 cocrystallized with various ligands and molecular modeling studies to expedite the discovery of potent compounds. These strategies enabled us to integrate the C-3 side chain on 2-aminoquinoline 1 extending deep into the P2' binding pocket of BACE1 and enhancing the ligand's potency. We were able to improve the BACE1 potency to subnanomolar range, over 10(6)-fold more potent than the initial hit (900 μM). Further elaboration of the physical properties of the lead compounds to those more consistent with good blood-brain barrier permeability led to inhibitors with greatly improved cellular activity and permeability. Compound 59 showed an IC(50) value of 11 nM on BACE1 and cellular activity of 80 nM. This compound was advanced into rat pharmacokinetic and pharmacodynamic studies and demonstrated significant reduction of Aβ levels in cerebrospinal fluid (CSF).
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Affiliation(s)
- Yuan Cheng
- Chemistry Research and Discovery, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320, USA.
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23
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24
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Johnson S, Barile E, Farina B, Purves A, Wei J, Chen LH, Shiryaev S, Zhang Z, Rodionova I, Agrawal A, Cohen SM, Osterman A, Strongin A, Pellecchia M. Targeting metalloproteins by fragment-based lead discovery. Chem Biol Drug Des 2011; 78:211-23. [PMID: 21564556 DOI: 10.1111/j.1747-0285.2011.01136.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
It has been estimated that nearly one-third of functional proteins contain a metal ion. These constitute a wide variety of possible drug targets including metalloproteinases, dehydrogenases, oxidoreductases, hydrolases, deacetylases, or many others in which the metal ion is either of catalytic or of structural nature. Despite the predominant role of a metal ion in so many classes of drug targets, current high-throughput screening techniques do not usually produce viable hits against these proteins, likely due to the lack of proper metal-binding pharmacophores in the current screening libraries. Herein, we describe a novel fragment-based drug discovery approach using a metal-targeting fragment library that is based on a variety of distinct classes of metal-binding groups designed to reliably anchor the fragments at the target's metal ions. We show that the approach can effectively identify novel, potent and selective agents that can be readily developed into metalloprotein-targeted therapeutics.
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Affiliation(s)
- Sherida Johnson
- Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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25
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Wilson CGM, Arkin MR. Small-molecule inhibitors of IL-2/IL-2R: lessons learned and applied. Curr Top Microbiol Immunol 2011; 348:25-59. [PMID: 20703966 DOI: 10.1007/82_2010_93] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The IL-2:IL-2R protein-protein interaction is of central importance to both healthy and diseased immune responses, and is one of the earliest examples of successful small-molecule inhibitor discovery against this target class. Drug-like inhibitors of IL-2 have been identified through a combination of fragment discovery, structure-based design, and medicinal chemistry; this discovery approach illustrates the importance of using a diverse range of complementary screening methods and analytical tools to achieve a comprehensive understanding of molecular recognition. The IL-2 story also provides insight into the dynamic nature of protein-protein interaction surfaces, their potential druggability, and the physical and chemical properties of effective small-molecule ligands. These lessons, from IL-2 and similar discovery programs, underscore an increasing awareness of the principles governing the development of drugs for protein-protein interactions.
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Affiliation(s)
- C G M Wilson
- Small Molecule Discovery Center, University of California, San Francisco, CA 94158, USA
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26
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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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27
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Huang D, Caflisch A. Fragment-Based Approaches in Virtual Screening. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1002/9783527633326.ch17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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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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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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Goettig P, Magdolen V, Brandstetter H. Natural and synthetic inhibitors of kallikrein-related peptidases (KLKs). Biochimie 2010; 92:1546-67. [PMID: 20615447 PMCID: PMC3014083 DOI: 10.1016/j.biochi.2010.06.022] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 06/29/2010] [Indexed: 01/21/2023]
Abstract
Including the true tissue kallikrein KLK1, kallikrein-related peptidases (KLKs) represent a family of fifteen mammalian serine proteases. While the physiological roles of several KLKs have been at least partially elucidated, their activation and regulation remain largely unclear. This obscurity may be related to the fact that a given KLK fulfills many different tasks in diverse fetal and adult tissues, and consequently, the timescale of some of their physiological actions varies significantly. To date, a variety of endogenous inhibitors that target distinct KLKs have been identified. Among them are the attenuating Zn(2+) ions, active site-directed proteinaceous inhibitors, such as serpins and the Kazal-type inhibitors, or the huge, unspecific compartment forming α(2)-macroglobulin. Failure of these inhibitory systems can lead to certain pathophysiological conditions. One of the most prominent examples is the Netherton syndrome, which is caused by dysfunctional domains of the Kazal-type inhibitor LEKTI-1 which fail to appropriately regulate KLKs in the skin. Small synthetic inhibitory compounds and natural polypeptidic exogenous inhibitors have been widely employed to characterize the activity and substrate specificity of KLKs and to further investigate their structures and biophysical properties. Overall, this knowledge leads not only to a better understanding of the physiological tasks of KLKs, but is also a strong fundament for the synthesis of small compound drugs and engineered biomolecules for pharmaceutical approaches. In several types of cancer, KLKs have been found to be overexpressed, which makes them clinically relevant biomarkers for prognosis and monitoring. Thus, down regulation of excessive KLK activity in cancer and in skin diseases by small inhibitor compounds may represent attractive therapeutical approaches.
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Affiliation(s)
- Peter Goettig
- Division of Structural Biology, Department of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria.
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31
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Li R, Pourpak A, Morris SW. Inhibition of the insulin-like growth factor-1 receptor (IGF1R) tyrosine kinase as a novel cancer therapy approach. J Med Chem 2010; 52:4981-5004. [PMID: 19610618 DOI: 10.1021/jm9002395] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rongshi Li
- Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Oncologic Sciences, University of South Florida, 12902 Magnolia Drive, Tampa, FL 33612, USA.
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32
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Liu F, Hakami RM, Dyas B, Bahta M, Lountos GT, Waugh DS, Ulrich RG, Burke TR. A rapid oxime linker-based library approach to identification of bivalent inhibitors of the Yersinia pestis protein-tyrosine phosphatase, YopH. Bioorg Med Chem Lett 2010; 20:2813-6. [PMID: 20350805 DOI: 10.1016/j.bmcl.2010.03.058] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 03/10/2010] [Accepted: 03/11/2010] [Indexed: 10/19/2022]
Abstract
A bivalent tethered approach toward YopH inhibitor development is presented that joins aldehydes with mixtures of bis-aminooxy-containing linkers using oxime coupling. The methodology is characterized by its facility and ease of use and its ability to rapidly identify low micromolar affinity inhibitors. The generality of the approach may potentially make it amenable to the development of bivalent inhibitors directed against other phosphatases.
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Affiliation(s)
- Fa Liu
- Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, NCI-Frederick, Frederick, MD 21702, USA
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33
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Zhu Z, Cuozzo J. Review article: high-throughput affinity-based technologies for small-molecule drug discovery. ACTA ACUST UNITED AC 2010; 14:1157-64. [PMID: 19822881 DOI: 10.1177/1087057109350114] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
High-throughput affinity-based technologies are rapidly growing in use as primary screening methods in drug discovery. In this review, their principles and applications are described and their impact on small-molecule drug discovery is evaluated. In general, these technologies can be divided into 2 groups: those that detect binding interactions by measuring changes to the protein target and those that detect bound compounds. Technologies detecting binding interactions by focusing on the protein have limited throughput but can reveal mechanistic information about the binding interaction; technologies detecting bound compounds have very high throughput, some even significantly higher than current high-throughput screening technologies, but offer limited information about the binding interaction. In addition, the appropriate use of affinity-based technologies is discussed. Finally, nanotechnology is predicted to generate a significant impact on the future of affinity-based technologies.
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Cudic M, Burstein GD, Fields GB, Lauer-Fields J. Analysis of flavonoid-based pharmacophores that inhibit aggrecanases (ADAMTS-4 and ADAMTS-5) and matrix metalloproteinases through the use of topologically constrained peptide substrates. Chem Biol Drug Des 2009; 74:473-82. [PMID: 19793184 DOI: 10.1111/j.1747-0285.2009.00885.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polyphenolic natural products from green tea and red wine have been identified as metalloproteinase inhibitors. Members from the flavonoid and stilbene families found to possess metalloproteinase inhibitory activities include (-)-epigallocatechin gallate, (-)-epicatechin gallate and piceatannol, but their minimally active pharmacophores have not been evaluated. The present study has examined compounds that are structural components of or structurally related to (-)-epigallocatechin gallate, (-)-epicatechin gallate and piceatannol for inhibition of aggrecanases and four representative matrix metalloproteinases. Piceatannol and pyrogallol were found to inhibit all aggrecanases and matrix metalloproteinases studied, indicating a crucial reliance on multiple hydroxyl groups for (-)-epigallocatechin gallate, (-)-epicatechin gallate and piceatannol activity. Differences in K(i) values for pyrogallol as determined with two structurally distinct substrates indicated the likelihood that this compound binds in a non-competitive modality. Further analysis showed that pyrogallol acts as an exosite inhibitor, consistent with the action of (-)-epigallocatechin gallate. In contrast, piceatannol was shown to be a competitive binding inhibitor and showed no differences in apparent K(i) values as determined by distinct substrates, illustrating the benefits of using two structurally distinct substrates to assist the analysis of protease inhibitors. The compounds identified here could be utilized to develop novel metalloproteinase probes or as fragment components of more active inhibitors.
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Affiliation(s)
- Mare Cudic
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, 33431, USA
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Heitner TR, Hansen NJV. Streamlining hit discovery and optimization with a yoctoliter scale DNA reactor. Expert Opin Drug Discov 2009; 4:1201-13. [DOI: 10.1517/17460440903206940] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Moore CD, Wu H, Bolaños B, Bergqvist S, Brooun A, Pauly T, Nowlin D. Structural and Biophysical Characterization of XIAP BIR3 G306E Mutant: Insights in Protein Dynamics and Application for Fragment-Based Drug Design. Chem Biol Drug Des 2009; 74:212-23. [DOI: 10.1111/j.1747-0285.2009.00862.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Schmidt M, El-Dahshan A, Keller S, Rademann J. Selektive Detektion kooperativ bindender Fragmente in einem Hochdurchsatz-Ligationsassay zur Entwicklung eines pikomolaren Caspase-3-Inhibitors. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200901647] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Schmidt M, El-Dahshan A, Keller S, Rademann J. Selective Identification of Cooperatively Binding Fragments in a High-Throughput Ligation Assay Enables Development of a Picomolar Caspase-3 Inhibitor. Angew Chem Int Ed Engl 2009; 48:6346-9. [DOI: 10.1002/anie.200901647] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Janga SC, Tzakos A. Structure and organization of drug-target networks: insights from genomic approaches for drug discovery. MOLECULAR BIOSYSTEMS 2009; 5:1536-48. [DOI: 10.1039/b908147j] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Journal Watch. Pharmaceut Med 2008. [DOI: 10.1007/bf03256711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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