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Cheng MY, Hsu IC, Huang SY, Chuang YT, Ke TY, Chang HW, Chu TH, Chen CY, Cheng YB. Marine Prostanoids with Cytotoxic Activity from Octocoral Clavularia spp. Mar Drugs 2024; 22:219. [PMID: 38786610 PMCID: PMC11122631 DOI: 10.3390/md22050219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Octocoral of the genus Clavularia is a kind of marine invertebrate possessing abundant cytotoxic secondary metabolites, such as prostanoids and dolabellanes. In our continuous natural product study of C. spp., two previously undescribed prostanoids [clavulone I-15-one (1) and 12-O-deacetylclavulone I (2)] and eleven known analogs (3-13) were identified. The structures of these new compounds were elucidated based on analysis of their 1D and 2D NMR, HRESIMS, and IR data. Additionally, all tested prostanoids (1 and 3-13) showed potent cytotoxic activities against the human oral cancer cell line (Ca9-22). The major compound 3 showed cytotoxic activity against the Ca9-22 cells with the IC50 value of 2.11 ± 0.03 μg/mL, which echoes the cytotoxic effect of the coral extract. In addition, in silico tools were used to predict the possible effects of isolated compounds on human tumor cell lines and nitric oxide production, as well as the pharmacological potentials.
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Affiliation(s)
- Ming-Ya Cheng
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 804201, Taiwan; (M.-Y.C.); (T.-Y.K.)
| | - I-Chi Hsu
- Division of Pharmacy, Zuoying Armed Forces General Hospital, Kaohsiung 813204, Taiwan;
| | - Shi-Ying Huang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China;
| | - Ya-Ting Chuang
- PhD Program in Life Sciences, Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung 807378, Taiwan; (Y.-T.C.); (H.-W.C.)
| | - Tzi-Yi Ke
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 804201, Taiwan; (M.-Y.C.); (T.-Y.K.)
| | - Hsueh-Wei Chang
- PhD Program in Life Sciences, Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung 807378, Taiwan; (Y.-T.C.); (H.-W.C.)
- Center for Cancer Research, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 807378, Taiwan
| | - Tian-Huei Chu
- Medical Laboratory, Medical Education and Research Center, Kaohsiung Armed Forces General Hospital, Kaohsiung 802301, Taiwan;
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 804201, Taiwan
| | - Ching-Yeu Chen
- Department of Physical Therapy, Tzu-Hui Institute of Technology, Pingtung 926001, Taiwan;
| | - Yuan-Bin Cheng
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 804201, Taiwan; (M.-Y.C.); (T.-Y.K.)
- Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 807378, Taiwan
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2
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Marsili G, Acchioni C, Remoli AL, Amatore D, Sgarbanti R, De Angelis M, Orsatti R, Acchioni M, Astolfi A, Iraci N, Puzelli S, Facchini M, Perrotti E, Cecchetti V, Sabatini S, Superti F, Agamennone M, Barreca ML, Hiscott J, Nencioni L, Sgarbanti M. Identification of Anti-Influenza A Compounds Inhibiting the Viral Non-Structural Protein 1 (NS1) Using a Type I Interferon-Driven Screening Strategy. Int J Mol Sci 2023; 24:10495. [PMID: 37445672 DOI: 10.3390/ijms241310495] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
There is an urgent need to identify efficient antiviral compounds to combat existing and emerging RNA virus infections, particularly those related to seasonal and pandemic influenza outbreaks. While inhibitors of the influenza viral integral membrane proton channel protein (M2), neuraminidase (NA), and cap-dependent endonuclease are available, circulating influenza viruses acquire resistance over time. Thus, the need for the development of additional anti-influenza drugs with novel mechanisms of action exists. In the present study, a cell-based screening assay and a small molecule library were used to screen for activities that antagonized influenza A non-structural protein 1 (NS1), a highly conserved, multifunctional accessory protein that inhibits the type I interferon response against influenza. Two potential anti-influenza agents, compounds 157 and 164, were identified with anti-NS1 activity, resulting in the reduction of A/PR/8/34(H1N1) influenza A virus replication and the restoration of IFN-β expression in human lung epithelial A549 cells. A 3D pharmacophore modeling study of the active compounds provided a glimpse of the structural motifs that may contribute to anti-influenza virus activity. This screening approach is amenable to a broader analysis of small molecule compounds to inhibit other viral targets.
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Affiliation(s)
- Giulia Marsili
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Chiara Acchioni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Anna Lisa Remoli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Donatella Amatore
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University, 00185 Rome, Italy
| | - Rossella Sgarbanti
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University, 00185 Rome, Italy
| | - Marta De Angelis
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University, 00185 Rome, Italy
- Laboratory of Virology, Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy
| | - Roberto Orsatti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Marta Acchioni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Andrea Astolfi
- Department of Pharmaceutical Sciences, Università degli Studi di Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Nunzio Iraci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Simona Puzelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Marzia Facchini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Edvige Perrotti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Violetta Cecchetti
- Department of Pharmaceutical Sciences, Università degli Studi di Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Stefano Sabatini
- Department of Pharmaceutical Sciences, Università degli Studi di Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Fabiana Superti
- National Centre for Innovative Technologies in Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Mariangela Agamennone
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
| | - Maria Letizia Barreca
- Department of Pharmaceutical Sciences, Università degli Studi di Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - John Hiscott
- Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy
| | - Lucia Nencioni
- Department of Public Health and Infectious Diseases, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University, 00185 Rome, Italy
| | - Marco Sgarbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
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3
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Liao Y, Chin Chan S, Welsh EA, Fang B, Sun L, Schönbrunn E, Koomen JM, Duckett DR, Haura EB, Monastyrskyi A, Rix U. Chemical Proteomics with Novel Fully Functionalized Fragments and Stringent Target Prioritization Identifies the Glutathione-Dependent Isomerase GSTZ1 as a Lung Cancer Target. ACS Chem Biol 2023; 18:251-264. [PMID: 36630201 DOI: 10.1021/acschembio.2c00587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Photoreactive fragment-like probes have been applied to discover target proteins that constitute novel cellular vulnerabilities and to identify viable chemical hits for drug discovery. Through forming covalent bonds, functionalized probes can achieve stronger target engagement and require less effort for on-target mechanism validation. However, the design of probe libraries, which directly affects the biological target space that is interrogated, and effective target prioritization remain critical challenges of such a chemical proteomic platform. In this study, we designed and synthesized a diverse panel of 20 fragment-based probes containing natural product-based privileged structural motifs for small-molecule lead discovery. These probes were fully functionalized with orthogonal diazirine and alkyne moieties and used for protein crosslinking in live lung cancer cells, target enrichment via "click chemistry," and subsequent target identification through label-free quantitative liquid chromatography-tandem mass spectrometry analysis. Pair-wise comparison with a blunted negative control probe and stringent prioritization via individual cross-comparisons against the entire panel identified glutathione S-transferase zeta 1 (GSTZ1) as a specific and unique target candidate. DepMap database query, RNA interference-based gene silencing, and proteome-wide tyrosine reactivity profiling suggested that GSTZ1 cooperated with different oncogenic alterations by supporting survival signaling in refractory non-small cell lung cancer cells. This finding may form the basis for developing novel GSTZ1 inhibitors to improve the therapeutic efficacy of oncogene-directed targeted drugs. In summary, we designed a novel fragment-based probe panel and developed a target prioritization scheme with improved stringency, which allows for the identification of unique target candidates, such as GSTZ1 in refractory lung cancer.
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Affiliation(s)
- Yi Liao
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States
| | - Sean Chin Chan
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States.,Cancer Chemical Biology Ph.D. Program, University of South Florida, Tampa, Florida 33620, United States
| | - Eric A Welsh
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States
| | - Bin Fang
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States
| | - Luxin Sun
- Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States
| | - Ernst Schönbrunn
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States.,Chemical Biology Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States
| | - John M Koomen
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States.,Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States
| | - Derek R Duckett
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States.,Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States
| | - Andrii Monastyrskyi
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States.,Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States.,Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida 33612, United States.,Department of Oncologic Sciences, University of South Florida, Tampa, Florida 33620, United States
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Martín-Acosta P, Amesty Á, Guerra-Rodríguez M, Guerra B, Fernández-Pérez L, Estévez-Braun A. Modular Synthesis and Antiproliferative Activity of New Dihydro-1 H-pyrazolo[1,3- b]pyridine Embelin Derivatives. Pharmaceuticals (Basel) 2021; 14:ph14101026. [PMID: 34681250 PMCID: PMC8541493 DOI: 10.3390/ph14101026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 11/24/2022] Open
Abstract
A set of new dihydro-1H-pyrazolo[1,3-b]pyridine and pyrazolo[1,3-b]pyridine embelin derivatives was synthesized through a multicomponent reaction from natural embelin, 3-substituted-5-aminopyrazoles and aldehydes. The synthesized compounds were evaluated against three hematologic tumor cell lines, HEL (acute erythroid leukemia), K-562 (chronic myeloid leukemia) and HL-60 (acute myeloid leukemia), and five breast cancer cell lines (SKBR3, MCF-7, MDA-MB-231, BT-549, HS-578T). The primate non-malignant kidney Vero cell line was used as the control of cytotoxicity. From the obtained results, some structure–activity relationships were outlined. Furthermore, in silico prediction of physicochemical properties and ADME parameters were determined for the derivatives with the best antiproliferative values.
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Affiliation(s)
- Pedro Martín-Acosta
- Departamento de Química Orgánica, Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez No. 2, 38206 Tenerife, Spain; (P.M.-A.); (Á.A.)
| | - Ángel Amesty
- Departamento de Química Orgánica, Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez No. 2, 38206 Tenerife, Spain; (P.M.-A.); (Á.A.)
| | - Miguel Guerra-Rodríguez
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Farmacología Molecular y Traslacional (BIOPharm), Universidad de Las Palmas de Gran Canaria (ULPGC), 35001 Las Palmas de Gran Canaria, Spain; (M.G.-R.); (B.G.)
| | - Borja Guerra
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Farmacología Molecular y Traslacional (BIOPharm), Universidad de Las Palmas de Gran Canaria (ULPGC), 35001 Las Palmas de Gran Canaria, Spain; (M.G.-R.); (B.G.)
| | - Leandro Fernández-Pérez
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Farmacología Molecular y Traslacional (BIOPharm), Universidad de Las Palmas de Gran Canaria (ULPGC), 35001 Las Palmas de Gran Canaria, Spain; (M.G.-R.); (B.G.)
- Correspondence: (L.F.-P.); (A.E.-B.)
| | - Ana Estévez-Braun
- Departamento de Química Orgánica, Instituto Universitario de Bio-Orgánica Antonio González, Universidad de La Laguna, Avda. Astrofísico Francisco Sánchez No. 2, 38206 Tenerife, Spain; (P.M.-A.); (Á.A.)
- Correspondence: (L.F.-P.); (A.E.-B.)
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5
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4-Nitro styrylquinoline is an antimalarial inhibiting multiple stages of Plasmodium falciparum asexual life cycle. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2017; 7:120-129. [PMID: 28285258 PMCID: PMC5350499 DOI: 10.1016/j.ijpddr.2017.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 01/07/2023]
Abstract
Drugs against malaria are losing their effectiveness because of emerging drug resistance. This underscores the need for novel therapeutic options for malaria with mechanism of actions distinct from current antimalarials. To identify novel pharmacophores against malaria we have screened compounds containing structural features of natural products that are pharmacologically relevant. This screening has identified a 4-nitro styrylquinoline (SQ) compound with submicromolar antiplasmodial activity and excellent selectivity. SQ exhibits a cellular action distinct from current antimalarials, acting early on malaria parasite's intraerythrocytic life cycle including merozoite invasion. The compound is a fast-acting parasitocidal agent and also exhibits curative property in the rodent malaria model when administered orally. In this report, we describe the synthesis, preliminary structure-function analysis, and the parasite developmental stage specific action of the SQ scaffold.
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6
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Ferry JJ, Smith RF, Denney N, Walsh CP, McCauley L, Qian J, Ma H, Horiuchi KY, Howitz KT. Development and Use of Assay Conditions Suited to Screening for and Profiling of SET-Domain-Targeted Inhibitors of the MLL/SET1 Family of Lysine Methyltransferases. Assay Drug Dev Technol 2016; 13:221-34. [PMID: 26065558 DOI: 10.1089/adt.2015.646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Methylation of histone H3 lysine-4 (H3K4) is an important, regulatory, epigenetic post-translational modification associated with actively transcribed genes. In humans, the principal mediators of this modification are part of the MLL/SET1 family of methyltransferases, which comprises six members, MLLs1-4 and SET1A/SET1B. Aberrations in the structure, expression, and regulation of these enzymes are implicated in various disease states, making them important potential targets for drug discovery, particularly for oncology indications. The MLL/SET1 family members are most enzymatically active when part of a "core complex," the catalytic SET-domain-containing subunits bound to a subcomplex consisting of the proteins WDR5, RbBP5, Ash2L and a homodimer of DPY-30 (WRAD2). The necessity of MLL/SET1 members to bind WRAD2 for full activity is the basis of a particular drug development strategy, which seeks to disrupt the interaction between the MLL/SET1 subunits and WDR5. This strategy is not without its theoretical and practical drawbacks, some of which relate to the ease with which complexes of Escherichia coli-expressed MLL/SET1 and WRAD2 fall apart. As an alternative strategy, we explore ways to stabilize the complex, focusing on the use of an excess of WRAD2 to drive the binding equilibria toward complex formation while maintaining low concentrations of the catalytic subunits. The purpose of this approach is to seek inhibitors that bind the SET domain, an approach proven successful with the related, but inherently more stable, enhancer of zeste homolog 2 (EZH2) complex.
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Affiliation(s)
- Joseph J Ferry
- 1 Department of Biochemistry, Reaction Biology Corporation , Malvern, Pennsylvania
| | - Robert F Smith
- 2 Department of Protein Sciences, Reaction Biology Corporation , Malvern, Pennsylvania
| | - Natalie Denney
- 2 Department of Protein Sciences, Reaction Biology Corporation , Malvern, Pennsylvania
| | - Colin P Walsh
- 2 Department of Protein Sciences, Reaction Biology Corporation , Malvern, Pennsylvania
| | - Lauren McCauley
- 2 Department of Protein Sciences, Reaction Biology Corporation , Malvern, Pennsylvania
| | - Jie Qian
- 3 Department of Cell Biology, Reaction Biology Corporation , Malvern, Pennsylvania
| | - Haiching Ma
- 2 Department of Protein Sciences, Reaction Biology Corporation , Malvern, Pennsylvania
| | - Kurumi Y Horiuchi
- 1 Department of Biochemistry, Reaction Biology Corporation , Malvern, Pennsylvania
| | - Konrad T Howitz
- 2 Department of Protein Sciences, Reaction Biology Corporation , Malvern, Pennsylvania
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Baell JB. Feeling Nature's PAINS: Natural Products, Natural Product Drugs, and Pan Assay Interference Compounds (PAINS). JOURNAL OF NATURAL PRODUCTS 2016; 79:616-28. [PMID: 26900761 DOI: 10.1021/acs.jnatprod.5b00947] [Citation(s) in RCA: 351] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We have previously reported on classes of compounds that can interfere with bioassays via a number of different mechanisms and termed such compounds Pan Assay INterference compoundS, or PAINS. These compounds were defined on the basis of high-throughput data derived from vendor-supplied synthetics. The question therefore arises whether the concept of PAINS is relevant to compounds of natural origin. Here, it is shown that this is indeed the case, but that the context of the biological readout is an important factor that must be brought into consideration.
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Affiliation(s)
- Jonathan B Baell
- Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus) , 381 Royal Parade, Parkville, Victoria 3084, Australia
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8
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Roberts BF, Iyamu ID, Lee S, Lee E, Ayong L, Kyle DE, Yuan Y, Manetsch R, Chakrabarti D. Spirocyclic chromanes exhibit antiplasmodial activities and inhibit all intraerythrocytic life cycle stages. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2016; 6:85-92. [PMID: 27054067 PMCID: PMC4805781 DOI: 10.1016/j.ijpddr.2016.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/28/2016] [Accepted: 02/09/2016] [Indexed: 11/27/2022]
Abstract
We screened a collection of synthetic compounds consisting of natural-product-like substructural motifs to identify a spirocyclic chromane as a novel antiplasmodial pharmacophore using an unbiased cell-based assay. The most active spirocyclic compound UCF 201 exhibits a 50% effective concentration (EC50) of 350 nM against the chloroquine-resistant Dd2 strain and a selectivity over 50 using human liver HepG2 cells. Our analyses of physicochemical properties of UCF 201 showed that it is in compliance with Lipinski's parameters and has an acceptable physicochemical profile. We have performed a limited structure-activity-relationship study with commercially available chromanes preserving the spirocyclic motif. Our evaluation of stage specificities of UCF 201 indicated that the compound is early-acting in blocking parasite development at ring, trophozoite and schizont stages of development as well as merozoite invasion. SPC is an attractive lead candidate scaffold because of its ability to act on all stages of parasite's aexual life cycle unlike current antimalarials. SPC is a novel antiplasmodial scaffold. SPC has an EC50 of 350 nM against chloroquine-resistant parasite and is selective. SPC inhibits all stages of parasite growth in erythrocytes.
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Affiliation(s)
- Bracken F Roberts
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Iredia D Iyamu
- Department of Chemistry and Chemical Biology and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Sukjun Lee
- Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Eunyoung Lee
- Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Lawrence Ayong
- Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Dennis E Kyle
- Department of Global Health, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Yu Yuan
- Department of Chemistry, University of Central Florida, Orlando, FL, USA
| | - Roman Manetsch
- Department of Chemistry and Chemical Biology and Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, USA
| | - Debopam Chakrabarti
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA.
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9
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Agamennone M, Pietrantoni A, Superti F. Identification of small molecules acting against H1N1 influenza A virus. Virology 2015; 488:249-58. [PMID: 26655243 DOI: 10.1016/j.virol.2015.11.024] [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: 09/14/2015] [Revised: 10/04/2015] [Accepted: 11/20/2015] [Indexed: 10/22/2022]
Abstract
Influenza virus represents a serious threat to public health. The lack of effective drugs against flu prompted researchers to identify more promising viral target. In this respect hemagglutinin (HA) can represent an interesting option because of its pivotal role in the infection process. With this aim we collected a small library of commercially available compounds starting from a large database and performing a diversity-based selection to reduce the number of screened compounds avoiding structural redundancy of the library. Selected compounds were tested for their hemagglutination-inhibiting (HI) ability against two different A/H1N1 viral strains (one of which is oseltamivir sensitive), and 17 of them showed the ability to interact with HA. Five drug-like molecules, in particular, were able to impair hemagglutination of both A/H1N1 viral strains under study and to inhibit cytopathic effect and hemolysis at sub-micromolar level.
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Affiliation(s)
- Mariangela Agamennone
- Department of Pharmacy, University "G. d'Annunzio", Via dei Vestini 31, 66100 Chieti, Italy
| | - Agostina Pietrantoni
- Department of Technology and Health, National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy
| | - Fabiana Superti
- Department of Technology and Health, National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy.
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10
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To screen or not to screen: an impassioned plea for smarter chemical libraries to improve drug lead finding. Future Med Chem 2014; 6:497-502. [PMID: 24649953 DOI: 10.4155/fmc.14.21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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11
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A minimalist fragment approach for the design of natural-product-like synthetic scaffolds. Drug Discov Today 2012; 17:1170-4. [DOI: 10.1016/j.drudis.2012.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 05/12/2012] [Accepted: 05/22/2012] [Indexed: 11/22/2022]
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12
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Nechayev MA, Gorobets NY, Borisov AV, Kovalenko SM, Tolmachev AA. The synthesis of low molecular weight pyrrolo[2,3-c]pyridine-7-one scaffold. Mol Divers 2012; 16:749-57. [PMID: 23108947 DOI: 10.1007/s11030-012-9410-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
Abstract
A facile method for the synthesis of substituted pyrrolo[2,3-c]pyridine-7-ones is developed that applies an acid-promoted intramolecular cyclization of 2-pyrrolecarboxylic acid amidoacetals as key step. The synthesis is easily scaled up to 1.5 mol quantity with no yield decrease. The alkylation/arylation reaction of the pyrrolo[2,3-c]pyridine-7-ones proceeds regioselectively giving N6-substituted derivatives.
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Affiliation(s)
- Maxim A Nechayev
- National University of Pharmacy, Pushkinska Str. 53, Kharkiv 61002, Ukraine
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Bruns RF, Watson IA. Rules for Identifying Potentially Reactive or Promiscuous Compounds. J Med Chem 2012; 55:9763-72. [DOI: 10.1021/jm301008n] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Robert F. Bruns
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana
46285, United States
| | - Ian A. Watson
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana
46285, United States
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Abstract
Natural products (NPs) have historically been a fertile source of new drugs for the pharmaceutical industry. However, this once-popular approach has waned considerably over the past two decades as the high-throughput screening of megalibraries comprised mainly of molecules with non-natural (synthetic) motifs has unfolded. Contemporary high-throughput screening libraries contain molecules compliant with physicochemical profiles considered essential for downstream development. Until recently, there was no strategy that aligned NP screening with the same physicochemical profiles. An approach based on Log P has addressed these concerns and, together with advances in isolation, afforded NP leads in timelines compatible with pure compound screening. Concomitant progress related to access of biological resources has provided long-awaited legal certainty to further facilitate NP drug discovery.
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15
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Cerulli V, Banfi L, Basso A, Rocca V, Riva R. Diversity oriented and chemoenzymatic synthesis of densely functionalized pyrrolidines through a highly diastereoselective Ugi multicomponent reaction. Org Biomol Chem 2012; 10:1255-74. [DOI: 10.1039/c1ob06632c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Thomas GL, Johannes CW. Natural product-like synthetic libraries. Curr Opin Chem Biol 2011; 15:516-22. [PMID: 21684804 DOI: 10.1016/j.cbpa.2011.05.022] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 05/09/2011] [Accepted: 05/23/2011] [Indexed: 02/03/2023]
Abstract
There is a paucity of chemical matter suitably poised for effective drug development. Improving the quality and efficiency of research early on in the drug discovery process has been a long standing objective for the drug industry and improvements to the accessibility and quality of compound screening decks might have a significant and positive impact. In the absence of specific molecular information that can be modeled and used predicatively we are far from identifying which small molecules are most relevant to emerging biological targets such as protein-protein interactions. Natural products have been historically successful as an entry point for drug discovery and recently screening libraries are being synthesized to emulate natural product like features.
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Affiliation(s)
- Gemma L Thomas
- Institute of Chemical and Engineering Sciences, Organic Chemistry, 11 Biopolis Way, Helios, Singapore 138667, Singapore
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17
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Boehm M. Virtual Screening of Chemical Space: From Generic Compound Collections to Tailored Screening Libraries. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/9783527633326.ch1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
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18
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Viswanadhan VN, Rajesh H, Balaji VN. Atom type preferences, structural diversity, and property profiles of known drugs, leads, and nondrugs: a comparative assessment. ACS COMBINATORIAL SCIENCE 2011; 13:327-36. [PMID: 21480669 DOI: 10.1021/co2000168] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new characterization of known drug, lead, and representative nondrug databases was performed taking into account several properties at the atomic and molecular levels. This characterization included atom type preferences, intrinsic structural diversity (Atom Type Diversity, ATD), and other well-known physicochemical properties, as an approach for rapid assessment of druglikeness for small molecule libraries. To characterize ATD, an elaborate united atom classification, UALOGP (United Atom Log P), with 148 atom types, was developed along with associated atomic physicochemical parameters. This classification also enabled an analysis of atom type and physicochemical property distributions (for calculated log P, molar refractivity, molecular weight, total atom count, and ATD) of drug, lead, and nondrug databases, a reassessment of the Ro5 (Rule of Five) and GVW (Ghose−Viswanadhan−Wendoloski) criteria, and development of new criteria and ranges more accurately reflecting the chemical space occupied by small molecule drugs. A relative druglikeness parameter was defined for atom types in drugs, identifying the most preferred types. The present work demonstrates that drug molecules are constitutionally more diverse relative to nondrugs, while being less diverse than leads.
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Affiliation(s)
- Vellarkad N. Viswanadhan
- Department of Computational Chemistry, Jubilant Biosys Limited, #96, Industrial Suburb, second Stage, Yeshwanthpur, Bangalore 560 064, India
| | - Hariharan Rajesh
- Department of Computational Chemistry, Jubilant Biosys Limited, #96, Industrial Suburb, second Stage, Yeshwanthpur, Bangalore 560 064, India
| | - Vitukudi N. Balaji
- Department of Computational Chemistry, Jubilant Biosys Limited, #96, Industrial Suburb, second Stage, Yeshwanthpur, Bangalore 560 064, India
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19
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20
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Huggins DJ, Venkitaraman AR, Spring DR. Rational methods for the selection of diverse screening compounds. ACS Chem Biol 2011; 6:208-17. [PMID: 21261294 PMCID: PMC4765079 DOI: 10.1021/cb100420r] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Traditionally a pursuit of large pharmaceutical companies, high-throughput screening assays are becoming increasingly common within academic and government laboratories. This shift has been instrumental in enabling projects that have not been commercially viable, such as chemical probe discovery and screening against high-risk targets. Once an assay has been prepared and validated, it must be fed with screening compounds. Crafting a successful collection of small molecules for screening poses a significant challenge. An optimized collection will minimize false positives while maximizing hit rates of compounds that are amenable to lead generation and optimization. Without due consideration of the relevant protein targets and the downstream screening assays, compound filtering and selection can fail to explore the great extent of chemical diversity and eschew valuable novelty. Herein, we discuss the different factors to be considered and methods that may be employed when assembling a structurally diverse compound collection for screening. Rational methods for selecting diverse chemical libraries are essential for their effective use in high-throughput screens.
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Affiliation(s)
- David J. Huggins
- University of Cambridge, TCM Group, Cavendish Laboratory, 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
- University of Cambridge, Cambridge Molecular Therapeutics Programme, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom
- University of Cambridge, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW, United Kingdom
| | - Ashok R. Venkitaraman
- University of Cambridge, Cambridge Molecular Therapeutics Programme, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom
| | - David R. Spring
- University of Cambridge, Cambridge Molecular Therapeutics Programme, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 2XZ, United Kingdom
- University of Cambridge, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW, United Kingdom
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21
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When pharmaceutical companies publish large datasets: an abundance of riches or fool's gold? Drug Discov Today 2010; 15:812-5. [DOI: 10.1016/j.drudis.2010.08.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 07/29/2010] [Accepted: 08/16/2010] [Indexed: 12/22/2022]
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22
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Selecting diversified compounds to build a tangible library for biological and biochemical assays. Molecules 2010; 15:5031-44. [PMID: 20657406 PMCID: PMC6257665 DOI: 10.3390/molecules15075031] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 07/14/2010] [Accepted: 07/19/2010] [Indexed: 11/17/2022] Open
Abstract
The quality of diverse compound selection mainly depends on cluster algorithms, descriptors, the combinations of the descriptors, and similarity metrics. The Jarvis-Patrick algorithm, MDL search keys, and Daylight fingerprints are a well accepted algorithm and structure descriptors for compound library diversity analysis. Based upon our 288 experiments on selecting compounds from various descriptor combinations, we have found (1) hybrid Daylight and MDL structural descriptors for diversity analyses can produce worse results; (2) selections based purely on 2,048-bit Daylight fingerprints yield better results than the ones based purely on MDL 166-bit search keys; (3) when Daylight fingerprints and MDL search keys are combined, it is better to compute the similarities independently, then to take the smaller value for the outcome. This will yield better average separation of clusters; (4) regarding the consistency of different clustering approaches, the Daylight fingerprints based clustering is more consistent with the SCA approach than it does with the MDL search keys based approach; (5) The MDL search keys based selection approach tends to select a greater number of compounds from larger clusters. As the Daylight fingerprint is folded two and three times, respectively, information is lost, and this approach tends to select a greater number of compounds from larger clusters as well. These results have not been reported before to our knowledge.
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23
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Drewry DH, Macarron R. Enhancements of screening collections to address areas of unmet medical need: an industry perspective. Curr Opin Chem Biol 2010; 14:289-98. [PMID: 20413343 DOI: 10.1016/j.cbpa.2010.03.024] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 02/19/2010] [Accepted: 03/24/2010] [Indexed: 01/31/2023]
Abstract
The past 20 years have witnessed an impressive expansion of the 'drug space'; defined as the intersection of the Medicinal Chemistry space and the Biologically Active space relevant in the quest for new treatments for disease. Despite the success of known lead discovery tactics, areas of unmet medical need are often linked to challenging or novel targets and are poorly served by current screening collections. A successful strategy to fill the gaps is to diversify the approaches taken in the enhancement of screening collections. Possible strategies include investments through proven methods, exploring areas of chemical space previously neglected (e.g. hydrophilic compounds, natural product mimics), and applying tactics to the lead discovery process that are complementary to HTS (e.g. fragment based screening or multidisciplinary team efforts to tackle new target classes).
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Affiliation(s)
- David H Drewry
- Molecular Discovery Research, GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, NC 27709, USA.
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24
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A Marriage of Convenience: Combining the Power of Isocyanide‐Based Multicomponent Reactions with the Versatility of (Hetero)norbornene Chemistry. European J Org Chem 2010. [DOI: 10.1002/ejoc.200901438] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Kysil V, Khvat A, Tsirulnikov S, Tkachenko S, Williams C, Churakova M, Ivachtchenko A. General Multicomponent Strategy for the Synthesis of 2-Amino-1,4-diazaheterocycles: Scope, Limitations, and Utility. European J Org Chem 2010. [DOI: 10.1002/ejoc.200901360] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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26
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Ekins S, Williams AJ. Meta-analysis of molecular property patterns and filtering of public datasets of antimalarial “hits” and drugs. MEDCHEMCOMM 2010. [DOI: 10.1039/c0md00129e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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27
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Leeson PD, Empfield JR. Reducing the Risk of Drug Attrition Associated with Physicochemical Properties. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2010. [DOI: 10.1016/s0065-7743(10)45024-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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28
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Boyd SM, de Kloe GE. Fragment library design: efficiently hunting drugs in chemical space. DRUG DISCOVERY TODAY. TECHNOLOGIES 2010; 7:e147-e202. [PMID: 24103769 DOI: 10.1016/j.ddtec.2010.11.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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29
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Oprea TI, Bologa CG, Boyer S, Curpan RF, Glen RC, Hopkins AL, Lipinski CA, Marshall GR, Martin YC, Ostopovici-Halip L, Rishton G, Ursu O, Vaz RJ, Waller C, Waldmann H, Sklar LA. A crowdsourcing evaluation of the NIH chemical probes. Nat Chem Biol 2009; 5:441-7. [PMID: 19536101 PMCID: PMC3596119 DOI: 10.1038/nchembio0709-441] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Between 2004 and 2008, the US National Institutes of Health Molecular Libraries and Imaging initiative pilot phase funded 10 high-throughput screening centers, resulting in the deposition of 691 assays into PubChem and the nomination of 64 chemical probes. We crowdsourced the Molecular Libraries and Imaging initiative output to 11 experts, who expressed medium or high levels of confidence in 48 of these 64 probes.
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Affiliation(s)
- Tudor I. Oprea
- UNM Center for Molecular Discovery University of New Mexico School of Medicine 2703 Frontier NE Albuquerque NM 87131, USA
| | - Cristian G. Bologa
- UNM Center for Molecular Discovery University of New Mexico School of Medicine 2703 Frontier NE Albuquerque NM 87131, USA
| | - Scott Boyer
- Global Safety Assessment AstraZeneca R&D, S-431 83 Mölndal, Sweden
| | - Ramona F. Curpan
- UNM Center for Molecular Discovery University of New Mexico School of Medicine 2703 Frontier NE Albuquerque NM 87131, USA
- Institute of Chemistry, Romanian Academy, 24 Mihai Viteazul, Timisoara 300223, Romania
| | - Robert C. Glen
- Unilever Centre for Molecular Science Informatics Department of Chemistry Lensfield Road Cambridge CB2 1EW, UK
| | - Andrew L. Hopkins
- Division of Biological Chemistry and Drug Discovery College of Life Science, University of Dundee, Dow Street, Dundee DD1 3DF, UK
| | | | - Garland R. Marshall
- Center for Computational Biology Washington University 700 S. Euclid Ave., Box 8036 St. Louis, MO 63110
| | | | - Liliana Ostopovici-Halip
- UNM Center for Molecular Discovery University of New Mexico School of Medicine 2703 Frontier NE Albuquerque NM 87131, USA
- Institute of Chemistry, Romanian Academy, 24 Mihai Viteazul, Timisoara 300223, Romania
| | - Gilbert Rishton
- Channel Islands Alzheimer’s Institute, California State University, Channel Islands, One University Drive, Camarillo, CA 93012, USA
| | - Oleg Ursu
- UNM Center for Molecular Discovery University of New Mexico School of Medicine 2703 Frontier NE Albuquerque NM 87131, USA
| | - Roy J. Vaz
- Sanofi-Aventis Pharmaceuticals 1041 Route 202-206, PO Box 5915 Bridgewater, NJ 08807, USA
| | - Chris Waller
- Chemistry Informatics Pfizer Global R&D Pfizer, Eastern Point Road, Groton, CT 06340, USA
| | - Herbert Waldmann
- Max-Planck Institut für Molekulare Physiologie Abteilung IV -Chemische Biologie Otto-Hahn-Strasse 11 D-44229 Dortmund, Germany and Technische Universität Dortmund, Faculty of Chemistry, Chemical Biology
| | - Larry A. Sklar
- UNM Center for Molecular Discovery University of New Mexico School of Medicine 2703 Frontier NE Albuquerque NM 87131, USA
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Kombarov R, Altieri A, Genis D, Kirpichenok M, Kochubey V, Rakitina N, Titarenko Z. BioCores: identification of a drug/natural product-based privileged structural motif for small-molecule lead discovery. Mol Divers 2009; 14:193-200. [PMID: 19468851 DOI: 10.1007/s11030-009-9157-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Accepted: 04/29/2009] [Indexed: 11/25/2022]
Abstract
The analysis of known drugs (Comprehensive Medicinal Chemistry database (2008 version): http://www.mdl.com/products/knowledge/medicinal_chem/index.jsp ) and natural products (Koch et al., Proc Natl Acad Sci USA 102:17272-17277, 2008) has led to the identification of privileged saturated and aromatic heterocyclic ring pairs that we have termed as "BioCores." This article explains how the BioCores can be used for the design of novel lead-like scaffolds.
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Affiliation(s)
- Roman Kombarov
- ASINEX Ltd, 20 Geroev Panfilovtzev Str. Bldg 1, Moscow, 125480, Russia.
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