1
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Li R, Yao L, Wang YB, Zhu JY, Zhang L, Fu JY, Zhang CB, Zhao L. Divergent Metal-Free [4 + 2] Cascade Reaction of 1-Indanylidenemalononitrile with 3-Benzylidenebenzofuran-2(3 H)-one: Access to Spiro-dihydrofluorene-benzofuranone and Axially Chiral Fluorenylamine-phenol Derivatives. Org Lett 2021; 23:5611-5615. [PMID: 34240601 DOI: 10.1021/acs.orglett.1c01510] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An efficient cascade reaction of 1-indanylidenemalononitrile with 3-benzylidenebenzofuran-2(3H)-one divergently promoted by DABCO or chiral organocatalyst was developed under mild reaction conditions, and various spiro-dihydrofluorene-benzofuranones were produced in gratifying results, respectively. It is worth noting that both the spiro and axially chiral products can be obtained by tuning the reaction conditions. The mechanism of the transformation was also studied by quantum chemical calculations.
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Affiliation(s)
- Ran Li
- Institute of Functional Organic Molecular Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, China
| | - Lei Yao
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yan-Bo Wang
- Institute of Functional Organic Molecular Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, China
| | - Jun-Yan Zhu
- Institute of Functional Organic Molecular Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, China
| | - Lixiong Zhang
- College of Chemical Engineering, State Key Laboratory of Materials-oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ji-Ya Fu
- Institute of Functional Organic Molecular Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, China
| | - Chuan-Bao Zhang
- School of Pharmacy, Zhengzhou Railway Vocational & Technical College, Zhengzhou 450052, China
| | - Lili Zhao
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
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2
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Li Q. Application of Fragment-Based Drug Discovery to Versatile Targets. Front Mol Biosci 2020; 7:180. [PMID: 32850968 PMCID: PMC7419598 DOI: 10.3389/fmolb.2020.00180] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/10/2020] [Indexed: 12/14/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is a powerful method to develop potent small-molecule compounds starting from fragments binding weakly to targets. As FBDD exhibits several advantages over high-throughput screening campaigns, it becomes an attractive strategy in target-based drug discovery. Many potent compounds/inhibitors of diverse targets have been developed using this approach. Methods used in fragment screening and understanding fragment-binding modes are critical in FBDD. This review elucidates fragment libraries, methods utilized in fragment identification/confirmation, strategies applied in growing the identified fragments into drug-like lead compounds, and applications of FBDD to different targets. As FBDD can be readily carried out through different biophysical and computer-based methods, it will play more important roles in drug discovery.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangdong Academy of Sciences, Guangzhou, China
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3
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Abstract
Abstract
Natural product (NP)-derived drugs can be extracts, biological macromolecules, or purified small molecule substances. Small molecule drugs can be originally purified from NPs, can represent semisynthetic molecules, natural fragments containing small molecules, or are fully synthetic molecules that mimic natural compounds. New semisynthetic NP-like drugs are entering the pharmaceutical market almost every year and reveal growing interests in the application of fragment-based approaches for NPs. Thus, several NP databases were constructed to be implemented in the fragment-based drug design (FBDD) workflows. FBDD has been established previously as an approach for hit identification and lead generation. Several biophysical and computational methods are used for fragment screening to identify potential hits. Once the fragments within the binding pocket of the protein are identified, they can be grown, linked, or merged to design more active compounds. This work discusses applications of NPs and NP scaffolds to FBDD. Moreover, it briefly reviews NP databases containing fragments and reports on case studies where the approach has been successfully applied for the design of antimalarial and anticancer drug candidates.
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4
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Luise N, Wyatt EW, Tarver GJ, Wyatt PG. A Continuous Flow Strategy for the Facile Synthesis and Elaboration of Semi-Saturated Heterobicyclic Fragments. European J Org Chem 2019. [DOI: 10.1002/ejoc.201801684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nicola Luise
- Drug Discovery Unit; School of Life Sciences; University of Dundee; Dow Street 5EH Dundee, DD1 Scotland, UK
| | - Eleanor W. Wyatt
- Drug Discovery Unit; School of Life Sciences; University of Dundee; Dow Street 5EH Dundee, DD1 Scotland, UK
| | - Gary J. Tarver
- Drug Discovery Unit; School of Life Sciences; University of Dundee; Dow Street 5EH Dundee, DD1 Scotland, UK
| | - Paul G. Wyatt
- Drug Discovery Unit; School of Life Sciences; University of Dundee; Dow Street 5EH Dundee, DD1 Scotland, UK
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5
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Ashenden SK. Screening Library Design. Methods Enzymol 2018; 610:73-96. [PMID: 30390806 DOI: 10.1016/bs.mie.2018.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Thanks to technological advances and a greater understanding of the biological and chemical natures of targets and related diseases, high-throughput screening (HTS) has been allowed to be faster, cheaper, and more accessible. Yet, despite these increased technologies and understandings, the frequency of novel and drugs are being approved each year has not being increasing over the years. 2017 was considered a "bumper" year with a total of 46 approved drugs, over double that of the previous year. However, it is thought that part of the problem that HTS has not lived up to expectations is because of the contents of current chemical libraries. Therefore, new methods to design screening libraries are of great interest.
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Affiliation(s)
- Stephanie Kay Ashenden
- Department of Chemistry, Cambridge University, Cambridge, United Kingdom; Discovery Sciences, IMed Biotech Unit, AstraZeneca R&D, Cambridge, United Kingdom.
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6
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A Fragment-Based Approach for the Development of G-Quadruplex Ligands: Role of the Amidoxime Moiety. Molecules 2018; 23:molecules23081874. [PMID: 30060461 PMCID: PMC6222391 DOI: 10.3390/molecules23081874] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 11/16/2022] Open
Abstract
G-quadruplex (G4) nucleic acid structures have been reported to be involved in several human pathologies, including cancer, neurodegenerative disorders and infectious diseases; however, G4 targeting compounds still need implementation in terms of drug-like properties and selectivity in order to reach the clinical use. So far, G4 ligands have been mainly identified through high-throughput screening methods or design of molecules with pre-set features. Here, we describe the development of new heterocyclic ligands through a fragment-based drug discovery (FBDD) approach. The ligands were designed against the major G4 present in the long terminal repeat (LTR) promoter region of the human immunodeficiency virus-1 (HIV-1), the stabilization of which has been shown to suppress viral gene expression and replication. Our method is based on the generation of molecular fragment small libraries, screened against the target to further elaborate them into lead compounds. We screened 150 small molecules, composed by structurally and chemically different fragments, selected from commercially available and in-house compounds; synthetic elaboration yielded several G4 ligands and two final G4 binders, both embedding an amidoxime moiety; one of these two compounds showed preferential binding for the HIV-1 LTR G4. This work presents the discovery of a novel potential pharmacophore and highlights the possibility to apply a fragment-based approach to develop G4 ligands with unexpected chemical features.
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7
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Borysko P, Moroz YS, Vasylchenko OV, Hurmach VV, Starodubtseva A, Stefanishena N, Nesteruk K, Zozulya S, Kondratov IS, Grygorenko OO. Straightforward hit identification approach in fragment-based discovery of bromodomain-containing protein 4 (BRD4) inhibitors. Bioorg Med Chem 2018; 26:3399-3405. [DOI: 10.1016/j.bmc.2018.05.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/24/2018] [Accepted: 05/08/2018] [Indexed: 02/07/2023]
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8
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Göth M, Badock V, Weiske J, Pagel K, Kuropka B. Critical Evaluation of Native Electrospray Ionization Mass Spectrometry for Fragment-Based Screening. ChemMedChem 2017; 12:1201-1211. [PMID: 28618179 DOI: 10.1002/cmdc.201700177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/19/2017] [Indexed: 12/24/2022]
Abstract
Fragment-based screening presents a promising alternative to high-throughput screening and has gained great attention in recent years. So far, only a few studies have discussed mass spectrometry as a screening technology for fragments. Herein, we report the application of native electrospray ionization mass spectrometry (MS) for screening defined sets of fragments against four different target proteins. Fragments were selected from a primary screening conducted with a thermal shift assay (TSA) and represented different binding categories. Our data indicated that, beside specific complex formation, many fragments show extensive multiple binding and also charge-state shifts. Both of these factors complicate automated data analysis and decrease the attractiveness of native MS as a primary screening tool for fragments. A comparison of the hits identified by native MS and TSA showed good agreement for two of the proteins. Furthermore, we discuss general challenges, including the determination of an optimal fragment concentration and the question of how to rank fragment hits according to their affinity. In conclusion, we consider native MS to be a highly valuable tool for the validation and deeper investigation of promising fragment hits rather than a method for primary screening.
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Affiliation(s)
- Melanie Göth
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195, Berlin, Germany.,Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Volker Badock
- Protein Technologies, Lead Discovery Berlin, Bayer AG, Müllerstraße 178, 13353, Berlin, Germany
| | - Jörg Weiske
- Protein Technologies, Lead Discovery Berlin, Bayer AG, Müllerstraße 178, 13353, Berlin, Germany
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195, Berlin, Germany.,Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195, Berlin, Germany
| | - Benno Kuropka
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany.,Protein Technologies, Lead Discovery Berlin, Bayer AG, Müllerstraße 178, 13353, Berlin, Germany
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9
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Drwal MN, Jacquemard C, Perez C, Desaphy J, Kellenberger E. Do Fragments and Crystallization Additives Bind Similarly to Drug-like Ligands? J Chem Inf Model 2017; 57:1197-1209. [PMID: 28414463 DOI: 10.1021/acs.jcim.6b00769] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The success of fragment-based drug design (FBDD) hinges upon the optimization of low-molecular-weight compounds (MW < 300 Da) with weak binding affinities to lead compounds with high affinity and selectivity. Usually, structural information from fragment-protein complexes is used to develop ideas about the binding mode of similar but drug-like molecules. In this regard, crystallization additives such as cryoprotectants or buffer components, which are highly abundant in crystal structures, are frequently ignored. Thus, the aim of this study was to investigate the information present in protein complexes with fragments as well as those with additives and how they relate to the binding modes of their drug-like counterparts. We present a thorough analysis of the binding modes of crystallographic additives, fragments, and drug-like ligands bound to four diverse targets of wide interest in drug discovery and highly represented in the Protein Data Bank: cyclin-dependent kinase 2, β-secretase 1, carbonic anhydrase 2, and trypsin. We identified a total of 630 unique molecules bound to the catalytic binding sites, among them 31 additives, 222 fragments, and 377 drug-like ligands. In general, we observed that, independent of the target, protein-fragment interaction patterns are highly similar to those of drug-like ligands and mostly cover the residues crucial for binding. Crystallographic additives are also able to show conserved binding modes and recover the residues important for binding in some of the cases. Moreover, we show evidence that the information from fragments and drug-like ligands can be applied to rescore docking poses in order to improve the prediction of binding modes.
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Affiliation(s)
- Malgorzata N Drwal
- Laboratoire d'Innovation Thérapeutique UMR 7200, CNRS-Université de Strasbourg , 74 Route du Rhin, 674000 Illkirch, France
| | - Célien Jacquemard
- Laboratoire d'Innovation Thérapeutique UMR 7200, CNRS-Université de Strasbourg , 74 Route du Rhin, 674000 Illkirch, France
| | - Carlos Perez
- Eli Lilly Research Laboratories , Avenida de la Industria 30, 28108 Alcobendas, Madrid, Spain
| | - Jérémy Desaphy
- Lilly Research Laboratories, Eli Lilly and Company , Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Esther Kellenberger
- Laboratoire d'Innovation Thérapeutique UMR 7200, CNRS-Université de Strasbourg , 74 Route du Rhin, 674000 Illkirch, France
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10
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Grixti JM, O'Hagan S, Day PJ, Kell DB. Enhancing Drug Efficacy and Therapeutic Index through Cheminformatics-Based Selection of Small Molecule Binary Weapons That Improve Transporter-Mediated Targeting: A Cytotoxicity System Based on Gemcitabine. Front Pharmacol 2017; 8:155. [PMID: 28396636 PMCID: PMC5366350 DOI: 10.3389/fphar.2017.00155] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/10/2017] [Indexed: 12/23/2022] Open
Abstract
The transport of drug molecules is mainly determined by the distribution of influx and efflux transporters for which they are substrates. To enable tissue targeting, we sought to develop the idea that we might affect the transporter-mediated disposition of small-molecule drugs via the addition of a second small molecule that of itself had no inhibitory pharmacological effect but that influenced the expression of transporters for the primary drug. We refer to this as a “binary weapon” strategy. The experimental system tested the ability of a molecule that on its own had no cytotoxic effect to increase the toxicity of the nucleoside analog gemcitabine to Panc1 pancreatic cancer cells. An initial phenotypic screen of a 500-member polar drug (fragment) library yielded three “hits.” The structures of 20 of the other 2,000 members of this library suite had a Tanimoto similarity greater than 0.7 to those of the initial hits, and each was itself a hit (the cheminformatics thus providing for a massive enrichment). We chose the top six representatives for further study. They fell into three clusters whose members bore reasonable structural similarities to each other (two were in fact isomers), lending strength to the self-consistency of both our conceptual and experimental strategies. Existing literature had suggested that indole-3-carbinol might play a similar role to that of our fragments, but in our hands it was without effect; nor was it structurally similar to any of our hits. As there was no evidence that the fragments could affect toxicity directly, we looked for effects on transporter transcript levels. In our hands, only the ENT1-3 uptake and ABCC2,3,4,5, and 10 efflux transporters displayed measurable transcripts in Panc1 cultures, along with a ribonucleoside reductase RRM1 known to affect gemcitabine toxicity. Very strikingly, the addition of gemcitabine alone increased the expression of the transcript for ABCC2 (MRP2) by more than 12-fold, and that of RRM1 by more than fourfold, and each of the fragment “hits” served to reverse this. However, an inhibitor of ABCC2 was without significant effect, implying that RRM1 was possibly the more significant player. These effects were somewhat selective for Panc cells. It seems, therefore, that while the effects we measured were here mediated more by efflux than influx transporters, and potentially by other means, the binary weapon idea is hereby fully confirmed: it is indeed possible to find molecules that manipulate the expression of transporters that are involved in the bioactivity of a pharmaceutical drug. This opens up an entirely new area, that of chemical genomics-based drug targeting.
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Affiliation(s)
- Justine M Grixti
- Faculty of Biology, Medicine and Health, University of ManchesterManchester, UK; Manchester Institute of Biotechnology, University of ManchesterManchester, UK
| | - Steve O'Hagan
- Manchester Institute of Biotechnology, University of ManchesterManchester, UK; School of Chemistry, University of ManchesterManchester, UK; Centre for Synthetic Biology of Fine and Speciality Chemicals, University of ManchesterManchester, UK
| | - Philip J Day
- Faculty of Biology, Medicine and Health, University of ManchesterManchester, UK; Manchester Institute of Biotechnology, University of ManchesterManchester, UK
| | - Douglas B Kell
- Manchester Institute of Biotechnology, University of ManchesterManchester, UK; School of Chemistry, University of ManchesterManchester, UK; Centre for Synthetic Biology of Fine and Speciality Chemicals, University of ManchesterManchester, UK
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11
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Borthwick JA, Ancellin N, Bertrand SM, Bingham RP, Carter PS, Chung CW, Churcher I, Dodic N, Fournier C, Francis PL, Hobbs A, Jamieson C, Pickett SD, Smith SE, Somers DO, Spitzfaden C, Suckling CJ, Young RJ. Structurally Diverse Mitochondrial Branched Chain Aminotransferase (BCATm) Leads with Varying Binding Modes Identified by Fragment Screening. J Med Chem 2016; 59:2452-67. [DOI: 10.1021/acs.jmedchem.5b01607] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jennifer A. Borthwick
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
- Department
of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral
Street, Glasgow, G1 1XL, U.K
| | - Nicolas Ancellin
- Les Ulis, Centre de Recherche, GlaxoSmithKline R&D, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Sophie M. Bertrand
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
- Department
of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral
Street, Glasgow, G1 1XL, U.K
| | - Ryan P. Bingham
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Paul S. Carter
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Chun-wa Chung
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Ian Churcher
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Nerina Dodic
- Les Ulis, Centre de Recherche, GlaxoSmithKline R&D, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Charlène Fournier
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Peter L. Francis
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Andrew Hobbs
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Craig Jamieson
- Department
of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral
Street, Glasgow, G1 1XL, U.K
| | - Stephen D. Pickett
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Sarah E. Smith
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Donald O’N. Somers
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Claus Spitzfaden
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Colin J. Suckling
- Department
of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral
Street, Glasgow, G1 1XL, U.K
| | - Robert J. Young
- Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
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12
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Xue Y, Olsson T, Johansson CA, Öster L, Beisel HG, Rohman M, Karis D, Bäckström S. Fragment Screening of Soluble Epoxide Hydrolase for Lead Generation-Structure-Based Hit Evaluation and Chemistry Exploration. ChemMedChem 2016; 11:497-508. [PMID: 26845235 DOI: 10.1002/cmdc.201500575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 12/20/2022]
Abstract
Soluble epoxide hydrolase (sEH) is involved in the regulation of many biological processes by metabolizing the key bioactive lipid mediator, epoxyeicosatrienoic acids. For the development of sEH inhibitors with improved physicochemical properties, we performed both a fragment screening and a high-throughput screening aiming at an integrated hit evaluation and lead generation. Followed by a joint dose-response analysis to confirm the hits, the identified actives were then effectively triaged by a structure-based hit-classification approach to three prioritized series. Two distinct scaffolds were identified as tractable starting points for potential lead chemistry work. The oxoindoline series bind at the right-hand side of the active-site pocket with hydrogen bonds to the protein. The 2-phenylbenzimidazole-4-sulfonamide series bind at the central channel with significant induced fit, which has not been previously reported. On the basis of the encouraging initial results, we envision that a new lead series with improved properties could be generated if a vector is found that could merge the cyclohexyl functionality of the oxoindoline series with the trifluoromethyl moiety of the 2-phenylbenzimidazole-4-sulfonamide series.
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Affiliation(s)
- Yafeng Xue
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Thomas Olsson
- Department Medicinal Chemistry, CVMD iMED, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Carina A Johansson
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Linda Öster
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Hans-Georg Beisel
- Department Medicinal Chemistry, CVMD iMED, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Mattias Rohman
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - David Karis
- Department Medicinal Chemistry, CVMD iMED, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Stefan Bäckström
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden.
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13
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Varnes JG, Geschwindner S, Holmquist CR, Forst J, Wang X, Dekker N, Scott CW, Tian G, Wood MW, Albert JS. Fragment-assisted hit investigation involving integrated HTS and fragment screening: Application to the identification of phosphodiesterase 10A (PDE10A) inhibitors. Bioorg Med Chem Lett 2015; 26:197-202. [PMID: 26597534 DOI: 10.1016/j.bmcl.2015.10.100] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/26/2015] [Accepted: 10/30/2015] [Indexed: 12/29/2022]
Abstract
Fragment-based drug design (FBDD) relies on direct elaboration of fragment hits and typically requires high resolution structural information to guide optimization. In fragment-assisted drug discovery (FADD), fragments provide information to guide selection and design but do not serve as starting points for elaboration. We describe FADD and high-throughput screening (HTS) campaign strategies conducted in parallel against PDE10A where fragment hit co-crystallography was not available. The fragment screen led to prioritized fragment hits (IC50's ∼500μM), which were used to generate a hypothetical core scaffold. Application of this scaffold as a filter to HTS output afforded a 4μM hit, which, after preparation of a small number of analogs, was elaborated into a 16nM lead. This approach highlights the strength of FADD, as fragment methods were applied despite the absence of co-crystallographical information to efficiently identify a lead compound for further optimization.
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Affiliation(s)
- Jeffrey G Varnes
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA.
| | | | - Christopher R Holmquist
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA
| | - Janet Forst
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA
| | - Xia Wang
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA
| | - Niek Dekker
- Discovery Sciences, AstraZeneca R&D, SE-431 83 Mölndal, Sweden
| | - Clay W Scott
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA
| | - Gaochao Tian
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA
| | - Michael W Wood
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA
| | - Jeffrey S Albert
- CNS Discovery Research, AstraZeneca Pharmaceuticals, 1800 Concord Pike, PO Box 15437, Wilmington, DE 19850-5437, USA.
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14
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Successful generation of structural information for fragment-based drug discovery. Drug Discov Today 2015; 20:1104-11. [DOI: 10.1016/j.drudis.2015.04.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/12/2015] [Accepted: 04/20/2015] [Indexed: 12/25/2022]
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15
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Wang Z, Hwang SH, Huang B, Lim SS. Identification of tyrosinase specific inhibitors from Xanthium strumarium fruit extract using ultrafiltration-high performance liquid chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1002:319-28. [PMID: 26367464 DOI: 10.1016/j.jchromb.2015.08.030] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/18/2015] [Accepted: 08/20/2015] [Indexed: 12/26/2022]
Abstract
In this study, a strategy based on ultrafiltration-high performance liquid chromatography coupled with diode array detection (UF-HPLC-DAD) was proposed for screening tyrosinase specific inhibitors in Xanthii fructus. The false negatives were distinguished by optimizing the UF-HPLC-DAD parameters to reduce the background noise; the false positives were distinguished by introducing a blocked tyrosinase in the control group for comparison. To obtain the best blocker, the competitive experiments were performed using various known ligands. Using this strategy, three competitive inhibitors (protocatechuic acid; 3,5-di-O-caffeoylquinic acid; and 1,5-di-O-caffeoylquinic acid) and one mixed-type inhibitor (chlorogenic acid) were identified. These results were verified using tyrosinase inhibition assay, kinetic analysis, and structural simulation of the complex. Our experimental results suggest that the proposed strategy could be useful for high-throughput identification of tyrosinase specific inhibitors in natural products.
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Affiliation(s)
- Zhiqiang Wang
- Department of Food Science and Nutrition, Hallym University, Chuncheon 200-702, South Korea; Institute of Korean Nutrition, Hallym University, Chuncheon 200-702, South Korea
| | - Seung Hwan Hwang
- Department of Food Science and Nutrition, Hallym University, Chuncheon 200-702, South Korea; Institute of Korean Nutrition, Hallym University, Chuncheon 200-702, South Korea
| | - Bo Huang
- College of Food Science and Engineering, Liaoning Medical University, Jinzhou 121-000, China
| | - Soon Sung Lim
- Department of Food Science and Nutrition, Hallym University, Chuncheon 200-702, South Korea; Institute of Korean Nutrition, Hallym University, Chuncheon 200-702, South Korea; Institute of Natural Medicine, Hallym University, Chuncheon 200-702, South Korea.
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16
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Chen X, Qin S, Chen S, Li J, Li L, Wang Z, Wang Q, Lin J, Yang C, Shui W. A ligand-observed mass spectrometry approach integrated into the fragment based lead discovery pipeline. Sci Rep 2015; 5:8361. [PMID: 25666181 PMCID: PMC4322365 DOI: 10.1038/srep08361] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/19/2015] [Indexed: 02/07/2023] Open
Abstract
In fragment-based lead discovery (FBLD), a cascade combining multiple orthogonal technologies is required for reliable detection and characterization of fragment binding to the target. Given the limitations of the mainstream screening techniques, we presented a ligand-observed mass spectrometry approach to expand the toolkits and increase the flexibility of building a FBLD pipeline especially for tough targets. In this study, this approach was integrated into a FBLD program targeting the HCV RNA polymerase NS5B. Our ligand-observed mass spectrometry analysis resulted in the discovery of 10 hits from a 384-member fragment library through two independent screens of complex cocktails and a follow-up validation assay. Moreover, this MS-based approach enabled quantitative measurement of weak binding affinities of fragments which was in general consistent with SPR analysis. Five out of the ten hits were then successfully translated to X-ray structures of fragment-bound complexes to lay a foundation for structure-based inhibitor design. With distinctive strengths in terms of high capacity and speed, minimal method development, easy sample preparation, low material consumption and quantitative capability, this MS-based assay is anticipated to be a valuable addition to the repertoire of current fragment screening techniques.
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Affiliation(s)
- Xin Chen
- College of Life Sciences, Nankai University, Tianjin 300071, China
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Shanshan Qin
- College of Life Sciences, Nankai University, Tianjin 300071, China
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Shuai Chen
- College of Life Sciences, Nankai University, Tianjin 300071, China
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Jinlong Li
- College of Life Sciences, Nankai University, Tianjin 300071, China
- State Key Laboratory of Medicinal Chemical and Department of Pharmacy, Nankai University, Tianjin 300071, China
| | - Lixin Li
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Zhongling Wang
- College of Life Sciences, Nankai University, Tianjin 300071, China
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Quan Wang
- College of Life Sciences, Nankai University, Tianjin 300071, China
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
| | - Jianping Lin
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
- State Key Laboratory of Medicinal Chemical and Department of Pharmacy, Nankai University, Tianjin 300071, China
| | - Cheng Yang
- High-throughput Molecular Drug Discovery Center, Tianjin Joint Academy of Biotechnology and Medicine, Tianjin 300457, China
- State Key Laboratory of Medicinal Chemical and Department of Pharmacy, Nankai University, Tianjin 300071, China
| | - Wenqing Shui
- College of Life Sciences, Nankai University, Tianjin 300071, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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17
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Multiscale quantum chemical approaches to QSAR modeling and drug design. Drug Discov Today 2014; 19:1921-7. [DOI: 10.1016/j.drudis.2014.09.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/01/2014] [Accepted: 09/26/2014] [Indexed: 12/24/2022]
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18
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Bisignano P, Doerr S, Harvey MJ, Favia AD, Cavalli A, De Fabritiis G. Kinetic characterization of fragment binding in AmpC β-lactamase by high-throughput molecular simulations. J Chem Inf Model 2014; 54:362-6. [PMID: 24444037 DOI: 10.1021/ci4006063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Small molecules used in fragment-based drug discovery form multiple, promiscuous binding complexes difficult to capture experimentally. Here, we identify such binding poses and their associated energetics and kinetics using molecular dynamics simulations on AmpC β-lactamase. Only one of the crystallographic binding poses was found to be thermodynamically favorable; however, the ligand shows several binding poses within the pocket. This study demonstrates free-binding molecular simulations in the context of fragment-to-lead development and its potential application in drug design.
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Affiliation(s)
- P Bisignano
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia , via Morego, 30, 16163 Genova, Italy
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19
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Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design. J Mol Graph Model 2013; 41:31-42. [PMID: 23467020 DOI: 10.1016/j.jmgm.2013.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 01/25/2013] [Accepted: 01/25/2013] [Indexed: 12/30/2022]
Abstract
We develop an inter-fragment interaction energy (IFIE) analysis based on the three- and four-body corrected fragment molecular orbital (FMO3 and FMO4) method to evaluate the interactions of functional group units in structure-based drug design context. The novel subdividing fragmentation method for a ligand (in units of their functional groups) and amino acid residues (in units of their main and side chains) enables us to understand the ligand-binding mechanism in more detail without sacrificing chemical accuracy of the total energy and IFIEs by using the FMO4 method. We perform FMO4 calculations with the second order Møller-Plesset perturbation theory for an estrogen receptor (ER) and the 17β-estradiol (EST) complex using the proposed fragmentation method and assess the interaction for each ligand-binding site by the FMO4-IFIE analysis. When the steroidal EST is divided into two functional units including "A ring" and "D ring", respectively, the FMO4-IFIE analysis reveals their binding affinity with surrounding fragments of the amino acid residues; the "A ring" of EST has polarization interaction with the main chain of Thr347 and two hydrogen bonds with the side chains of Glu353 and Arg394; the "D ring" of EST has a hydrogen bond with the side chain of His524. In particular, the CH/π interactions of the "A ring" of EST with the side chains of Leu387 and Phe404 are easily identified in cooperation with the CHPI program. The FMO4-IFIE analysis using our novel subdividing fragmentation method, which provides higher resolution than the conventional IFIE analysis in units of ligand and each amino acid reside in the framework of two-body approximation, is a useful tool for revealing ligand-binding mechanism and would be applicable to rational drug design such as structure-based drug design and fragment-based drug design.
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20
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Doak BC, Morton CJ, Simpson JS, Scanlon MJ. Design and Evaluation of the Performance of an NMR Screening Fragment Library. Aust J Chem 2013. [DOI: 10.1071/ch13280] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The design of a suitable library is an essential prerequisite to establish a fragment-based screening capability. Several pharmaceutical companies have described their approaches to establishing fragment libraries; however there are few detailed reports of both design and analysis of performance for a fragment library maintained in an academic setting. Here we report our efforts towards the design of a fragment library for nuclear magnetic resonance spectroscopy-based screening, demonstrate the performance of the library through analysis of 14 screens, and present a comparison to previously reported fragment libraries.
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21
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Bisignano P, Lambruschini C, Bicego M, Murino V, Favia AD, Cavalli A. In silico deconstruction of ATP-competitive inhibitors of glycogen synthase kinase-3β. J Chem Inf Model 2012. [PMID: 23198830 DOI: 10.1021/ci300355p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fragment-based methods have emerged in the last two decades as alternatives to traditional high throughput screenings for the identification of chemical starting points in drug discovery. One arguable yet popular assumption about fragment-based design is that the fragment binding mode remains conserved upon chemical expansion. For instance, the question of the binding conservation upon fragmentation of a molecule is still unclear. A number of papers have challenged this hypothesis by means of experimental techniques, with controversial results, "underlining" the idea that a simple generalization, maybe, is not possible. From a computational standpoint, the issue has been rarely addressed and mostly to test novel protocols on limited data sets. To fill this gap, we here report on a computational retrospective study concerned with the in silico deconstruction of leadlike compounds, active on the pharmaceutically relevant enzyme glycogen synthase kinase-3β.
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Affiliation(s)
- Paola Bisignano
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genova, Italy
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22
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Stoddart L, Vernall A, Denman J, Briddon S, Kellam B, Hill S. Fragment screening at adenosine-A(3) receptors in living cells using a fluorescence-based binding assay. CHEMISTRY & BIOLOGY 2012; 19:1105-15. [PMID: 22999879 PMCID: PMC3456874 DOI: 10.1016/j.chembiol.2012.07.014] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 06/22/2012] [Accepted: 07/17/2012] [Indexed: 10/31/2022]
Abstract
G protein-coupled receptors (GPCRs) comprise the largest family of transmembrane proteins. For GPCR drug discovery, it is important that ligand affinity is determined in the correct cellular environment and preferably using an unmodified receptor. We developed a live cell high-content screening assay that uses a fluorescent antagonist, CA200645, to determine binding affinity constants of competing ligands at human adenosine-A(1) and -A(3) receptors. This method was validated as a tool to screen a library of low molecular weight fragments, and identified a hit with submicromolar binding affinity (K(D)). This fragment was structurally unrelated to substructures of known adenosine receptor antagonists and was optimized to show selectivity for the adenosine-A(3) receptor. This technology represents a significant advance that will allow the determination of ligand and fragment affinities at receptors in their native membrane environment.
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Affiliation(s)
- Leigh A. Stoddart
- Institute of Cell Signalling, School of Biomedical Science, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Andrea J. Vernall
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Jessica L. Denman
- Institute of Cell Signalling, School of Biomedical Science, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Stephen J. Briddon
- Institute of Cell Signalling, School of Biomedical Science, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Barrie Kellam
- School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Stephen J. Hill
- Institute of Cell Signalling, School of Biomedical Science, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
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23
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Boyd SM, Turnbull AP, Walse B. Fragment library design considerations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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24
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Maple HJ, Garlish RA, Rigau-Roca L, Porter J, Whitcombe I, Prosser CE, Kennedy J, Henry AJ, Taylor RJ, Crump MP, Crosby J. Automated Protein–Ligand Interaction Screening by Mass Spectrometry. J Med Chem 2012; 55:837-51. [DOI: 10.1021/jm201347k] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hannah J. Maple
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
| | - Rachel A. Garlish
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Laura Rigau-Roca
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
| | - John Porter
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Ian Whitcombe
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | | | - Jeff Kennedy
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Alistair J. Henry
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Richard J. Taylor
- UCB Pharma, 216 Bath Road, Slough, Berkshire SL1 4EN, United Kingdom
| | - Matthew P. Crump
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
| | - John Crosby
- School of Chemistry, University of Bristol, Cantock’s
Close, Clifton, Bristol BS8 1TS, United Kingdom
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25
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Nakano T, Mochizuki Y, Yamashita K, Watanabe C, Fukuzawa K, Segawa K, Okiyama Y, Tsukamoto T, Tanaka S. Development of the four-body corrected fragment molecular orbital (FMO4) method. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2011.12.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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26
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Edink E, Akdemir A, Jansen C, van Elk R, Zuiderveld O, de Kanter FJJ, van Muijlwijk-Koezen JE, Smit AB, Leurs R, de Esch IJP. Structure-based design, synthesis and structure-activity relationships of dibenzosuberyl- and benzoate-substituted tropines as ligands for acetylcholine-binding protein. Bioorg Med Chem Lett 2011; 22:1448-54. [PMID: 22243960 DOI: 10.1016/j.bmcl.2011.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 11/30/2011] [Accepted: 12/01/2011] [Indexed: 12/26/2022]
Abstract
Using structure-based optimization procedures on in silico hits, dibenzosuberyl- and benzoate substituted tropines were designed as ligands for acetylcholine-binding protein (AChBP). This protein is a homolog to the ligand binding domain of the nicotinic acetylcholine receptor (nAChR). Distinct SAR is observed between two AChBP species variants and between the α7 and α4β2 nAChR subtype. The AChBP species differences are indicative of a difference in accessibility of a ligand-inducible subpocket. Hereby, we have identified a region that can be scrutinized to achieve selectivity for nicotinic receptor subtypes.
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Affiliation(s)
- Ewald Edink
- Leiden/Amsterdam Center of Drug Research, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands
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27
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Nakagawa S, Bainbridge KA, Butcher K, Ellis D, Klute W, Ryckmans T. Application of Barluenga Boronic Coupling (BBC) to the Parallel Synthesis of Drug-like and Drug Fragment-like Molecules. ChemMedChem 2011; 7:233-6. [DOI: 10.1002/cmdc.201100339] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 10/20/2011] [Indexed: 11/07/2022]
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28
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Favia AD, Bottegoni G, Nobeli I, Bisignano P, Cavalli A. SERAPhiC: A Benchmark for in Silico Fragment-Based Drug Design. J Chem Inf Model 2011; 51:2882-96. [DOI: 10.1021/ci2003363] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Angelo D. Favia
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Giovanni Bottegoni
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Irene Nobeli
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, WC1E 7HX London, United Kingdom
| | - Paola Bisignano
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | - Andrea Cavalli
- Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
- Dipartimento di Scienze Farmaceutiche, Università di Bologna, via Belmeloro 6, 40126 Bologna, Italy
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29
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Abstract
Rapid advances in our collective understanding of biomolecular structure and, in concert, of biochemical systems, coupled with developments in computational methods, have massively impacted the field of medicinal chemistry over the past two decades, with even greater changes appearing on the horizon. In this perspective, we endeavor to profile some of the most prominent determinants of change and speculate as to further evolution that may consequently occur during the next decade. The five main angles to be addressed are: protein-protein interactions; peptides and peptidomimetics; molecular diversity and pharmacological space; molecular pharmacodynamics (significance, potential and challenges); and early-stage clinical efficacy and safety. We then consider, in light of these, the future of medicinal chemistry and the educational preparation that will be required for future medicinal chemists.
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Affiliation(s)
- Seetharama D Satyanarayanajois
- Basic Pharmaceutical Sciences, College of Pharmacy, University of Louisiana at Monroe, 1800 Bienville Drive, Monroe LA 71201, USA.
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30
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Gordon MS, Fedorov DG, Pruitt SR, Slipchenko LV. Fragmentation Methods: A Route to Accurate Calculations on Large Systems. Chem Rev 2011; 112:632-72. [DOI: 10.1021/cr200093j] [Citation(s) in RCA: 836] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Dmitri G. Fedorov
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Spencer R. Pruitt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Lyudmila V. Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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31
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Abstract
‘Fragments’ refer to particularly small molecular starting points in medicinal chemistry. The small size of fragments requires adapted techniques for their screening and subsequent elaboration. The detection of the weak binding affinity of fragments for their target, and associated screening issues, have been debated at length. Since it is now clear that fragments can be developed into clinical candidates, the discussion is shifting to the design of good-quality lead compounds from fragment hits. The increasing ability to control and tailor this construction process highlights the potential benefits of fragment-based drug discovery.
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32
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Ichihara O, Barker J, Law RJ, Whittaker M. Compound Design by Fragment-Linking. Mol Inform 2011; 30:298-306. [PMID: 27466947 DOI: 10.1002/minf.201000174] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 02/14/2010] [Indexed: 12/21/2022]
Abstract
The linking together of two fragment compounds that bind to distinct protein sub-sites can lead to a superadditivity of binding affinities, in which the binding free energy of the linked fragments exceeds the simple sum of the binding energies of individual fragments (linking coefficient E<1). However, a review of the literature shows that such events are relatively rare and, in the majority of the cases, linking coefficients are far from optimal being much greater than 1. It is critical to design a linker that does not disturb the original binding poses of each fragment in order to achieve successful linking. However, such an ideal linker is often difficult to design and even more difficult to actually synthesize. We suggest that the chance of achieving successful fragment linking can be significantly improved by choosing a fragment pair that consists of one fragment that binds by strong H-bonds (or non-classical equivalents) and a second fragment that is more tolerant of changes in binding mode (hydrophobic or vdW binders). We also propose that the fragment molecular orbital (FMO) calculations can be used to analyse the nature of the binding interactions of the fragment hits for the selection of fragments for evolution, merging and linking in order to optimize the chance of success.
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Affiliation(s)
- Osamu Ichihara
- Evotec (UK) Ltd, 114 Milton Park, Abingdon, OXON, OX14 4SA, UK phone: +44(0)1235 441238
| | - John Barker
- Evotec (UK) Ltd, 114 Milton Park, Abingdon, OXON, OX14 4SA, UK phone: +44(0)1235 441238
| | - Richard J Law
- Evotec (UK) Ltd, 114 Milton Park, Abingdon, OXON, OX14 4SA, UK phone: +44(0)1235 441238
| | - Mark Whittaker
- Evotec (UK) Ltd, 114 Milton Park, Abingdon, OXON, OX14 4SA, UK phone: +44(0)1235 441238.
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