1
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Vandyshev DY, Shikhaliev KS. Recyclization of Maleimides by Binucleophiles as a General Approach for Building Hydrogenated Heterocyclic Systems. Molecules 2022; 27:5268. [PMID: 36014507 PMCID: PMC9416709 DOI: 10.3390/molecules27165268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
The building of heterocyclic systems containing hydrogenated fragments is an important step towards the creation of biologically-active compounds with a wide spectrum of pharmacological activity. Among the numerous methods for creating such systems, a special place is occupied by processes using N-substituted maleimides as the initial substrate. This molecule easily reacts in Diels-Alder/retro-Diels-Alder reactions, Michael additions with various nucleophiles, and co-polymerization processes, as have been described in numerous detailed reviews. However, information on the use of maleimides in cascade heterocyclization reactions is currently limited. This study is devoted to a review and analysis of existing literature data on the processes of recyclization of N-substituted maleimides with various C,N-/N,N-/S,N-di- and polynucleophilic agents, such as amidines, guanidines, diamines, aliphatic ketazines, aminouracils, amino- and mercaptoazoles, aminothiourea, and thiocarbomoyl pyrazolines, among others. The significant structural diversity of the recyclization products described in this study illustrates the powerful potential of maleimides as a building block in the organic synthesis of biologically-active compounds with hydrogenated heterocyclic fragments.
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Affiliation(s)
- Dmitriy Yu. Vandyshev
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, Universitetskaya Sq. 1, 394018 Voronezh, Russia
| | - Khidmet S. Shikhaliev
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, Universitetskaya Sq. 1, 394018 Voronezh, Russia
- TekhnoKhim, 50 Let Sovetskoi Vlasti Str. 8, 394050 Voronezh, Russia
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2
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Solid-phase synthetic method for N-alkyl-4-alkylamino-6-arylthieno[3,2-d]pyrimidine-2-carboxamide derivatives. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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3
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Caplin MJ, Foley DJ. Emergent synthetic methods for the modular advancement of sp 3-rich fragments. Chem Sci 2021; 12:4646-4660. [PMID: 34168751 PMCID: PMC8179648 DOI: 10.1039/d1sc00161b] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 02/28/2021] [Indexed: 12/29/2022] Open
Abstract
Fragment-based drug discovery is an important and increasingly reliable technology for the delivery of clinical candidates. Notably, however, sp3-rich fragments are a largely untapped resource in molecular discovery, in part due to the lack of general and suitably robust chemical methods available to aid their development into higher affinity lead and drug compounds. This Perspective describes the challenges associated with developing sp3-rich fragments, and succinctly highlights recent advances in C(sp3)-H functionalisations of high potential value towards advancing fragment hits by 'growing' functionalised rings and chains from unconventional, carbon-centred vectors.
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Affiliation(s)
- Max J Caplin
- School of Physical and Chemical Sciences, University of Canterbury Christchurch New Zealand
| | - Daniel J Foley
- School of Physical and Chemical Sciences, University of Canterbury Christchurch New Zealand
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4
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Li X, Yan X, Yang Y, Gu Q, Zhou H, Du Y, Lu Y, Liao J, Xu J. LSA: a local-weighted structural alignment tool for pharmaceutical virtual screening. RSC Adv 2019; 9:3912-3917. [PMID: 35518105 PMCID: PMC9060470 DOI: 10.1039/c8ra08915a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 01/23/2019] [Indexed: 11/21/2022] Open
Abstract
Similar structures having similar activities is a dogma for identifying new functional molecules. However, it is not rare that a minor structural change can cause a significant activity change. Methods to measure the molecular similarity can be classified into two categories of overall three-dimensional shape based methods and local substructure based methods. The former states the relation between overall similarity and activity, and is represented by conventional similarity algorithms. The latter states the relation between local substructure and activity, and is represented by conventional substructure match algorithms. Practically, the similarity of two molecules with similar activity depends on the contributions from both overall similarity and local substructure match. We report a new tool termed as a local-weighted structural alignment (LSA) tool for pharmaceutical virtual screening, which computes the similarity of two molecular structures by considering the contributions of both overall similarity and local substructure match. LSA consists of three steps: (1) mapping a common substructure between two molecular topological structures; (2) superimposing two three-dimensional molecular structures with substructure focus; (3) computing the similarity score based on superimposing. LSA has been validated with 102 testing compound libraries from DUD-E collection with the average AUC (the area under a receiver-operating characteristic curve) value of 0.82 and an average EF1% (the enrichment factor at top 1%) of 27.0, which had consistently better performance than conventional approaches. LSA is implemented in C++ and run on Linux and Windows systems. A local-weighted structural alignment tool by considering the contributions of both overall similarity and local substructure match.![]()
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Affiliation(s)
- Xiuming Li
- Research Center for Drug Discovery
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- China
| | - Xin Yan
- Research Center for Drug Discovery
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- China
| | - Yuedong Yang
- National Supercomputer Center in Guangzhou
- School of Data and Computer Science
- Sun Yat-Sen University
- Guangzhou 510006
- China
| | - Qiong Gu
- Research Center for Drug Discovery
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- China
| | - Huihao Zhou
- Research Center for Drug Discovery
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- China
| | - Yunfei Du
- National Supercomputer Center in Guangzhou
- School of Data and Computer Science
- Sun Yat-Sen University
- Guangzhou 510006
- China
| | - Yutong Lu
- National Supercomputer Center in Guangzhou
- School of Data and Computer Science
- Sun Yat-Sen University
- Guangzhou 510006
- China
| | - Jielou Liao
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei 230026
- China
| | - Jun Xu
- Research Center for Drug Discovery
- School of Pharmaceutical Sciences
- Sun Yat-Sen University
- Guangzhou 510006
- China
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5
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Birchall K, Merritt A, Sattikar A, Kettleborough C, Saxty B. Design of the LifeArc Index Set and Retrospective Review of Its Performance: A Collection for Sharing. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2018; 24:332-345. [PMID: 30290126 DOI: 10.1177/2472555218803696] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Building, curating, and maintaining a compound collection is an expensive operation, beyond the scope of most academic organizations. Here we describe the selection criteria used to compile the LifeArc diversity set from commercial suppliers and the process we undertook to generate our representative LifeArc index set. The aim was to avoid a "junk in, junk out" screen collection to increase chemical tractability going forward, while maximizing diversity. Using historical LifeArc screening data, we demonstrate that the index set was predictive of ligandability and that progressable hits could be identified by mining associated clusters within our larger diversity set. Indeed, a higher percentage of index-derived hit clusters were found to have been progressed into hit-to-lead programs, reflecting better drug-likeness. In practice, the library has been shared widely with academic groups and used routinely within LifeArc to assess the ligandability of novel targets. Its small size is well suited to meet the needs of medium-throughput screening in labs with either limited automation, limited precious or expensive reagents, or complex cellular assays. The strategy of screening a small set in combination with rapid hit analog follow-up has demonstrated the utility of finding active clusters for potential development against challenging targets.
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Affiliation(s)
| | - Andy Merritt
- 1 LifeArc, Centre for Therapeutic Discovery, Stevenage, UK
| | - Afrah Sattikar
- 1 LifeArc, Centre for Therapeutic Discovery, Stevenage, UK
| | | | - Barbara Saxty
- 1 LifeArc, Centre for Therapeutic Discovery, Stevenage, UK
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6
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Pavić K, Perković I, Pospíšilová Š, Machado M, Fontinha D, Prudêncio M, Jampilek J, Coffey A, Endersen L, Rimac H, Zorc B. Primaquine hybrids as promising antimycobacterial and antimalarial agents. Eur J Med Chem 2017; 143:769-779. [PMID: 29220797 DOI: 10.1016/j.ejmech.2017.11.083] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
Abstract
Four series of primaquine (PQ) derivatives were screened for antitubercular and antiplasmodial activity: amides 1a-k, ureas 2a-s, semicarbazides 3a-c and bis-ureas 4a-u. Antimycobacterial activity of PQ derivatives against Mycobacterium tuberculosis (MTB), M. avium complex (MAC) and M. avium subsp. paratuberculosis (MAP) were evaluated in vitro and compared with PQ and the standard antitubercular drugs. In general, the PQ derivatives showed higher potency than the parent compound. Most of the compounds of series 1 and 2 showed high activity against MAP, comparable or even higher than the relevant drug ciprofloxacin, and weak or no activity against MTB and MAC. bis-Trifluoromethylated cinnamamide 1k showed low cytotoxicity and high activity against all three Mycobacterium species and their activities were comparable or slightly higher than those of the reference drugs. PQ urea derivatives with hydroxyl, halogen and trifluoromethyl substituents on benzene ring 2f-p exerted very strong antimycobacterial activity towards all tested mycobacteria, stronger than PQ and the relevant standard drug(s). Unfortunately, these compounds had relatively high cytotoxicity, except bromo 2l and trifluoromethyl 2m, 2n derivatives. In general, meta-substituted derivatives were more active than analogues para-derivatives. Phenyl ureas were also more active than cycloalkyl or hydroxyalkyl ureas. Semicarbazide 3a showed similar activity as PQ, while the other two semicarbazides were inactive. Bis-urea derivatives 4 were generally less active than the urea derivatives sharing the same scaffold, differing only in the spacer type. Out of 21 evaluated bis-urea derivatives, only p-Cl/m-CF3 phenyl derivative 4p, benzhydryl derivatives 4t and 4u and bis-PQ derivative 4s showed high activity, higher than all three reference drugs. After comparison of activity and cytotoxicity, urea 2m and bis-urea 4u could be considered as the most promising agents. Antimalarial potential of PQ derivatives in vitro against the liver stage of P. berghei was evaluated as well. 3-(4-Chlorophenyl)-1-[({4-[(6-methoxyquinolin-8-yl)amino]pentyl}carbamoyl)amino]urea (4l) was the most active compound (IC50 = 42 nM; cytotoxicity/activity ratio >2000). Our results bring new insights into development of novel anti-TB and antimalarial compounds.
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Affiliation(s)
- Kristina Pavić
- University of Zagreb, Faculty of Pharmacy and Biochemistry, A. Kovačića 1, 10 000 Zagreb, Croatia
| | - Ivana Perković
- University of Zagreb, Faculty of Pharmacy and Biochemistry, A. Kovačića 1, 10 000 Zagreb, Croatia
| | - Šárka Pospíšilová
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University, Odbojárov 10, 83232 Bratislava, Slovakia
| | - Marta Machado
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Diana Fontinha
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Miguel Prudêncio
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - Josef Jampilek
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University, Odbojárov 10, 83232 Bratislava, Slovakia.
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
| | - Lorraine Endersen
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
| | - Hrvoje Rimac
- University of Zagreb, Faculty of Pharmacy and Biochemistry, A. Kovačića 1, 10 000 Zagreb, Croatia
| | - Branka Zorc
- University of Zagreb, Faculty of Pharmacy and Biochemistry, A. Kovačića 1, 10 000 Zagreb, Croatia.
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7
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Heo YJ, Jeon MK. A novel solid-phase synthetic method for production of N -alkyl-4-alkylamino-1-aryl-1 H -pyrazolo[3,4- d ]pyrimidine-6-carboxamide library. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.08.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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8
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Drwal MN, Bret G, Kellenberger E. Multi-target Fragments Display Versatile Binding Modes. Mol Inform 2017; 36. [PMID: 28691374 DOI: 10.1002/minf.201700042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/30/2017] [Indexed: 11/10/2022]
Abstract
Promiscuity is an interesting concept in fragment-based drug design as fragments with low specificity can be advantageous for finding many screening hits. We present a PDB-wide analysis of multi-target fragments and their binding mode conservation. Focussing on multi-target fragments, we found that the majority shows non-conserved binding modes, even if they bind in a similar conformation or similar protein targets. Surprisingly, fragment properties alone are not able to predict whether a fragment will exhibit a versatile or conserved binding mode, emphasizing the interplay between protein and fragment features during a binding event and the importance of structure-based modelling.
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Affiliation(s)
- Malgorzata N Drwal
- UMR 7200 - Laboratoire d'Innovation Thérapeutique, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401, Illkirch, France phone: +33 3 68 85 42 21 fax: +33 3 68 85 43 10
| | - Guillaume Bret
- UMR 7200 - Laboratoire d'Innovation Thérapeutique, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401, Illkirch, France phone: +33 3 68 85 42 21 fax: +33 3 68 85 43 10
| | - Esther Kellenberger
- UMR 7200 - Laboratoire d'Innovation Thérapeutique, Université de Strasbourg, Faculté de Pharmacie, 74 Route du Rhin, 67401, Illkirch, France phone: +33 3 68 85 42 21 fax: +33 3 68 85 43 10
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9
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Mello JDFRE, Gomes RA, Vital-Fujii DG, Ferreira GM, Trossini GHG. Fragment-based drug discovery as alternative strategy to the drug development for neglected diseases. Chem Biol Drug Des 2017; 90:1067-1078. [PMID: 28547936 DOI: 10.1111/cbdd.13030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/12/2017] [Accepted: 05/08/2017] [Indexed: 12/24/2022]
Abstract
Neglected diseases (NDs) affect large populations and almost whole continents, representing 12% of the global health burden. In contrast, the treatment available today is limited and sometimes ineffective. Under this scenery, the Fragment-Based Drug Discovery emerged as one of the most promising alternatives to the traditional methods of drug development. This method allows achieving new lead compounds with smaller size of fragment libraries. Even with the wide Fragment-Based Drug Discovery success resulting in new effective therapeutic agents against different diseases, until this moment few studies have been applied this approach for NDs area. In this article, we discuss the basic Fragment-Based Drug Discovery process, brief successful ideas of general applications and show a landscape of its use in NDs, encouraging the implementation of this strategy as an interesting way to optimize the development of new drugs to NDs.
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Affiliation(s)
- Juliana da Fonseca Rezende E Mello
- Litec, Laboratório de Integração Entre Técnicas Computacionais e Experimentais no Planejamento de Fármacos, Departamento de Farmácia, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Renan Augusto Gomes
- Litec, Laboratório de Integração Entre Técnicas Computacionais e Experimentais no Planejamento de Fármacos, Departamento de Farmácia, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Drielli Gomes Vital-Fujii
- Litec, Laboratório de Integração Entre Técnicas Computacionais e Experimentais no Planejamento de Fármacos, Departamento de Farmácia, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Glaucio Monteiro Ferreira
- Litec, Laboratório de Integração Entre Técnicas Computacionais e Experimentais no Planejamento de Fármacos, Departamento de Farmácia, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-graduação em Toxicologia e Análises Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
| | - Gustavo Henrique Goulart Trossini
- Litec, Laboratório de Integração Entre Técnicas Computacionais e Experimentais no Planejamento de Fármacos, Departamento de Farmácia, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil.,Programa de Pós-graduação em Toxicologia e Análises Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brazil
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10
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Proschak E, Heitel P, Kalinowsky L, Merk D. Opportunities and Challenges for Fatty Acid Mimetics in Drug Discovery. J Med Chem 2017; 60:5235-5266. [PMID: 28252961 DOI: 10.1021/acs.jmedchem.6b01287] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Fatty acids beyond their role as an endogenous energy source and storage are increasingly considered as signaling molecules regulating various physiological effects in metabolism and inflammation. Accordingly, the molecular targets involved in formation and physiological activities of fatty acids hold significant therapeutic potential. A number of these fatty acid targets are addressed by some of the oldest and most widely used drugs such as cyclooxygenase inhibiting NSAIDs, whereas others remain unexploited. Compounds orthosterically binding to proteins that endogenously bind fatty acids are considered as fatty acid mimetics. On the basis of their structural resemblance, fatty acid mimetics constitute a family of bioactive compounds showing specific binding thermodynamics and following similar pharmacokinetic mechanisms. This perspective systematically evaluates targets for fatty acid mimetics, investigates their common structural characteristics, and highlights demands in their discovery and design. In summary, fatty acid mimetics share particularly favorable characteristics justifying the conclusion that their therapeutic potential vastly outweighs the challenges in their design.
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Affiliation(s)
- Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Pascal Heitel
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Lena Kalinowsky
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt , Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
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11
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Twigg DG, Kondo N, Mitchell SL, Galloway WRJD, Sore HF, Madin A, Spring DR. Partially Saturated Bicyclic Heteroaromatics as an sp(3) -Enriched Fragment Collection. Angew Chem Int Ed Engl 2016; 55:12479-83. [PMID: 27596095 PMCID: PMC5091628 DOI: 10.1002/anie.201606496] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/01/2016] [Indexed: 12/12/2022]
Abstract
Fragment‐based lead generation has proven to be an effective means of identifying high‐quality lead compounds for drug discovery programs. However, the fragment screening sets often used are principally comprised of sp2‐rich aromatic compounds, which limits the structural (and hence biological) diversity of the library. Herein, we describe strategies for the synthesis of a series of partially saturated bicyclic heteroaromatic scaffolds with enhanced sp3 character. Subsequent derivatization led to a fragment collection featuring regio‐ and stereo‐controlled introduction of substituents on the saturated ring system, often with formation of new stereocenters.
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Affiliation(s)
- David G Twigg
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK
| | - Noriyasu Kondo
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK.,Shionogi & Co. Ltd., 1-1, Futaba-cho 3-chome, Toyonaka, Osaka, 561-0825, Japan
| | - Sophie L Mitchell
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK
| | - Warren R J D Galloway
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK
| | - Hannah F Sore
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK
| | - Andrew Madin
- AstraZeneca UK Ltd., 310 Cambridge Science Park, Milton Rd, Cambridge, CB4 0FZ, UK
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW, UK.
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12
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Twigg DG, Kondo N, Mitchell SL, Galloway WRJD, Sore HF, Madin A, Spring DR. Partially Saturated Bicyclic Heteroaromatics as an sp3
-Enriched Fragment Collection. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606496] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- David G. Twigg
- Department of Chemistry; University of Cambridge; Lensfield Rd Cambridge CB2 1EW UK
| | - Noriyasu Kondo
- Department of Chemistry; University of Cambridge; Lensfield Rd Cambridge CB2 1EW UK
- Shionogi & Co. Ltd.; 1-1, Futaba-cho 3-chome, Toyonaka Osaka 561-0825 Japan
| | - Sophie L. Mitchell
- Department of Chemistry; University of Cambridge; Lensfield Rd Cambridge CB2 1EW UK
| | | | - Hannah F. Sore
- Department of Chemistry; University of Cambridge; Lensfield Rd Cambridge CB2 1EW UK
| | - Andrew Madin
- AstraZeneca UK Ltd.; 310 Cambridge Science Park, Milton Rd Cambridge CB4 0FZ UK
| | - David R. Spring
- Department of Chemistry; University of Cambridge; Lensfield Rd Cambridge CB2 1EW UK
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13
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Jeon MK, Kim JG, Lee DH. Novel Solid-phase and Solution-phase Synthetic Methods for Trisubstituted Thieno[3,2- d]pyrimidine Derivatives. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Moon-Kook Jeon
- Bio & Drug Discovery Division; Korea Research Institute of Chemical Technology; 141 Gajeong-ro, Yuseong-gu Daejeon 305-600 Republic of Korea
| | - Jung-Gyu Kim
- Bio & Drug Discovery Division; Korea Research Institute of Chemical Technology; 141 Gajeong-ro, Yuseong-gu Daejeon 305-600 Republic of Korea
- Department of Chemistry; Sogang University; 1 Sogangdae-gil, Mapo-gu Seoul 121-742 Republic of Korea
| | - Duck-Hyung Lee
- Department of Chemistry; Sogang University; 1 Sogangdae-gil, Mapo-gu Seoul 121-742 Republic of Korea
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14
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Keserű GM, Erlanson DA, Ferenczy GG, Hann MM, Murray CW, Pickett SD. Design Principles for Fragment Libraries: Maximizing the Value of Learnings from Pharma Fragment-Based Drug Discovery (FBDD) Programs for Use in Academia. J Med Chem 2016; 59:8189-206. [DOI: 10.1021/acs.jmedchem.6b00197] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- György M. Keserű
- Research
Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
körútja 2, H-1117, Budapest, Hungary
| | - Daniel A. Erlanson
- Carmot Therapeutics, Inc. 409 Illinois Street, San Francisco, California 94158, United States
| | - György G. Ferenczy
- Research
Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok
körútja 2, H-1117, Budapest, Hungary
| | - Michael M. Hann
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Christopher W. Murray
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton
Road, Cambridge CB4 0QA, U.K
| | - Stephen D. Pickett
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
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15
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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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16
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Aretz J, Kondoh Y, Honda K, Anumala UR, Nazaré M, Watanabe N, Osada H, Rademacher C. Chemical fragment arrays for rapid druggability assessment. Chem Commun (Camb) 2016; 52:9067-70. [DOI: 10.1039/c5cc10457b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Incorporation of early druggability assessment in the drug discovery process provides a means to prioritize target proteins for high-throughput screening.
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Affiliation(s)
- J. Aretz
- Department of Biomolecular Systems
- Max Planck Institute of Colloids and Interfaces
- Potsdam
- Germany
- Department of Biology
| | - Y. Kondoh
- Antibiotics Laboratory
- RIKEN
- Wako
- Japan
- Chemical Biology Research Group
| | - K. Honda
- Antibiotics Laboratory
- RIKEN
- Wako
- Japan
- Chemical Biology Research Group
| | - U. R. Anumala
- Leibniz Institut für Molekulare Pharmakologie (FMP)
- Berlin
- Germany
| | - M. Nazaré
- Leibniz Institut für Molekulare Pharmakologie (FMP)
- Berlin
- Germany
| | - N. Watanabe
- Antibiotics Laboratory
- RIKEN
- Wako
- Japan
- Chemical Biology Research Group
| | - H. Osada
- Antibiotics Laboratory
- RIKEN
- Wako
- Japan
- Chemical Biology Research Group
| | - C. Rademacher
- Department of Biomolecular Systems
- Max Planck Institute of Colloids and Interfaces
- Potsdam
- Germany
- Department of Biology
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17
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Abstract
A powerful early approach to evaluating the druggability of proteins involved determining the hit rate in NMR-based screening of a library of small compounds. Here, we show that a computational analog of this method, based on mapping proteins using small molecules as probes, can reliably reproduce druggability results from NMR-based screening and can provide a more meaningful assessment in cases where the two approaches disagree. We apply the method to a large set of proteins. The results show that, because the method is based on the biophysics of binding rather than on empirical parametrization, meaningful information can be gained about classes of proteins and classes of compounds beyond those resembling validated targets and conventionally druglike ligands. In particular, the method identifies targets that, while not druggable by druglike compounds, may become druggable using compound classes such as macrocycles or other large molecules beyond the rule-of-five limit.
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Affiliation(s)
- Dima Kozakov
- Department of Applied Mathematics & Statistics, Stony Brook University , Stony Brook, New York 11794, United States
| | - David R Hall
- Acpharis Inc. , Holliston, Massachusetts 01746, United States
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18
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Abstract
Fragment-based screening is now recognised as a powerful method for the design of novel potent molecules against therapeutic protein targets including challenging targets. Here, the main concepts used in the fragment-based drug design approach are reviewed, together with the reasons for its success. Methods and strategies used to identify, validate and select fragments are discussed. Future challenges and developments that are expected for the next decade are presented.
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Affiliation(s)
- Isabelle Krimm
- Institut des sciences analytiques, UMR CNRS 5280, 5, rue de La Doua, 69100 Villeurbanne, France
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19
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Abstract
Very few chemically novel agents have been approved for antibacterial chemotherapies during the last 50 yr. Yet new antibacterial drugs are needed to reduce the impact on global health of an increasing number of drug-resistant infections, including highly drug-resistant forms of tuberculosis. This review discusses how genetic approaches can be used to study the mechanism of action of whole-cell screening hits and facilitate target-driven strategies for antimicrobial drug development.
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Affiliation(s)
- Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065
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20
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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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21
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Miller TR, Rutherford TJ, Birchall K, Chugh J, Fiedler M, Bienz M. Competitive binding of a benzimidazole to the histone-binding pocket of the Pygo PHD finger. ACS Chem Biol 2014; 9:2864-74. [PMID: 25323450 PMCID: PMC4330097 DOI: 10.1021/cb500585s] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/16/2014] [Indexed: 01/01/2023]
Abstract
The Pygo-BCL9 complex is a chromatin reader, facilitating β-catenin-mediated oncogenesis, and is thus emerging as a potential therapeutic target for cancer. Its function relies on two ligand-binding surfaces of Pygo's PHD finger that anchor the histone H3 tail methylated at lysine 4 (H3K4me) with assistance from the BCL9 HD1 domain. Here, we report the first use of fragment-based screening by NMR to identify small molecules that block protein-protein interactions by a PHD finger. This led to the discovery of a set of benzothiazoles that bind to a cleft emanating from the PHD-HD1 interface, as defined by X-ray crystallography. Furthermore, we discovered a benzimidazole that docks into the H3K4me specificity pocket and displaces the native H3K4me peptide from the PHD finger. Our study demonstrates the ligandability of the Pygo-BCL9 complex and uncovers a privileged scaffold as a template for future development of lead inhibitors of oncogenesis.
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Affiliation(s)
- Thomas
C. R. Miller
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Trevor J. Rutherford
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Kristian Birchall
- MRC
Technology, 1-3 Burtonhole
Lane, Mill Hill, London, NW7 1AD, United Kingdom
| | - Jasveen Chugh
- MRC
Technology, 1-3 Burtonhole
Lane, Mill Hill, London, NW7 1AD, United Kingdom
| | - Marc Fiedler
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Mariann Bienz
- MRC
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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22
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Lucas X, Günther S. Using chiral molecules as an approach to address low-druggability recognition sites. J Comput Chem 2014; 35:2114-21. [PMID: 25223950 DOI: 10.1002/jcc.23726] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/13/2014] [Accepted: 08/20/2014] [Indexed: 11/07/2022]
Abstract
The content of chiral carbon atoms or structural complexity, which is known to correlate well with relevant physicochemical properties of small molecules, represents a promising descriptor that could fill the gap in existing drug discovery between ligand library filtering rules and the corresponding properties of the target's recognition site. Herein, we present an in silico study on the yet unclear underlying correlations between molecular complexity and other more sophisticated physicochemical and biological properties. By analyzing thousands of protein-ligand complexes from DrugBank, we show that increasing molecular complexity of drugs is an approach to addressing particularly low-druggability and polar recognition sites. We also show that biologically relevant protein classes characteristically bind molecules with a certain degree of structural complexity. Three distinct behaviors toward drug recognition are described. The reported results set the basis for a better understanding of protein-drug recognition, and open the possibility of including target information in the filtering of large ligand libraries for screening.
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Affiliation(s)
- Xavier Lucas
- Pharmaceutical Bioinformatics, Institute of Pharmaceutical Sciences, University of Freiburg, 79104, Germany
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23
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Barelier S, Eidam O, Fish I, Hollander J, Figaroa F, Nachane R, Irwin JJ, Shoichet BK, Siegal G. Increasing chemical space coverage by combining empirical and computational fragment screens. ACS Chem Biol 2014; 9:1528-35. [PMID: 24807704 PMCID: PMC4215856 DOI: 10.1021/cb5001636] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Most libraries for fragment-based drug discovery are restricted to 1,000-10,000 compounds, but over 500,000 fragments are commercially available and potentially accessible by virtual screening. Whether this larger set would increase chemotype coverage, and whether a computational screen can pragmatically prioritize them, is debated. To investigate this question, a 1281-fragment library was screened by nuclear magnetic resonance (NMR) against AmpC β-lactamase, and hits were confirmed by surface plasmon resonance (SPR). Nine hits with novel chemotypes were confirmed biochemically with KI values from 0.2 to low mM. We also computationally docked 290,000 purchasable fragments with chemotypes unrepresented in the empirical library, finding 10 that had KI values from 0.03 to low mM. Though less novel than those discovered by NMR, the docking-derived fragments filled chemotype holes from the empirical library. Crystal structures of nine of the fragments in complex with AmpC β-lactamase revealed new binding sites and explained the relatively high affinity of the docking-derived fragments. The existence of chemotype holes is likely a general feature of fragment libraries, as calculation suggests that to represent the fragment substructures of even known biogenic molecules would demand a library of minimally over 32,000 fragments. Combining computational and empirical fragment screens enables the discovery of unexpected chemotypes, here by the NMR screen, while capturing chemotypes missing from the empirical library and tailored to the target, with little extra cost in resources.
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Affiliation(s)
- Sarah Barelier
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall, San Francisco, California 94158, United States
| | - Oliv Eidam
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall, San Francisco, California 94158, United States
| | - Inbar Fish
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall, San Francisco, California 94158, United States
- Department
of Biochemistry and Molecular Biology, George S. Wise Faculty of Life
SciencesTel-Aviv University, Ramat Aviv, Israel
| | | | | | - Ruta Nachane
- ZoBio, Eisteinweg 55, 2300-RA Leiden, The Netherlands
| | - John J. Irwin
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall, San Francisco, California 94158, United States
- Leslie
Dan Faculty of Pharmacy, University of Toronto, Donnelly Centre Suite 604, 160 College
Street, Toronto, Ontario, Canada M5S 3E1
| | - Brian K. Shoichet
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th St., Byers Hall, San Francisco, California 94158, United States
- Leslie
Dan Faculty of Pharmacy, University of Toronto, Donnelly Centre Suite 604, 160 College
Street, Toronto, Ontario, Canada M5S 3E1
| | - Gregg Siegal
- ZoBio, Eisteinweg 55, 2300-RA Leiden, The Netherlands
- Leiden University, Eisteinweg 55, 2300-RA Leiden, The Netherlands
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24
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Vu H, Roullier C, Campitelli M, Trenholme KR, Gardiner DL, Andrews KT, Skinner-Adams T, Crowther GJ, Van Voorhis WC, Quinn RJ. Plasmodium gametocyte inhibition identified from a natural-product-based fragment library. ACS Chem Biol 2013; 8:2654-9. [PMID: 24079418 DOI: 10.1021/cb400582b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Fragment-based screening is commonly used to identify compounds with relatively weak but efficient localized binding to protein surfaces. We used mass spectrometry to study fragment-sized three-dimensional natural products. We identified seven securinine-related compounds binding to Plasmodium falciparum 2'-deoxyuridine 5'-triphosphate nucleotidohydrolase (PfdUTPase). Securinine bound allosterically to PfdUTPase, enhancing enzyme activity and inhibiting viability of both P. falciparum gametocyte (sexual) and blood (asexual) stage parasites. Our results provide a new insight into mechanisms that may be applicable to transmission-blocking agents.
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Affiliation(s)
- Hoan Vu
- Eskitis
Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Catherine Roullier
- Eskitis
Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Marc Campitelli
- Eskitis
Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Katharine R. Trenholme
- Queensland Institute of Medical Research, Herston, Queensland, Australia
- School
of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Donald L. Gardiner
- Queensland Institute of Medical Research, Herston, Queensland, Australia
| | - Katherine T. Andrews
- Eskitis
Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Tina Skinner-Adams
- Eskitis
Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Gregory J. Crowther
- Department
of Medicine, University of Washington, Seattle, Washington, United States
| | - Wesley C. Van Voorhis
- Department
of Medicine, University of Washington, Seattle, Washington, United States
| | - Ronald J. Quinn
- Eskitis
Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
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25
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Abstract
The incidence of malignant melanoma is increasing annually. Early stages can be cured with surgical intervention but metastatic disease has generally had a dismal prognosis with few effective interventions. A half of all melanomas possess a BRAF mutation, which can be targeted by specific inhibitors. Vemurafenib is an orally active, purposely designed mutant BRAF inhibitor, which has recently been shown to have a survival benefit measured in months in metastatic patients. In this article, the authors discuss the scientific rationale, drug development process and clinical trials that have led to vemurafenib becoming the first BRAF inhibitor approved for the treatment of patients with mutant BRAF metastatic melanoma.
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Affiliation(s)
- Heather M Shaw
- Mount Vernon Cancer Centre, Rickmansworth Road, Northwood, Middlesex, HA6 2RN, UK
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26
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Virtual and biophysical screening targeting the γ-tubulin complex--a new target for the inhibition of microtubule nucleation. PLoS One 2013; 8:e63908. [PMID: 23691113 PMCID: PMC3655011 DOI: 10.1371/journal.pone.0063908] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 04/08/2013] [Indexed: 01/11/2023] Open
Abstract
Microtubules are the main constituents of mitotic spindles. They are nucleated in large amounts during spindle assembly, from multiprotein complexes containing γ-tubulin and associated γ-tubulin complex proteins (GCPs). With the aim of developing anti-cancer drugs targeting these nucleating complexes, we analyzed the interface between GCP4 and γ-tubulin proteins usually located in a multiprotein complex named γ-TuRC (γ-Tubulin Ring Complex). 10 ns molecular dynamics simulations were performed on the heterodimers to obtain a stable complex in silico and to analyze the residues involved in persistent protein-protein contacts, responsible for the stability of the complex. We demonstrated in silico the existence of a binding pocket at the interface between the two proteins upon complex formation. By combining virtual screening using a fragment-based approach and biophysical screening, we found several small molecules that bind specifically to this pocket. Sub-millimolar fragments have been experimentally characterized on recombinant proteins using differential scanning fluorimetry (DSF) for validation of these compounds as inhibitors. These results open a new avenue for drug development against microtubule-nucleating γ-tubulin complexes.
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27
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Lee JH, Park S, Hyun H, Bordo MW, Oketokoun R, Nasr KA, Frangioni JV, Choi HS. High-throughput screening of small molecule ligands targeted to live bacteria surface. Anal Chem 2013; 85:3508-14. [PMID: 23461528 DOI: 10.1021/ac303199x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The discovery of small molecule ligands targeted to the surface of live pathogenic bacteria would enable an entirely new class of antibiotics. We report the development and validation of a microarray-based high-throughput screening platform for bacteria that exploits 300 μm diameter chemical spots in a 1 in. × 3 in. nanolayered glass slide format. Using 24 model compounds and 4 different bacterial strains, we optimized the screening technology, including fluorophore-based optical deconvolution for automated scoring of affinity and cyan-magenta-yellow-key (CMYK) color-coding for scoring of both affinity and specificity. The latter provides a lossless, one-dimensional view of multidimensional data. By linking in silico analysis with cell binding affinity and specificity, we could also begin to identify the physicochemical factors that affect ligand performance. The technology we describe could form the foundation for developing new classes of antibiotics.
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Affiliation(s)
- Jeong Heon Lee
- Center for Molecular Imaging, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, United States
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28
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Guo Y, Partch CL, Key J, Card PB, Pashkov V, Patel A, Bruick RK, Wurdak H, Gardner KH. Regulating the ARNT/TACC3 axis: multiple approaches to manipulating protein/protein interactions with small molecules. ACS Chem Biol 2013; 8:626-35. [PMID: 23240775 DOI: 10.1021/cb300604u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
For several well-documented reasons, it has been challenging to develop artificial small molecule inhibitors of protein/protein complexes. Such reagents are of particular interest for transcription factor complexes given links between their misregulation and disease. Here we report parallel approaches to identify regulators of a hypoxia signaling transcription factor complex, involving the ARNT subunit of the HIF (Hypoxia Inducible Factor) activator and the TACC3 (Transforming Acidic Coiled Coil Containing Protein 3) coactivator. In one route, we used in vitro NMR and biochemical screening to identify small molecules that selectively bind within the ARNT PAS (Per-ARNT-Sim) domain that recruits TACC3, identifying KG-548 as an ARNT/TACC3 disruptor. A parallel, cell-based screening approach previously implicated the small molecule KHS101 as an inhibitor of TACC3 signaling. Here, we show that KHS101 works indirectly on HIF complex formation by destabilizing both TACC3 and the HIF component HIF-1α. Overall, our data identify small molecule regulators for this important complex and highlight the utility of pursuing parallel strategies to develop protein/protein inhibitors.
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Affiliation(s)
| | | | | | | | | | - Anjana Patel
- Leeds Institute of Molecular Medicine, University of Leeds, St. James’s University
Hospital, Beckett Street, Leeds LS9 7TF, U.K
| | | | - Heiko Wurdak
- Leeds Institute of Molecular Medicine, University of Leeds, St. James’s University
Hospital, Beckett Street, Leeds LS9 7TF, U.K
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29
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Chen H, Yang Z, Ding C, Chu L, Zhang Y, Terry K, Liu H, Shen Q, Zhou J. Fragment-based drug design and identification of HJC0123, a novel orally bioavailable STAT3 inhibitor for cancer therapy. Eur J Med Chem 2013; 62:498-507. [PMID: 23416191 DOI: 10.1016/j.ejmech.2013.01.023] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 01/14/2013] [Accepted: 01/17/2013] [Indexed: 01/05/2023]
Abstract
Fragment-based drug design (FBDD) is a promising approach for the generation of lead molecules with enhanced activity and especially drug-like properties against therapeutic targets. Herein, we report the fragment-based drug design, systematic chemical synthesis and pharmacological evaluation of novel scaffolds as potent anticancer agents by utilizing six privileged fragments from known STAT3 inhibitors. Several new molecules such as compounds 5, 12, and 19 that may act as advanced chemical leads have been identified. The most potent compound 5 (HJC0123) has demonstrated to inhibit STAT3 promoter activity, downregulate phosphorylation of STAT3, increase the expression of cleaved caspase-3, inhibit cell cycle progression and promote apoptosis in breast and pancreatic cancer cells with low micromolar to nanomolar IC50 values. Furthermore, compound 5 significantly suppressed estrogen receptor (ER)-negative breast cancer MDA-MB-231 xenograft tumor growth in vivo (p.o.), indicating its great potential as an efficacious and orally bioavailable drug candidate for human cancer therapy.
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Affiliation(s)
- Haijun Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, United States
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30
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Abstract
The ability of many drugs, unintended most often, to interact with multiple proteins is commonly referred to as polypharmacology. Could this be a reminiscent chemical signature of early protein evolution?
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Affiliation(s)
- Xavier Jalencas
- Chemogenomics Laboratory
- Research Programme on Biomedical Informatics (GRIB)
- IMIM Hospital del Mar Research Institute and University Pompeu Fabra
- Parc de Recerca Biomèdica
- 08003 Barcelona
| | - Jordi Mestres
- Chemogenomics Laboratory
- Research Programme on Biomedical Informatics (GRIB)
- IMIM Hospital del Mar Research Institute and University Pompeu Fabra
- Parc de Recerca Biomèdica
- 08003 Barcelona
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31
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Fragment-based discovery of novel and selective mPGES-1 inhibitors Part 1: Identification of sulfonamido-1,2,3-triazole-4,5-dicarboxylic acid. Bioorg Med Chem Lett 2013; 23:75-80. [DOI: 10.1016/j.bmcl.2012.11.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 10/20/2012] [Accepted: 11/07/2012] [Indexed: 11/19/2022]
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32
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Schmidt MF, Korb O, Howard NI, Dias MVB, Blundell TL, Abell C. Discovery of Schaeffer’s Acid Analogues as Lead Structures ofMycobacterium tuberculosisType II Dehydroquinase Using a Rational Drug Design Approach. ChemMedChem 2012; 8:54-8. [DOI: 10.1002/cmdc.201200508] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Indexed: 11/11/2022]
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33
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Scott DE, Coyne AG, Hudson SA, Abell C. Fragment-Based Approaches in Drug Discovery and Chemical Biology. Biochemistry 2012; 51:4990-5003. [DOI: 10.1021/bi3005126] [Citation(s) in RCA: 324] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Duncan E. Scott
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Anthony G. Coyne
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Sean A. Hudson
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
| | - Chris Abell
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United
Kingdom
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34
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35
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Taboureau O, Baell JB, Fernández-Recio J, Villoutreix BO. Established and emerging trends in computational drug discovery in the structural genomics era. ACTA ACUST UNITED AC 2012; 19:29-41. [PMID: 22284352 DOI: 10.1016/j.chembiol.2011.12.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 12/05/2011] [Accepted: 12/08/2011] [Indexed: 12/01/2022]
Abstract
Bioinformatics and chemoinformatics approaches contribute to hit discovery, hit-to-lead optimization, safety profiling, and target identification and enhance our overall understanding of the health and disease states. A vast repertoire of computational methods has been reported and increasingly combined in order to address more and more challenging targets or complex molecular mechanisms in the context of large-scale integration of structure and bioactivity data produced by private and public drug research. This review explores some key computational methods directly linked to drug discovery and chemical biology with a special emphasis on compound collection preparation, virtual screening, protein docking, and systems pharmacology. A list of generally freely available software packages and online resources is provided, and examples of successful applications are briefly commented upon.
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Affiliation(s)
- Olivier Taboureau
- Center for Biological Sequences Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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36
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Emerging role of surface plasmon resonance in fragment-based drug discovery. Future Med Chem 2012; 3:1809-20. [PMID: 22004086 DOI: 10.4155/fmc.11.128] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Surface plasmon resonance (SPR) offers a method of biophysical fragment screening that is fast, efficient, cost effective and accurate. SPR is increasingly being adopted as a secondary assay to validate fragment hits. Recently, technical advances have resulted in the emergence of SPR as a primary screening methodology for fragment-based drug discovery. Moreover, SPR biosensor assays can be developed for a wide range of proteins, including membrane proteins, such as G-protein-coupled receptors. In this review, we discuss the advantages and limitations of SPR fragment screening including experimental consideration of reducing false positive and false negative rates to a minimum. We discuss how ligand efficiency can be used both as a method to eliminate false positives and to understand which fragments in a library may be a source of false negatives.
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Krimm I, Lancelin JM, Praly JP. Binding evaluation of fragment-based scaffolds for probing allosteric enzymes. J Med Chem 2012; 55:1287-95. [PMID: 22229710 DOI: 10.1021/jm201439b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fragment-based drug discovery has become a powerful method for the generation of drug leads against therapeutic targets. Beyond the identification of novel and effective starting points for drug design, fragments have emerged as reliable tools for assessing protein druggability and identifying protein hot spots. Here, we have examined fragments resulting from the deconstruction of known inhibitors from the glycogen phosphorylase enzyme, a therapeutic target against type 2 diabetes, with two motivations. First, we have analyzed the fragment binding to the multiple binding sites of the glycogen phosphorylase, and then we have investigated the use of fragments to study allosteric enzymes. The work we report illustrates the power of fragmentlike ligands not only for probing the various binding pockets of proteins, but also for uncovering cooperativity between these various binding sites.
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Affiliation(s)
- Isabelle Krimm
- Institut des Sciences Analytiques, UMR CNRS 5280, Université de Lyon, Université Claude Bernard Lyon 1, Bât. CPE Lyon, Domaine scientifique de la Doua, F-69622 Villeurbanne, France.
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Jordan JB, Poppe L, Xia X, Cheng AC, Sun Y, Michelsen K, Eastwood H, Schnier PD, Nixey T, Zhong W. Fragment Based Drug Discovery: Practical Implementation Based on 19F NMR Spectroscopy. J Med Chem 2012; 55:678-87. [DOI: 10.1021/jm201441k] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John B. Jordan
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Leszek Poppe
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Xiaoyang Xia
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Alan C. Cheng
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Yax Sun
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Klaus Michelsen
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Heather Eastwood
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Paul D. Schnier
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Thomas Nixey
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
| | - Wenge Zhong
- Department
of Molecular Structure, and ‡Chemistry Research and Discovery, Amgen, Inc., One Amgen Center Drive, Thousand Oaks,
California 91320, United States
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Krimm I. INPHARMA-based identification of ligand binding site in fragment-based drug design. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20035j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Dou D, He G, Mandadapu SR, Aravapalli S, Kim Y, Chang KO, Groutas WC. Inhibition of noroviruses by piperazine derivatives. Bioorg Med Chem Lett 2011; 22:377-9. [PMID: 22119464 DOI: 10.1016/j.bmcl.2011.10.122] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 10/27/2011] [Accepted: 10/31/2011] [Indexed: 11/27/2022]
Abstract
There is currently an unmet need for the development of small-molecule therapeutics for norovirus infection. The piperazine scaffold, a privileged structure embodied in many pharmacological agents, was used to synthesize an array of structurally-diverse derivatives which were screened for anti-norovius activity in a cell-based replicon system. The studies described herein demonstrate for the first time that functionalized piperazine derivatives possess anti-norovirus activity. Furthermore, these studies have led to the identification of two promising compounds (6a and 9l) that can be used as a launching pad for the optimization of potency, cytotoxicity, and drug-like characteristics.
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Affiliation(s)
- Dengfeng Dou
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA
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